diff --git a/organisms/stage/Aethina_tumida/trackList.json b/organisms/stage/Aethina_tumida/trackList.json
index fe0b337..97e119b 100644
--- a/organisms/stage/Aethina_tumida/trackList.json
+++ b/organisms/stage/Aethina_tumida/trackList.json
@@ -1,238 +1,232 @@
 {
-   "css" : "./plugins/NAL_CSS/css/contrib_styles.css",
-   "share_link" : 0,
-   "plugins" : [
-      {
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-         "name" : "WebApollo"
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+  "css": "./plugins/NAL_CSS/css/main.css",
+  "favicon": "./plugins/WebApollo/img/webapollo_favicon.ico",
+  "formatVersion": 1,
+  "names": {
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+    },
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+    },
+    {
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+      "bicolor_pivot": "0.5",
+      "category": "Reference Assembly",
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+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+      },
+      "scoreType": "avgScore",
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "rgba(255,255,0,50)",
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+      "urlTemplate": "bigwig/GCF_001937115.1_Atum_1.0_genomic_RefSeqIDs.fna.gc.bigwig"
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 }
diff --git a/organisms/stage/Agrilus_planipennis/trackList.json b/organisms/stage/Agrilus_planipennis/trackList.json
index 72b5b82..f6521e3 100644
--- a/organisms/stage/Agrilus_planipennis/trackList.json
+++ b/organisms/stage/Agrilus_planipennis/trackList.json
@@ -1,1343 +1,1337 @@
 {
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+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Cephalochordata proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
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+        "arrowheadClass": "webapollo-arrowhead",
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+    },
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+      "key": "protein2genome_Chelicerata",
+      "label": "protein2genome_Chelicerata",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Chelicerata proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
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+        "arrowheadClass": "webapollo-arrowhead",
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+      "key": "protein2genome_Cnidaria",
+      "label": "protein2genome_Cnidaria",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Cnidaria proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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+          "match_part": "protein2genome"
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Cnidaria/{refseq}/trackData.json"
+    },
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+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+      "key": "protein2genome_Craniata",
+      "label": "protein2genome_Craniata",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Craniata proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
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+          "match_part": "protein2genome"
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+      "urlTemplate": "tracks/protein2genome_Craniata/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Crustacea",
+      "label": "protein2genome_Crustacea",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Crustacea proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
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+          "match_part": "protein2genome"
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Crustacea/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Echinodermata",
+      "label": "protein2genome_Echinodermata",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Echinodermata proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
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+          "match_part": "protein2genome"
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Echinodermata/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Mollusca",
+      "label": "protein2genome_Mollusca",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Mollusca proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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+          "match_part": "protein2genome"
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+      "urlTemplate": "tracks/protein2genome_Mollusca/{refseq}/trackData.json"
+    },
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+      "key": "protein2genome_Nemata",
+      "label": "protein2genome_Nemata",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline."
+      },
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+        "arrowheadClass": "webapollo-arrowhead",
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+          "match_part": "protein2genome"
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+      "urlTemplate": "tracks/protein2genome_Nemata/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+      "key": "protein2genome_Nematomorpha",
+      "label": "protein2genome_Nematomorpha",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Nematomorpha proteins as part of the MAKER automated annotation pipeline."
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+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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+          "match_part": "protein2genome"
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Nematomorpha/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Onychophora",
+      "label": "protein2genome_Onychophora",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Onychophora proteins as part of the MAKER automated annotation pipeline."
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+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
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+        "arrowheadClass": "webapollo-arrowhead",
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+          "match_part": "protein2genome"
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+      "urlTemplate": "tracks/protein2genome_Onychophora/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+      "key": "protein2genome_Parazoa",
+      "label": "protein2genome_Parazoa",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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+          "match_part": "protein2genome"
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+      },
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Parazoa/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Placozoa",
+      "label": "protein2genome_Placozoa",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
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+          "match_part": "protein2genome"
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+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Placozoa/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Platyhelminthes",
+      "label": "protein2genome_Platyhelminthes",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
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+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Platyhelminthes/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Priapulida",
+      "label": "protein2genome_Priapulida",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
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+      },
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Priapulida/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Tardigrada",
+      "label": "protein2genome_Tardigrada",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
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+      },
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Tardigrada/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Tunicata",
+      "label": "protein2genome_Tunicata",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
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+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Tunicata/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_UNCATEGORISED",
+      "label": "protein2genome_UNCATEGORISED",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
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+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_UNCATEGORISED/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/2. Evidence/Repeats",
+      "compress": 0,
+      "key": "repeatmasker",
+      "label": "repeatmasker",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from RepeatMasker as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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+        "subfeatureClasses": {
+          "match_part": "repeat"
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+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/repeatmasker/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/2. Evidence/Repeats",
+      "compress": 0,
+      "key": "repeatrunner",
+      "label": "repeatrunner",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Repeatrunner as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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+        "subfeatureClasses": {
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+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/repeatrunner/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/1. Gene Sets/Supplementary Gene Predictions",
+      "compress": 0,
+      "key": "snap_masked",
+      "label": "snap_masked",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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+      },
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+      "urlTemplate": "tracks/snap_masked/{refseq}/trackData.json"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Reference Assembly",
+      "key": "Gaps in assembly",
+      "label": "Gaps in assembly",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "white",
+        "pos_color": "black"
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+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "bigwig/Aplan.scaffolds.50.fa.gaps.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "0.5",
+      "category": "Reference Assembly",
+      "key": "GC Content",
+      "label": "GC Content",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+      },
+      "scoreType": "avgScore",
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "rgba(255,255,0,50)",
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+      "urlTemplate": "bigwig/Aplan.scaffolds.50.fa.gc.bigwig"
+    },
+    {
+      "category": "2. NCBI Annotation Release 100/1. Gene Sets/Protein Coding",
+      "compress": 0,
+      "key": "NCBI Predicted protein coding genes, Annotation Release 100",
+      "label": "Agrilus_planipennis_Annotation_Release_100",
+      "metadata": {
+        "Data description": "ftp://ftp.ncbi.nlm.nih.gov/genomes/Agrilus_planipennis/README_CURRENT_RELEASE",
+        "Data provider": "NCBI",
+        "Data source": "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/699/045/GCF_000699045.1_Apla_1.0/GCF_000699045.1_Apla_1.0_genomic.gff.gz",
+        "Method": "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/",
+        "Note": "Some genes may have non-coding transcripts"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "description": "product,note, description",
+        "subfeatureClasses": {
+          "CDS": "primary_gene_set-cds",
+          "UTR": "primary_gene_set-utr",
+          "exon": "container-100pct",
+          "wholeCDS": null
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/Agrilus_planipennis_Annotation_Release_100/{refseq}/trackData.json"
+    },
+    {
+      "category": "2. NCBI Annotation Release 100/1. Gene Sets/Pseudogenes",
+      "compress": 0,
+      "key": "NCBI Predicted pseudogenes, Annotation Release 100",
+      "label": "NCBI_Annotation_Release_100_Pseudogene",
+      "metadata": {
+        "Data description": "ftp://ftp.ncbi.nlm.nih.gov/genomes/Agrilus_planipennis/README_CURRENT_RELEASE",
+        "Data provider": "NCBI",
+        "Data source": "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/699/045/GCF_000699045.1_Apla_1.0/GCF_000699045.1_Apla_1.0_genomic.gff.gz",
+        "Method": "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "CDS": "gnomon_CDS",
+          "UTR": "gnomon_UTR",
+          "exon": "container-100pct",
+          "wholeCDS": null
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/NCBI_Annotation_Release_100_Pseudogene/{refseq}/trackData.json"
+    },
+    {
+      "category": "2. NCBI Annotation Release 100/1. Gene Sets/Noncoding",
+      "compress": 0,
+      "key": "NCBI Predicted tRNAs, Annotation Release 100",
+      "label": "NCBI_Annotation_Release_100_tRNA",
+      "metadata": {
+        "Data description": "ftp://ftp.ncbi.nlm.nih.gov/genomes/Agrilus_planipennis/README_CURRENT_RELEASE",
+        "Data provider": "NCBI",
+        "Data source": "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/699/045/GCF_000699045.1_Apla_1.0/GCF_000699045.1_Apla_1.0_genomic.gff.gz",
+        "Method": "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "CDS": "gnomon_CDS",
+          "UTR": "gnomon_UTR",
+          "exon": "container-100pct",
+          "wholeCDS": null
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/NCBI_Annotation_Release_100_tRNA/{refseq}/trackData.json"
+    },
+    {
+      "category": "2. NCBI Annotation Release 100/2. Evidence",
+      "compress": 0,
+      "key": "cDNA match evidence from NCBI Annotation Release 100",
+      "label": "NCBI_Annotation_Release_100_cDNA_match",
+      "metadata": {
+        "Data description": "ftp://ftp.ncbi.nlm.nih.gov/genomes/Agrilus_planipennis/README_CURRENT_RELEASE",
+        "Data provider": "NCBI",
+        "Data source": "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/699/045/GCF_000699045.1_Apla_1.0/GCF_000699045.1_Apla_1.0_genomic.gff.gz",
+        "Method": "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}"
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/NCBI_Annotation_Release_100_cDNA_match/{refseq}/trackData.json"
+    },
+    {
+      "category": "2. NCBI Annotation Release 100/1. Gene Sets/Noncoding",
+      "compress": 0,
+      "key": "NCBI Predicted lncRNA, Annotation Release 100",
+      "label": "NCBI_Annotation_Release_100_lncRNA",
+      "metadata": {
+        "Data description": "ftp://ftp.ncbi.nlm.nih.gov/genomes/Agrilus_planipennis/README_CURRENT_RELEASE",
+        "Data provider": "NCBI",
+        "Data source": "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/699/045/GCF_000699045.1_Apla_1.0/GCF_000699045.1_Apla_1.0_genomic.gff.gz",
+        "Method": "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "description": "product,note, description",
+        "subfeatureClasses": {
+          "CDS": "gnomon_CDS",
+          "UTR": "gnomon_UTR",
+          "exon": "container-100pct",
+          "wholeCDS": null
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/NCBI_Annotation_Release_100_lncRNA/{refseq}/trackData.json"
+    }
+  ]
 }
diff --git a/organisms/stage/Amyelois_transitella/trackList.json b/organisms/stage/Amyelois_transitella/trackList.json
index 5f5ee9f..7785cc5 100644
--- a/organisms/stage/Amyelois_transitella/trackList.json
+++ b/organisms/stage/Amyelois_transitella/trackList.json
@@ -1,370 +1,423 @@
 {
-   "css" : "./plugins/NAL_CSS/css/contrib_styles.css",
+   "alwaysOnTracks" : "DNA,Annotations",
+   "css" : "./plugins/NAL_CSS/css/main.css",
+   "favicon" : "./plugins/WebApollo/img/webapollo_favicon.ico",
+   "formatVersion" : 1,
+   "names" : {
+      "type" : "Hash",
+      "url" : "names/"
+   },
    "share_link" : 0,
    "tracks" : [
       {
-         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
+         "category" : "Reference sequence",
          "chunkSize" : 20000,
-         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-",
+         "key" : "Reference sequence",
          "label" : "DNA",
+         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
          "type" : "SequenceTrack",
-         "category" : "Reference sequence",
-         "key" : "Reference sequence"
+         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-"
       },
       {
          "autocomplete" : "none",
+         "compress" : 0,
+         "key" : "User-created Annotations",
+         "label" : "Annotations",
+         "phase" : 0,
+         "storeClass" : "WebApollo/Store/SeqFeature/ScratchPad",
          "style" : {
-            "className" : "annot",
-            "renderClassName" : "annot-render",
-            "subfeatureClasses" : {
-               "non_canonical_three_prime_splice_site" : "noncanonical-splice-site",
-               "wholeCDS" : null,
-               "exon" : "container-100pct",
-               "CDS" : "annot-CDS",
-               "non_canonical_five_prime_splice_site" : "noncanonical-splice-site",
-               "UTR" : "annot-UTR"
-            },
-            "arrowheadClass" : "annot-arrowhead",
             "alternateClasses" : {
-               "transposable_element" : {
-                  "renderClassName" : "blue-ibeam-render",
-                  "className" : "blue-ibeam"
+               "miRNA" : {
+                  "className" : "brightgreen-80pct",
+                  "renderClassName" : "gray-center-30pct"
                },
-               "pseudogene" : {
-                  "renderClassName" : "gray-center-30pct",
-                  "className" : "light-purple-80pct"
+               "ncRNA" : {
+                  "className" : "brightgreen-80pct",
+                  "renderClassName" : "gray-center-30pct"
                },
-               "snRNA" : {
-                  "renderClassName" : "gray-center-30pct",
-                  "className" : "brightgreen-80pct"
+               "pseudogene" : {
+                  "className" : "light-purple-80pct",
+                  "renderClassName" : "gray-center-30pct"
                },
                "rRNA" : {
-                  "renderClassName" : "gray-center-30pct",
-                  "className" : "brightgreen-80pct"
-               },
-               "snoRNA" : {
-                  "renderClassName" : "gray-center-30pct",
-                  "className" : "brightgreen-80pct"
+                  "className" : "brightgreen-80pct",
+                  "renderClassName" : "gray-center-30pct"
                },
                "repeat_region" : {
                   "className" : "magenta-80pct"
                },
-               "tRNA" : {
-                  "renderClassName" : "gray-center-30pct",
-                  "className" : "brightgreen-80pct"
+               "snRNA" : {
+                  "className" : "brightgreen-80pct",
+                  "renderClassName" : "gray-center-30pct"
                },
-               "ncRNA" : {
-                  "renderClassName" : "gray-center-30pct",
-                  "className" : "brightgreen-80pct"
+               "snoRNA" : {
+                  "className" : "brightgreen-80pct",
+                  "renderClassName" : "gray-center-30pct"
                },
-               "miRNA" : {
-                  "renderClassName" : "gray-center-30pct",
-                  "className" : "brightgreen-80pct"
+               "tRNA" : {
+                  "className" : "brightgreen-80pct",
+                  "renderClassName" : "gray-center-30pct"
+               },
+               "transposable_element" : {
+                  "className" : "blue-ibeam",
+                  "renderClassName" : "blue-ibeam-render"
                }
             },
-            "uniqueIdField" : "id",
+            "arrowheadClass" : "annot-arrowhead",
             "centerSubFeature" : {
-               "non_canonical_three_prime_splice_site" : false,
-               "non_canonical_five_prime_splice_site" : false
-            }
-         },
-         "key" : "User-created Annotations",
-         "storeClass" : "WebApollo/Store/SeqFeature/ScratchPad",
-         "phase" : 0,
-         "compress" : 0,
-         "label" : "Annotations",
-         "type" : "WebApollo/View/Track/AnnotTrack",
-         "subfeatures" : 1
-      },
-      {
-         "style" : {
-            "className" : "container-16px",
+               "non_canonical_five_prime_splice_site" : false,
+               "non_canonical_three_prime_splice_site" : false
+            },
+            "className" : "annot",
+            "renderClassName" : "annot-render",
             "subfeatureClasses" : {
-               "wholeCDS" : null,
+               "CDS" : "annot-CDS",
+               "UTR" : "annot-UTR",
                "exon" : "container-100pct",
-               "CDS" : "primary_gene_set-cds",
-               "UTR" : "primary_gene_set-utr"
+               "non_canonical_five_prime_splice_site" : "noncanonical-splice-site",
+               "non_canonical_three_prime_splice_site" : "noncanonical-splice-site",
+               "wholeCDS" : null
             },
-            "arrowheadClass" : "trellis-arrowhead"
+            "uniqueIdField" : "id"
          },
-         "key" : "NCBI Predicted protein coding genes, Annotation Release 100",
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
-         "trackType" : null,
-         "urlTemplate" : "tracks/amytra_current_models/{refseq}/trackData.json",
+         "subfeatures" : 1,
+         "type" : "WebApollo/View/Track/AnnotTrack"
+      },
+      {
+         "category" : "NCBI Annotation Release 100/1. Gene Sets/Protein Coding",
          "compress" : 0,
+         "key" : "NCBI Predicted protein coding genes, Annotation Release 100",
+         "label" : "amytra_current_models",
          "metadata" : {
-            "Data source" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Amyelois_transitella/GFF/ref_ASM118610v1_scaffolds.gff3.gz",
-            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/",
+            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Amyelois_transitella/README_CURRENT_RELEASE",
             "Data provider" : "NCBI",
-            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Amyelois_transitella/README_CURRENT_RELEASE"
+            "Data source" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Amyelois_transitella/GFF/ref_ASM118610v1_scaffolds.gff3.gz",
+            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
          },
-         "category" : "NCBI Annotation Release 100/1. Gene Sets/Protein Coding",
-         "label" : "amytra_current_models",
-         "type" : "FeatureTrack"
-      },
-      {
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "neg_color" : "white",
-            "pos_color" : "black"
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "{type}",
+            "subfeatureClasses" : {
+               "CDS" : "primary_gene_set-cds",
+               "UTR" : "primary_gene_set-utr",
+               "exon" : "container-100pct",
+               "wholeCDS" : null
+            }
          },
-         "bicolor_pivot" : "zero",
-         "key" : "Gaps in assembly",
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/amytra_current_models/{refseq}/trackData.json"
+      },
+      {
          "autoscale" : "local",
-         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
-         "urlTemplate" : "bigwig/680683_ref_ASM118610v1_chrUn_refseq_IDS.fa.gaps.bigwig",
-         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "bicolor_pivot" : "zero",
          "category" : "Reference Assembly",
+         "key" : "Gaps in assembly",
+         "label" : "Gaps in assembly",
          "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
             "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
-            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank",
-            "Track contact" : "The i5k workspace@NAL"
+            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
          },
-         "label" : "Gaps in assembly"
-      },
-      {
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
          "style" : {
-            "pos_color" : "rgba(0,0,255,50)",
-            "neg_color" : "rgba(255,255,0,50)"
+            "neg_color" : "white",
+            "pos_color" : "black"
          },
-         "bicolor_pivot" : "0.5",
-         "autoscale" : "local",
-         "key" : "GC Content",
-         "scoreType": "avgScore",
-         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
-         "urlTemplate" : "bigwig/680683_ref_ASM118610v1_chrUn_refseq_IDS.fa.gc.bigwig",
          "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/680683_ref_ASM118610v1_chrUn_refseq_IDS.fa.gaps.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "0.5",
          "category" : "Reference Assembly",
+         "key" : "GC Content",
+         "label" : "GC Content",
          "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
             "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
-            "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track.",
-            "Track contact" : "The i5k workspace@NAL"
+            "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
          },
-         "label" : "GC Content"
-      },
-      {
+         "scoreType" : "avgScore",
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
          "style" : {
-            "className" : "container-16px",
-            "subfeatureClasses" : {
-               "wholeCDS" : null,
-               "exon" : "container-100pct",
-               "CDS" : "gnomon_CDS",
-               "UTR" : "gnomon_UTR"
-            },
-            "arrowheadClass" : "trellis-arrowhead"
+            "neg_color" : "rgba(255,255,0,50)",
+            "pos_color" : "rgba(0,0,255,50)"
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-         "key" : "NCBI Predicted low-quality protein coding genes, Annotation Release 100",
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
-         "trackType" : null,
-         "urlTemplate" : "tracks/NCBI_Annotation_Release_100_Protein_Coding_low_quality/{refseq}/trackData.json",
+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/680683_ref_ASM118610v1_chrUn_refseq_IDS.fa.gc.bigwig"
+      },
+      {
+         "category" : "NCBI Annotation Release 100/1. Gene Sets/Protein Coding",
          "compress" : 0,
+         "key" : "NCBI Predicted low-quality protein coding genes, Annotation Release 100",
          "label" : "NCBI_Annotation_Release_100_Protein_Coding_low_quality",
-         "category" : "NCBI Annotation Release 100/1. Gene Sets/Protein Coding",
          "metadata" : {
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-            "Data source" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Amyelois_transitella/GFF/ref_ASM118610v1_scaffolds.gff3.gz",
+            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Amyelois_transitella/README_CURRENT_RELEASE",
             "Data provider" : "NCBI",
-            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Amyelois_transitella/README_CURRENT_RELEASE"
+            "Data source" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Amyelois_transitella/GFF/ref_ASM118610v1_scaffolds.gff3.gz",
+            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
          },
-         "type" : "FeatureTrack"
-      },
-      {
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "className" : "container-16px",
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "{type}",
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-               "exon" : "container-100pct",
                "CDS" : "gnomon_CDS",
-               "UTR" : "gnomon_UTR"
-            },
-            "arrowheadClass" : "trellis-arrowhead"
+               "UTR" : "gnomon_UTR",
+               "exon" : "container-100pct",
+               "wholeCDS" : null
+            }
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-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "trackType" : null,
-         "urlTemplate" : "tracks/NCBI_Annotation_Release_100_lncRNA/{refseq}/trackData.json",
-         "compress" : 0,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/NCBI_Annotation_Release_100_Protein_Coding_low_quality/{refseq}/trackData.json"
+      },
+      {
          "category" : "NCBI Annotation Release 100/1. Gene Sets/Noncoding",
+         "compress" : 0,
+         "key" : "NCBI Predicted lncRNA, Annotation Release 100",
          "label" : "NCBI_Annotation_Release_100_lncRNA",
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          "metadata" : {
-            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/",
-            "Data source" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Amyelois_transitella/GFF/ref_ASM118610v1_scaffolds.gff3.gz",
+            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Amyelois_transitella/README_CURRENT_RELEASE",
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-         }
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+            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "className" : "container-16px",
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "{type}",
             "subfeatureClasses" : {
-               "wholeCDS" : null,
-               "exon" : "container-100pct",
                "CDS" : "gnomon_CDS",
-               "UTR" : "gnomon_UTR"
-            },
-            "arrowheadClass" : "trellis-arrowhead"
+               "UTR" : "gnomon_UTR",
+               "exon" : "container-100pct",
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-         "key" : "NCBI Predicted miscRNA, Annotation Release 100",
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "trackType" : null,
-         "urlTemplate" : "tracks/NCBI_Annotation_Release_100_misc_RNA/{refseq}/trackData.json",
-         "compress" : 0,
          "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/NCBI_Annotation_Release_100_lncRNA/{refseq}/trackData.json"
+      },
+      {
+         "category" : "NCBI Annotation Release 100/1. Gene Sets/Noncoding",
+         "compress" : 0,
+         "key" : "NCBI Predicted miscRNA, Annotation Release 100",
+         "label" : "NCBI_Annotation_Release_100_misc_RNA",
          "metadata" : {
-            "Data source" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Amyelois_transitella/GFF/ref_ASM118610v1_scaffolds.gff3.gz",
-            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/",
+            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Amyelois_transitella/README_CURRENT_RELEASE",
             "Data provider" : "NCBI",
-            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Amyelois_transitella/README_CURRENT_RELEASE"
+            "Data source" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Amyelois_transitella/GFF/ref_ASM118610v1_scaffolds.gff3.gz",
+            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
          },
-         "label" : "NCBI_Annotation_Release_100_misc_RNA",
-         "category" : "NCBI Annotation Release 100/1. Gene Sets/Noncoding"
-      },
-      {
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "className" : "container-16px",
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "{type}",
             "subfeatureClasses" : {
-               "wholeCDS" : null,
-               "exon" : "container-100pct",
                "CDS" : "gnomon_CDS",
-               "UTR" : "gnomon_UTR"
-            },
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index bb0e787..a12bef5 100644
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+      "key": "protein2genome_Craniata",
+      "label": "protein2genome_Craniata",
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+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Craniata proteins as part of the MAKER automated annotation pipeline."
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+      "label": "protein2genome_Crustacea",
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+        "Track legend": "Results from Protein2genome alignments of a set of Crustacea proteins as part of the MAKER automated annotation pipeline."
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+      "key": "protein2genome_Echinodermata",
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+        "Track legend": "Results from Protein2genome alignments of a set of Echinodermata proteins as part of the MAKER automated annotation pipeline."
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+        "Track legend": "Results from Protein2genome alignments of a set of Mollusca proteins as part of the MAKER automated annotation pipeline."
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+        "arrowheadClass": "webapollo-arrowhead",
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+    },
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+      "key": "protein2genome_Nemata",
+      "label": "protein2genome_Nemata",
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+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
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+        "Track legend": "Results from Protein2genome alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline."
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+        "arrowheadClass": "webapollo-arrowhead",
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+      "type": "FeatureTrack",
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+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+      "key": "protein2genome_Nematomorpha",
+      "label": "protein2genome_Nematomorpha",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
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+      "key": "protein2genome_Onychophora",
+      "label": "protein2genome_Onychophora",
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+        "Track legend": "Results from Protein2genome alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline."
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+      "key": "protein2genome_Placozoa",
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+      "key": "protein2genome_Platyhelminthes",
+      "label": "protein2genome_Platyhelminthes",
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+      "key": "protein2genome_Priapulida",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_UNCATEGORISED/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/2. Evidence/Repeats",
+      "compress": 0,
+      "key": "repeatrunner",
+      "label": "repeatrunner",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Repeatrunner as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "repeat"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/repeatrunner/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/1. Gene Sets/Supplementary Gene Predictions",
+      "compress": 0,
+      "key": "snap_masked",
+      "label": "snap_masked",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "snap"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/snap_masked/{refseq}/trackData.json"
+    },
+    {
+      "category": "Transcriptome/Mapped Reads",
+      "key": "female RNA-Seq",
+      "label": "Agla_RNA-female",
+      "metadata": {
+        "Alignment method": "TopHat 2.0, default parameters",
+        "Alignment summary": "http://de.iplantcollaborative.org/dl/d/931C1A50-6BB7-4170-8D6A-0A608D444C9B/align_summary.txt",
+        "Data Provider": "Baylor College of Medicine",
+        "Data Source 1": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Asian_long-horned_beetle/RNA_sequence/Agla_RNA-female_ICD_AGI5DM.DDM3004-F-1_1pA_D16AUACXX-4-ID01_1_sequence.txt.bz2",
+        "Data Source 2": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Asian_long-horned_beetle/RNA_sequence/Agla_RNA-female_ICD_AGI5DM.DDM3004-F-1_1pA_D16AUACXX-4-ID01_2_sequence.txt.bz2",
+        "Read cleaning method": "None"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "bam/BCM/Agla_RNA-female_ICD_AGI5DM.bam"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Transcriptome/Coverage plots (BigWig)",
+      "key": "female RNA-Seq coverage",
+      "label": "Agla_RNA-female_bigwig",
+      "metadata": {
+        "Alignment method": "TopHat 2.0, default parameters",
+        "Alignment summary": "http://de.iplantcollaborative.org/dl/d/931C1A50-6BB7-4170-8D6A-0A608D444C9B/align_summary.txt",
+        "Data Provider": "Baylor College of Medicine",
+        "Data Source 1": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Asian_long-horned_beetle/RNA_sequence/Agla_RNA-female_ICD_AGI5DM.DDM3004-F-1_1pA_D16AUACXX-4-ID01_1_sequence.txt.bz2",
+        "Data Source 2": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Asian_long-horned_beetle/RNA_sequence/Agla_RNA-female_ICD_AGI5DM.DDM3004-F-1_1pA_D16AUACXX-4-ID01_2_sequence.txt.bz2",
+        "Read cleaning method": "None"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "clip_marker_color": "red",
+        "height": 75,
+        "neg_color": "#0086B3",
+        "pos_color": "#00BFFF"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "bigwig/Agla_RNA-female_ICD_AGI5DM.bigwig"
+    },
+    {
+      "category": "Transcriptome/Mapped Reads",
+      "key": "male RNA-Seq",
+      "label": "Agla_RNA-male",
+      "metadata": {
+        "Alignment method": "TopHat 2.0, default parameters",
+        "Alignment summary": "http://de.iplantcollaborative.org/dl/d/B49C976B-1544-4C1C-AFA9-6735F7DB5AEB/align_summary.txt",
+        "Data Provider": "Baylor College of Medicine",
+        "Data Source 1": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Asian_long-horned_beetle/RNA_sequence/Agla_RNA-male_ICD_AGI5DM.DDM3005-M-1_1pA_D16AUACXX-4-ID02_1_sequence.txt.bz2",
+        "Data Source 2": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Asian_long-horned_beetle/RNA_sequence/Agla_RNA-male_ICD_AGI5DM.DDM3005-M-1_1pA_D16AUACXX-4-ID02_2_sequence.txt.bz2",
+        "Read cleaning method": "None"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "bam/BCM/Agla_RNA-male_ICD_AGI5DM.bam"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Transcriptome/Coverage plots (BigWig)",
+      "key": "male RNA-Seq coverage",
+      "label": "Agla_RNA-male_bigwig",
+      "metadata": {
+        "Alignment method": "TopHat 2.0, default parameters",
+        "Alignment summary": "http://de.iplantcollaborative.org/dl/d/B49C976B-1544-4C1C-AFA9-6735F7DB5AEB/align_summary.txt",
+        "Data Provider": "Baylor College of Medicine",
+        "Data Source 1": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Asian_long-horned_beetle/RNA_sequence/Agla_RNA-male_ICD_AGI5DM.DDM3005-M-1_1pA_D16AUACXX-4-ID02_1_sequence.txt.bz2",
+        "Data Source 2": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Asian_long-horned_beetle/RNA_sequence/Agla_RNA-male_ICD_AGI5DM.DDM3005-M-1_1pA_D16AUACXX-4-ID02_2_sequence.txt.bz2",
+        "Read cleaning method": "None"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "clip_marker_color": "red",
+        "height": 75,
+        "neg_color": "#0086B3",
+        "pos_color": "#00BFFF"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "bigwig/Agla_RNA-male_ICD_AGI5DM.bigwig"
+    },
+    {
+      "category": "Transcriptome/Mapped Reads",
+      "key": "Scully et al. larval RNA-Seq",
+      "label": "ALBwholelarva",
+      "metadata": {
+        "Alignment method": "Remaining pairs were mapped to the ALB genome using TopHat2 with the following non-default parameters:  --library-type fr-unstranded –mate-inner-dist -30 –mate-std-dev 50 –b2-sensitive.",
+        "Bioproject accession number": "PRJNA247974",
+        "Data provider": "Erin D. Scully (USDA-ARS-Grain, Forage, and Bioenergy Research Unit, Lincoln, NE), Scott M. Geib (USDA-ARS-Pacific Basin Agricultural Research Center, Hilo, HI), and Kelli Hoover (Pennsylvania State University, University Park, PA).",
+        "Library preparation": "Four whole larvae were homogenized and pooled together for RNA isolation.  Total RNA was isolated from whole larvae using the Power Microbiome RNA isolation kit (MoBio, Carlsbad, CA) and ribosomal RNA was depleted from the sample using the Ribominus Eukaryotic Kit for RNA Seq (Life Technologies, Carlsbad, CA).  The library was prepared using the TruSeq RNA Sample Prep Kit (Illumina, San Diego, CA) and the library was enriched for 175 nt fragments so that the paired ends overlapped by 30 nt.",
+        "Read cleaning method": "Paired reads were quality filtered using ea-utils.  Pairs where one or both reads had a mean quality score less of than 30 were discarded.",
+        "Rearing conditions": "Asian longhorned beetle adults were allowed to mate and oviposit onto potted sugar maple trees maintained at a USDA-approved quarantine greenhouse located at The Pennsylvania State University, University Park, PA.  60 days after the eggs hatched (indicated by the first appearance of frass), trees were harvested and third instar larvae were collected and surface sterilized with 70% ethanol.",
+        "SRA accession number": "SRR1290861 and SRR1292125",
+        "Sequencing": "Approximately 19 million 100 nt  unstranded paired end reads were sequenced on the Illumina HiSeq 2000 platform in two separate runs.  Data for runs 1 and 2 are available under the accession numbers SRR1290861 and SRR1292125, respectively.",
+        "Track legend": "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "bam/escully/ALBwholelarva.bam"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Reference Assembly",
+      "key": "Gaps in assembly",
+      "label": "Gaps in assembly",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "white",
+        "pos_color": "black"
+      },
+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "bigwig/Agla_Btl03082013.GAPS.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "0.5",
+      "category": "Reference Assembly",
+      "key": "GC Content",
+      "label": "GC Content",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+      },
+      "scoreType": "avgScore",
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "rgba(255,255,0,50)",
+        "pos_color": "rgba(0,0,255,50)"
+      },
+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "bigwig/Agla_Btl03082013.genome_GC.bigwig"
+    },
+    {
+      "category": "Official Gene Set/1. Protein Coding Genes",
+      "compress": 0,
+      "fmtDetailValue_Id": "function (id, feature) {  var name2 = id.replace(/-R./, '');  if(feature.get('type')=='mRNA') {    return '<a target=_blank href=https://i5k.nal.usda.gov/'+name2+'>'+id+'</a>';} else { return id;}}",
+      "key": "Official Gene Set v1.2 - protein-coding genes",
+      "label": "anogla_current_models",
+      "metadata": {
+        "Data contact": "The i5k workspace@NAL; Duane McKenna (University of Memphis)",
+        "Data description": "Official Gene Set generated in collaboration with the Baylor College of Medicine, the National Agricultural Library, and the Anoplophora glabripennis manual annotation community. The OGS is a merge of a Maker2 gene set generated by Dan Hughes at BCM (AGLA_v0.5.3-Models) and manual curated genes by the Anoplophora glabripennis manual annotation community.",
+        "Publication status": "unpublished - Please follow Ft. Lauderdale and Toronto agreements"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "CDS": "ogs-cds",
+          "UTR": "ogs-utr",
+          "exon": "container-100pct",
+          "five_prime_utr": "ogs-utr",
+          "three_prime_utr": "ogs-utr",
+          "wholeCDS": null
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/anogla_current_models/{refseq}/trackData.json"
+    },
+    {
+      "category": "Official Gene Set/2. Noncoding Genes",
+      "compress": 0,
+      "key": "Official Gene Set v1.2 - pseudogenes",
+      "label": "OGS_v1.2_pseudogene",
+      "metadata": {
+        "Data contact": "The i5k workspace@NAL; Duane McKenna (University of Memphis)",
+        "Data description": "Official Gene Set generated in collaboration with the Baylor College of Medicine, the National Agricultural Library, and the Anoplophora glabripennis manual annotation community. The OGS is a merge of a Maker2 gene set generated by Dan Hughes at BCM (AGLA_v0.5.3-Models) and manual curated genes by the Anoplophora glabripennis manual annotation community.",
+        "Publication status": "unpublished - Please follow Ft. Lauderdale and Toronto agreements"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "CDS": "ogs-cds",
+          "UTR": "ogs-utr",
+          "pseudogenic_exon": "ogs-utr",
+          "wholeCDS": null
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/OGS_v1.2_pseudogene/{refseq}/trackData.json"
+    }
+  ]
 }
diff --git a/organisms/stage/Apis_mellifera/trackList.json b/organisms/stage/Apis_mellifera/trackList.json
index 881b2f1..c557e3d 100644
--- a/organisms/stage/Apis_mellifera/trackList.json
+++ b/organisms/stage/Apis_mellifera/trackList.json
@@ -1,140 +1,142 @@
 {
-   "formatVersion" : 1,
-   "names" : {
-      "type" : "Hash",
-      "url" : "names/"
-   },
-   "tracks" : [
-      {
-         "category" : "Reference sequence",
-         "faiUrlTemplate" : "seq/GCF_000002195.4_Amel_4.5_genomic.fna.fai",
-         "key" : "Reference sequence",
-         "label" : "DNA",
-         "seqType" : "dna",
-         "storeClass" : "JBrowse/Store/Sequence/IndexedFasta",
-         "type" : "SequenceTrack",
-         "urlTemplate" : "seq/GCF_000002195.4_Amel_4.5_genomic.fna",
-         "useAsRefSeqStore" : 1
+  "formatVersion": 1,
+  "names": {
+    "type": "Hash",
+    "url": "names/"
+  },
+  "tracks": [
+    {
+      "category": "Reference sequence",
+      "faiUrlTemplate": "seq/GCF_000002195.4_Amel_4.5_genomic.fna.fai",
+      "key": "Reference sequence",
+      "label": "DNA",
+      "seqType": "dna",
+      "storeClass": "JBrowse/Store/Sequence/IndexedFasta",
+      "type": "SequenceTrack",
+      "urlTemplate": "seq/GCF_000002195.4_Amel_4.5_genomic.fna",
+      "useAsRefSeqStore": 1
+    },
+    {
+      "category": "Apis mellifera Official Gene Set version 3.3",
+      "compress": 0,
+      "fmtDetailValue_Id": "function(id, feature) { var name2 = id.replace(/-R./, ''); if(feature.get('type')=='mRNA') { return ''+id+' (Click for Gene page)';} else {return id}}",
+      "key": "apimel_OGSv3.3 Gene",
+      "label": "apimel_current_models",
+      "menuTemplate": [
+        {
+          "label": "View details"
+        },
+        {
+          "action": "newWindow",
+          "iconClass": "dijitIconDatabase",
+          "label": "function(track,feature){ return 'Search HymenopteraMine for '+feature.get('id')}",
+          "title": "function(track,feature){ return 'Search HymenopteraMine for '+feature.get('id')}",
+          "url": "function(track,feature){ return 'http://128.206.116.3:8080/hymenopteramine/keywordSearchResults.do?searchTerm='+feature.get('id')+'&searchSubmit=Search'}"
+        }
+      ],
+      "metadata": {
+        "Data description": "Honey Bee Genome Sequencing Consortium. 2014. doi: 10.1186/1471-2164-15-86; https://i5k.nal.usda.gov/node/739241",
+        "Data provider": "BeeBase, http://hymenopteragenome.org/beebase/?q=consortium_datasets",
+        "Data source": "BeeBase, http://hymenopteragenome.org/beebase/?q=consortium_datasets",
+        "Method": "Honey Bee Genome Sequencing Consortium. 2014. doi: 10.1186/1471-2164-15-86; https://i5k.nal.usda.gov/node/739241",
+        "Publication status": "Published, Honey Bee Genome Sequencing Consortium. 2014. doi: 10.1186/1471-2164-15-86"
       },
-      {
-         "compress" : 0,
-         "fmtDetailValue_Id" : "function(id, feature) { var name2 = id.replace(/-R./, ''); if(feature.get('type')=='mRN:A') { return ''+id+' (Click for Gene page)';} else {return id}}",
-         "menuTemplate" : [
-             {
-                "label" : "View details",
-             },
-             {
-              "label": "function(track,feature){ return 'Search HymenopteraMine for '+feature.get('id')}",
-              "title": "function(track,feature){ return 'Search HymenopteraMine for '+feature.get('id')}",
-              "iconClass" : "dijitIconDatabase",
-              "action": "newWindow",
-              "url" : "function(track,feature){ return 'http://128.206.116.3:8080/hymenopteramine/keywordSearchResults.do?searchTerm='+feature.get('id')+'&searchSubmit=Search'}",
-              },
-        ],
-         "key" : "apimel_OGSv3.3 Gene",
-         "category":"Apis mellifera Official Gene Set version 3.3",
-         "metadata" : {
-         "Data description":"Honey Bee Genome Sequencing Consortium. 2014. doi: 10.1186/1471-2164-15-86; https://i5k.nal.usda.gov/node/739241",
-         "Data source":"BeeBase, http://hymenopteragenome.org/beebase/?q=consortium_datasets",
-         "Data provider":"BeeBase, http://hymenopteragenome.org/beebase/?q=consortium_datasets",
-         "Method":"Honey Bee Genome Sequencing Consortium. 2014. doi: 10.1186/1471-2164-15-86; https://i5k.nal.usda.gov/node/739241",
-         "Publication status":"Published, Honey Bee Genome Sequencing Consortium. 2014. doi: 10.1186/1471-2164-15-86"},
-         "label" : "apimel_current_models",
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
-         "style" : {
-            "arrowheadClass" : "trellis-arrowhead",
-            "className" : "container-16px",
-            "subfeatureClasses" : {
-               "CDS" : "primary_gene_set-cds",
-               "UTR" : "primary_gene_set-utr",
-               "exon" : "container-100pct",
-               "wholeCDS" : null
-            }
-         },
-         "trackType" : null,
-         "type" : "ColorByType/View/Track/ColorByTypeDraggable",
-         "urlTemplate" : "tracks/apimel_current_models/{refseq}/trackData.json"
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "CDS": "primary_gene_set-cds",
+          "UTR": "primary_gene_set-utr",
+          "exon": "container-100pct",
+          "wholeCDS": null
+        }
       },
-      {
-         "autoscale" : "local",
-         "bicolor_pivot" : "zero",
-         "category" : "Reference Assembly",
-         "key" : "Gaps in assembly",
-         "label" : "Gaps in assembly",
-         "metadata" : {
-            "Track contact" : "The i5k workspace@NAL",
-            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
-            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
-         },
-         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
-         "style" : {
-            "neg_color" : "white",
-            "pos_color" : "black"
-         },
-         "type" : "JBrowse/View/Track/Wiggle/Density",
-         "urlTemplate" : "bigwig/GCF_000002195.4_Amel_4.5_genomic.fna.gaps.bigwig"
+      "trackType": null,
+      "type": "HTMLFeatures",
+      "urlTemplate": "tracks/apimel_current_models/{refseq}/trackData.json"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Reference Assembly",
+      "key": "Gaps in assembly",
+      "label": "Gaps in assembly",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
       },
-      {
-         "autoscale" : "local",
-         "bicolor_pivot" : "0.5",
-         "category" : "Reference Assembly",
-         "key" : "GC Content",
-         "label" : "GC Content",
-         "metadata" : {
-            "Track contact" : "The i5k workspace@NAL",
-            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
-            "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
-         },
-         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
-         "style" : {
-            "neg_color" : "rgba(255,255,0,50)",
-            "pos_color" : "rgba(0,0,255,50)"
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diff --git a/organisms/stage/Athalia_rosae/trackList.json b/organisms/stage/Athalia_rosae/trackList.json
index 4228a68..b3607cf 100644
--- a/organisms/stage/Athalia_rosae/trackList.json
+++ b/organisms/stage/Athalia_rosae/trackList.json
@@ -1,1821 +1,1815 @@
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-            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank",
-            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
-            "Track contact" : "The i5k workspace@NAL"
-         },
-         "category" : "Reference Assembly",
-         "type" : "JBrowse/View/Track/Wiggle/Density"
-      },
-      {
-         "style" : {
-            "className" : "container-10px",
-            "subfeatureClasses" : {
-               "match_part" : "est_gff"
-            },
-            "arrowheadClass" : "webapollo-arrowhead"
-         },
-         "key" : "A. rosae females-combined Trinity transcriptome",
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
-         "trackType" : null,
-         "urlTemplate" : "tracks/atro-females-comb_est2genome/{refseq}/trackData.json",
-         "compress" : 0,
-         "metadata" : {
-            "Data Source 3" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-66-1_2pA_D191TACXX-6-ID06_D191TACXX-6-ID06_1_sequence.txt.bz2",
-            "Data Source 1" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.W-1544-1_2pA_D191TACXX-6-ID05_D191TACXX-6-ID05_1_sequence.txt.bz2",
-            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
-            "Method" : "Raw reads cleaned with Trimmomatic v0.32, using the options ILLUMINACLIP:'costumadapterlist.fa':2:30:10, SLIDINGWINDOW:4:33 and MINLEN:45. Cleaned reads from two females were concatenated and then assembled using Trinity version trinityrnaseq_r20140413p1 using default settings. Assembled transcripts were mapped to the genome using Exonerate-gff3 (https://github.com/hotdogee/exonerate-gff3) with the options: --model est2genome --showtargetgff yes --gff3 yes --showalignment no --showvulgar no --geneseed 250 --bestn 2 --percent 50 --minintron 20 --maxintron 10000. Transcripts mapping to two locations were detected and marked with a note using a custom perl script (available from JP Oeyen (Univ. Bonn/ZFMK, ZMB), janphilipoyen@gmail.com)",
-            "Data Source 4" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-66-1_2pA_D191TACXX-6-ID06_D191TACXX-6-ID06_2_sequence.txt.bz2",
-            "Data Source 2" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.W-1544-1_2pA_D191TACXX-6-ID05_D191TACXX-6-ID05_2_sequence.txt.bz2"
-         },
-         "category" : "Transcriptome/Assembly",
-         "label" : "atro-females-comb_est2genome",
-         "type" : "FeatureTrack"
-      },
-      {
-         "style" : {
-            "className" : "container-10px",
-            "subfeatureClasses" : {
-               "match_part" : "est_gff"
-            },
-            "arrowheadClass" : "webapollo-arrowhead"
-         },
-         "key" : "A. rosae male-1 Trinity transcriptome",
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
-         "trackType" : null,
-         "urlTemplate" : "tracks/atro-male-1_est2genome/{refseq}/trackData.json",
-         "compress" : 0,
-         "metadata" : {
-            "Data Source 1" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.sw-1228-WT-63-1_2pA_D191TACXX-6-ID08_D191TACXX-6-ID08_1_sequence.txt.bz2",
-            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
-            "Method" : "Raw reads cleaned with Trimmomatic v0.32, using the options ILLUMINACLIP:'costumadapterlist.fa':2:30:10, SLIDINGWINDOW:4:33 and MINLEN:45. Cleaned reads were assembled using Trinity version trinityrnaseq_r20140413p1 using default settings. Assembled transcripts were mapped to the genome using Exonerate-gff3 (https://github.com/hotdogee/exonerate-gff3) with the options: --model est2genome --showtargetgff yes --gff3 yes --showalignment no --showvulgar no --geneseed 250 --bestn 2 --percent 50 --minintron 20 --maxintron 10000. Transcripts mapping to two locations were detected and marked with a note using a custom perl script (available from JP Oeyen (Univ. Bonn/ZFMK, ZMB), janphilipoyen@gmail.com)",
-            "Data Source 2" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.sw-1228-WT-63-1_2pA_D191TACXX-6-ID08_D191TACXX-6-ID08_2_sequence.txt.bz2"
-         },
-         "category" : "Transcriptome/Assembly",
-         "label" : "atro-male-1_est2genome",
-         "type" : "FeatureTrack"
-      },
-      {
-         "style" : {
-            "className" : "container-10px",
-            "subfeatureClasses" : {
-               "match_part" : "est_gff"
-            },
-            "arrowheadClass" : "webapollo-arrowhead"
-         },
-         "key" : "A. rosae male-2 Trinity transcriptome",
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
-         "trackType" : null,
-         "urlTemplate" : "tracks/atro-male-2_est2genome/{refseq}/trackData.json",
-         "compress" : 0,
-         "metadata" : {
-            "Data Source 1" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-63-1_2pA_D191TACXX-6-ID07_D191TACXX-6-ID07_1_sequence.txt.bz2",
-            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
-            "Method" : "Raw reads cleaned with Trimmomatic v0.32, using the options ILLUMINACLIP:'costumadapterlist.fa':2:30:10, SLIDINGWINDOW:4:33 and MINLEN:45. Cleaned reads were assembled using Trinity version trinityrnaseq_r20140413p1 using default settings. Assembled transcripts were mapped to the genome using Exonerate-gff3 (https://github.com/hotdogee/exonerate-gff3) with the options: --model est2genome --showtargetgff yes --gff3 yes --showalignment no --showvulgar no --geneseed 250 --bestn 2 --percent 50 --minintron 20 --maxintron 10000. Transcripts mapping to two locations were detected and marked with a note using a custom perl script (available from JP Oeyen (Univ. Bonn/ZFMK, ZMB), janphilipoyen@gmail.com)",
-            "Data Source 2" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-63-1_2pA_D191TACXX-6-ID07_D191TACXX-6-ID07_2_sequence.txt.bz2"
-         },
-         "category" : "Transcriptome/Assembly",
-         "label" : "atro-male-2_est2genome",
-         "type" : "FeatureTrack"
-      },
-      {
-         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
-         "urlTemplate" : "bam/janphilipoeyen/Athalia_rosae/cleaned-reads-tophat/aros_male-1_tophat-accepted_hits.bam",
-         "metadata" : {
-            "Data Source 1" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.sw-1228-WT-63-1_2pA_D191TACXX-6-ID08_D191TACXX-6-ID08_1_sequence.txt.bz2",
-            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
-            "Method" : "Raw reads cleaned with Trimmomatic v0.32, using the options ILLUMINACLIP:'costumadapterlist.fa':2:30:10, SLIDINGWINDOW:4:33 and MINLEN:45. Cleaned reads mapped with TopHat v2.0.12 using default settings.",
-            "Track legend" : "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)",
-            "Data Source 2" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.sw-1228-WT-63-1_2pA_D191TACXX-6-ID08_D191TACXX-6-ID08_2_sequence.txt.bz2"
-         },
-         "category" : "Transcriptome/Mapped Reads",
-         "label" : "aros_male-1_tophat-accepted_hits",
-         "type" : "WebApollo/View/Track/DraggableAlignments",
-         "key" : "A. rosae male-1 cleaned reads"
-      },
-      {
-         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
-         "urlTemplate" : "bam/janphilipoeyen/Athalia_rosae/cleaned-reads-tophat/aros_male-2_tophat-accepted_hits.bam",
-         "metadata" : {
-            "Data Source 1" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-63-1_2pA_D191TACXX-6-ID07_D191TACXX-6-ID07_1_sequence.txt.bz2",
-            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
-            "Method" : "Raw reads cleaned with Trimmomatic v0.32, using the options ILLUMINACLIP:'costumadapterlist.fa':2:30:10, SLIDINGWINDOW:4:33 and MINLEN:45. Cleaned reads mapped with TopHat v2.0.12 using default settings.",
-            "Track legend" : "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)",
-            "Data Source 2" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-63-1_2pA_D191TACXX-6-ID07_D191TACXX-6-ID07_2_sequence.txt.bz2"
-         },
-         "category" : "Transcriptome/Mapped Reads",
-         "label" : "aros_male-2_tophat-accepted_hits",
-         "type" : "WebApollo/View/Track/DraggableAlignments",
-         "key" : "A. rosae male-2 cleaned reads"
-      },
-      {
-         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
-         "urlTemplate" : "bam/janphilipoeyen/Athalia_rosae/cleaned-reads-tophat/aros_female-1_tophat-accepted_hits.bam",
-         "metadata" : {
-            "Data Source 1" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.W-1544-1_2pA_D191TACXX-6-ID05_D191TACXX-6-ID05_1_sequence.txt.bz2",
-            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
-            "Method" : "Raw reads cleaned with Trimmomatic v0.32, using the options ILLUMINACLIP:'costumadapterlist.fa':2:30:10, SLIDINGWINDOW:4:33 and MINLEN:45. Cleaned reads mapped with TopHat v2.0.12 using default settings.",
-            "Track legend" : "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)",
-            "Data Source 2" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.W-1544-1_2pA_D191TACXX-6-ID05_D191TACXX-6-ID05_2_sequence.txt.bz2"
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-         "category" : "Transcriptome/Mapped Reads",
-         "label" : "aros_female-1_tophat-accepted_hits",
-         "type" : "WebApollo/View/Track/DraggableAlignments",
-         "key" : "A. rosae female-1 cleaned reads"
-      },
-      {
-         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
-         "urlTemplate" : "bam/janphilipoeyen/Athalia_rosae/cleaned-reads-tophat/aros_female-2_tophat-accepted_hits.bam",
-         "metadata" : {
-            "Data Source 1" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-66-1_2pA_D191TACXX-6-ID06_D191TACXX-6-ID06_1_sequence.txt.bz2",
-            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
-            "Method" : "Raw reads cleaned with Trimmomatic v0.32, using the options ILLUMINACLIP:'costumadapterlist.fa':2:30:10, SLIDINGWINDOW:4:33 and MINLEN:45. Cleaned reads mapped with TopHat v2.0.12 using default settings.",
-            "Track legend" : "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)",
-            "Data Source 2" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-66-1_2pA_D191TACXX-6-ID06_D191TACXX-6-ID06_2_sequence.txt.bz2 "
-         },
-         "category" : "Transcriptome/Mapped Reads",
-         "label" : "aros_female-2_tophat-accepted_hits",
-         "type" : "WebApollo/View/Track/DraggableAlignments",
-         "key" : "A. rosae female-2 cleaned reads"
-      },
-      {
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-         "key" : " A. rosae female-1 cleaned reads, XY-plots",
-         "autoscale" : "local",
-         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
-         "urlTemplate" : "bigwig/janphilipoeyen/Athalia_rosae/cleaned-reads-tophat/aros_female-1_tophat-accepted_hits.bigwig",
-         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
-         "metadata" : {
-            "Data Source 1" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.W-1544-1_2pA_D191TACXX-6-ID05_D191TACXX-6-ID05_1_sequence.txt.bz2",
-            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
-            "Method" : "Raw reads cleaned with Trimmomatic v0.32, using the options ILLUMINACLIP:'costumadapterlist.fa':2:30:10, SLIDINGWINDOW:4:33 and MINLEN:45. Cleaned reads mapped with TopHat v2.0.12 using default settings. Alignment files were converted by the NAL to bigwig format; reads that failed QC, secondary and supplementary alignments, and optical or PCR duplicates were ignored.",
-            "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage.",
-            "Data Source 2" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.W-1544-1_2pA_D191TACXX-6-ID05_D191TACXX-6-ID05_2_sequence.txt.bz2"
-         },
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-         "label" : "aros_female-1_tophat-accepted_hits_bigwig"
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-         "key" : " A. rosae female-2 cleaned reads, XY-plots",
-         "autoscale" : "local",
-         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
-         "urlTemplate" : "bigwig/janphilipoeyen/Athalia_rosae/cleaned-reads-tophat/aros_female-2_tophat-accepted_hits.bigwig",
-         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
-         "metadata" : {
-            "Data Source 1" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-66-1_2pA_D191TACXX-6-ID06_D191TACXX-6-ID06_1_sequence.txt.bz2",
-            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
-            "Method" : "Raw reads cleaned with Trimmomatic v0.32, using the options ILLUMINACLIP:'costumadapterlist.fa':2:30:10, SLIDINGWINDOW:4:33 and MINLEN:45. Cleaned reads mapped with TopHat v2.0.12 using default settings. Alignment files were converted by the NAL to bigwig format; reads that failed QC, secondary and supplementary alignments, and optical or PCR duplicates were ignored.",
-            "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage.",
-            "Data Source 2" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-66-1_2pA_D191TACXX-6-ID06_D191TACXX-6-ID06_2_sequence.txt.bz2 "
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-         "urlTemplate" : "bigwig/janphilipoeyen/Athalia_rosae/cleaned-reads-tophat/aros_male-1_tophat-accepted_hits.bigwig",
-         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
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-            "Data Source 1" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.sw-1228-WT-63-1_2pA_D191TACXX-6-ID08_D191TACXX-6-ID08_1_sequence.txt.bz2",
-            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
-            "Method" : "Raw reads cleaned with Trimmomatic v0.32, using the options ILLUMINACLIP:'costumadapterlist.fa':2:30:10, SLIDINGWINDOW:4:33 and MINLEN:45. Cleaned reads mapped with TopHat v2.0.12 using default settings. Alignment files were converted by the NAL to bigwig format; reads that failed QC, secondary and supplementary alignments, and optical or PCR duplicates were ignored.",
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-         "urlTemplate" : "bigwig/janphilipoeyen/Athalia_rosae/cleaned-reads-tophat/aros_male-2_tophat-accepted_hits.bigwig",
-         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
-         "metadata" : {
-            "Data Source 1" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-63-1_2pA_D191TACXX-6-ID07_D191TACXX-6-ID07_1_sequence.txt.bz2",
-            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
-            "Method" : "Raw reads cleaned with Trimmomatic v0.32, using the options ILLUMINACLIP:'costumadapterlist.fa':2:30:10, SLIDINGWINDOW:4:33 and MINLEN:45. Cleaned reads mapped with TopHat v2.0.12 using default settings. Alignment files were converted by the NAL to bigwig format; reads that failed QC, secondary and supplementary alignments, and optical or PCR duplicates were ignored.",
-            "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage.",
-            "Data Source 2" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-63-1_2pA_D191TACXX-6-ID07_D191TACXX-6-ID07_2_sequence.txt.bz2"
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-         "label" : "aros_male-2_tophat-accepted_hits_bigwig"
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-         "bicolor_pivot" : "zero",
-         "key" : "A. rosae male-1 raw reads, XY-plots",
-         "autoscale" : "local",
-         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
-         "urlTemplate" : "bigwig/Aros_ID08.bigwig",
-         "category" : "Transcriptome/Coverage plots (BigWig)",
-         "metadata" : {
-            "Alignment summary" : "http://de.iplantcollaborative.org/dl/d/C72E8FAE-2A8F-48CC-8E81-E763757DC126/align_summary.txt",
-            "Data Source 1" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.sw-1228-WT-63-1_2pA_D191TACXX-6-ID08_D191TACXX-6-ID08_1_sequence.txt.bz2",
-            "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage.",
-            "File note" : "This track replaces the previous track, 'Aros_ID08'.",
-            "Alignment method" : "TopHat 2.0, default parameters. Alignment files were converted by the NAL to bigwig format; reads that failed QC, secondary and supplementary alignments, and optical or PCR duplicates were ignored.",
-            "Data Source 2" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.sw-1228-WT-63-1_2pA_D191TACXX-6-ID08_D191TACXX-6-ID08_2_sequence.txt.bz2",
-            "Read cleaning method" : "None",
-            "Data Provider" : "Baylor College of Medicine"
-         },
-         "label" : "aros_male-1_raw_reads_bigwig",
-         "type" : "JBrowse/View/Track/Wiggle/XYPlot"
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-      {
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-         "key" : "A. rosae male-2 raw reads, XY-plots",
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-         "urlTemplate" : "bigwig/Aros_ID07.bigwig",
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+        "Track legend": "Results from Blastx alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline."
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+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Blastx alignments of a set of Nematomorpha proteins as part of the MAKER automated annotation pipeline."
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+      "key": "blastx_Parazoa",
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+        "Track legend": "Results from Blastx alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline."
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+      "label": "blastx_Placozoa",
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+        "Track legend": "Results from Blastx alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline."
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+      "label": "blastx_Platyhelminthes",
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+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Blastx alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline."
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+      "key": "blastx_Priapulida",
+      "label": "blastx_Priapulida",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
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+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Blastx alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline."
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+      "key": "blastx_Tardigrada",
+      "label": "blastx_Tardigrada",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
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+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Blastx alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline."
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+      "label": "blastx_Tunicata",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
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+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Blastx alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline."
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+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Blastx alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline."
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
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+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from EST alignments resulting from the Cufflinks software as part of the MAKER automated annotation pipeline."
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Annelida proteins as part of the MAKER automated annotation pipeline."
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
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+        "Track legend": "Results from Protein2genome alignments of a set of Arthropoda proteins as part of the MAKER automated annotation pipeline."
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+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Atelocerata proteins as part of the MAKER automated annotation pipeline."
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+      "key": "protein2genome_Cephalochordata",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Cephalochordata proteins as part of the MAKER automated annotation pipeline."
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+      "urlTemplate": "tracks/protein2genome_Cephalochordata/{refseq}/trackData.json"
+    },
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+      "compress": 0,
+      "key": "protein2genome_Chelicerata",
+      "label": "protein2genome_Chelicerata",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Chelicerata proteins as part of the MAKER automated annotation pipeline."
+      },
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+        "arrowheadClass": "webapollo-arrowhead",
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Chelicerata/{refseq}/trackData.json"
+    },
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+      "key": "protein2genome_Cnidaria",
+      "label": "protein2genome_Cnidaria",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Cnidaria proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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+          "match_part": "protein2genome"
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+      "urlTemplate": "tracks/protein2genome_Cnidaria/{refseq}/trackData.json"
+    },
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+      "key": "protein2genome_Craniata",
+      "label": "protein2genome_Craniata",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Craniata proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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+          "match_part": "protein2genome"
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+    },
+    {
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+      "compress": 0,
+      "key": "protein2genome_Crustacea",
+      "label": "protein2genome_Crustacea",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Crustacea proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
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+          "match_part": "protein2genome"
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Crustacea/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Echinodermata",
+      "label": "protein2genome_Echinodermata",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Echinodermata proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
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+          "match_part": "protein2genome"
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Echinodermata/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Mollusca",
+      "label": "protein2genome_Mollusca",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Mollusca proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
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+          "match_part": "protein2genome"
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Mollusca/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Nemata",
+      "label": "protein2genome_Nemata",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline."
+      },
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+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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+          "match_part": "protein2genome"
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+      "urlTemplate": "tracks/protein2genome_Nemata/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Nematomorpha",
+      "label": "protein2genome_Nematomorpha",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Nematomorpha proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Nematomorpha/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Onychophora",
+      "label": "protein2genome_Onychophora",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Onychophora proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
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+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Onychophora/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Parazoa",
+      "label": "protein2genome_Parazoa",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Parazoa/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Placozoa",
+      "label": "protein2genome_Placozoa",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
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+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Placozoa/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Platyhelminthes",
+      "label": "protein2genome_Platyhelminthes",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Platyhelminthes/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Priapulida",
+      "label": "protein2genome_Priapulida",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
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+      },
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Priapulida/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Tardigrada",
+      "label": "protein2genome_Tardigrada",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Tardigrada/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Tunicata",
+      "label": "protein2genome_Tunicata",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Tunicata/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_UNCATEGORISED",
+      "label": "protein2genome_UNCATEGORISED",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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+        "subfeatureClasses": {
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+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_UNCATEGORISED/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/2. Evidence/Repeats",
+      "compress": 0,
+      "key": "repeatmasker",
+      "label": "repeatmasker",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from RepeatMasker as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
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+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/repeatmasker/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/2. Evidence/Repeats",
+      "compress": 0,
+      "key": "repeatrunner",
+      "label": "repeatrunner",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Repeatrunner as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "repeat"
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+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/repeatrunner/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/1. Gene Sets/Supplementary Gene Predictions",
+      "compress": 0,
+      "key": "snap_masked",
+      "label": "snap_masked",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "snap"
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+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/snap_masked/{refseq}/trackData.json"
+    },
+    {
+      "category": "Transcriptome/Mapped Reads",
+      "key": "A. rosae female-1 raw reads",
+      "label": "Aros_ID05",
+      "metadata": {
+        "Alignment method": "TopHat 2.0, default parameters",
+        "Alignment summary": "http://de.iplantcollaborative.org/dl/d/14EEEDD5-99A7-4C0E-98F2-2AE508F0ACE3/align_summary.txt",
+        "Data Provider": "Baylor College of Medicine",
+        "Data Source 1": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.W-1544-1_2pA_D191TACXX-6-ID05_D191TACXX-6-ID05_1_sequence.txt.bz2",
+        "Data Source 2": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.W-1544-1_2pA_D191TACXX-6-ID05_D191TACXX-6-ID05_2_sequence.txt.bz2",
+        "File note": "This track replaces the previous track, 'Aros_ID05'.",
+        "Read cleaning method": "None",
+        "Track legend": "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "bam/Aros_ID05.bam"
+    },
+    {
+      "category": "Transcriptome/Mapped Reads",
+      "key": "A. rosae female-2 raw reads",
+      "label": "Aros_ID06",
+      "metadata": {
+        "Alignment method": "TopHat 2.0, default parameters",
+        "Alignment summary": "http://de.iplantcollaborative.org/dl/d/5D8FF6D9-C9E8-43AB-B492-85B96244F147/align_summary.txt",
+        "Data Provider": "Baylor College of Medicine",
+        "Data Source 1": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-66-1_2pA_D191TACXX-6-ID06_D191TACXX-6-ID06_1_sequence.txt.bz2",
+        "Data Source 2": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-66-1_2pA_D191TACXX-6-ID06_D191TACXX-6-ID06_2_sequence.txt.bz2",
+        "File note": "This track replaces the previous track, 'Aros_ID06'.",
+        "Read cleaning method": "None",
+        "Track legend": "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "bam/Aros_ID06.bam"
+    },
+    {
+      "category": "Transcriptome/Mapped Reads",
+      "key": "A. rosae male-2 raw reads",
+      "label": "Aros_ID07",
+      "metadata": {
+        "Alignment method": "TopHat 2.0, default parameters",
+        "Alignment summary": "http://de.iplantcollaborative.org/dl/d/DFED2491-A36F-41E0-BE8B-DDEDAE6050FD/align_summary.txt",
+        "Data Provider": "Baylor College of Medicine",
+        "Data Source 1": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-63-1_2pA_D191TACXX-6-ID07_D191TACXX-6-ID07_1_sequence.txt.bz2",
+        "Data Source 2": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-63-1_2pA_D191TACXX-6-ID07_D191TACXX-6-ID07_2_sequence.txt.bz2",
+        "File note": "This track replaces the previous track, 'Aros_ID07'.",
+        "Read cleaning method": "None",
+        "Track legend": "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "bam/Aros_ID07.bam"
+    },
+    {
+      "category": "Transcriptome/Mapped Reads",
+      "key": "A. rosae male-1 raw reads",
+      "label": "Aros_ID08",
+      "metadata": {
+        "Alignment method": "TopHat 2.0, default parameters",
+        "Alignment summary": "http://de.iplantcollaborative.org/dl/d/C72E8FAE-2A8F-48CC-8E81-E763757DC126/align_summary.txt",
+        "Data Provider": "Baylor College of Medicine",
+        "Data Source 1": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.sw-1228-WT-63-1_2pA_D191TACXX-6-ID08_D191TACXX-6-ID08_1_sequence.txt.bz2",
+        "Data Source 2": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.sw-1228-WT-63-1_2pA_D191TACXX-6-ID08_D191TACXX-6-ID08_2_sequence.txt.bz2",
+        "File note": "This track replaces the previous track, 'Aros_ID08'.",
+        "Read cleaning method": "None",
+        "Track legend": "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "bam/Aros_ID08.bam"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "0.5",
+      "category": "Reference Assembly",
+      "key": "GC Content",
+      "label": "GC Content",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+      },
+      "scoreType": "avgScore",
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "rgba(255,255,0,50)",
+        "pos_color": "rgba(0,0,255,50)"
+      },
+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "bigwig/Aros01112013-genome_GC.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Reference Assembly",
+      "key": "Gaps in assembly",
+      "label": "Gaps in assembly",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "white",
+        "pos_color": "black"
+      },
+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "bigwig/Aros01112013-GAPS.bigwig"
+    },
+    {
+      "category": "Transcriptome/Assembly",
+      "compress": 0,
+      "key": "A. rosae females-combined Trinity transcriptome",
+      "label": "atro-females-comb_est2genome",
+      "metadata": {
+        "Data Source 1": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.W-1544-1_2pA_D191TACXX-6-ID05_D191TACXX-6-ID05_1_sequence.txt.bz2",
+        "Data Source 2": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.W-1544-1_2pA_D191TACXX-6-ID05_D191TACXX-6-ID05_2_sequence.txt.bz2",
+        "Data Source 3": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-66-1_2pA_D191TACXX-6-ID06_D191TACXX-6-ID06_1_sequence.txt.bz2",
+        "Data Source 4": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-66-1_2pA_D191TACXX-6-ID06_D191TACXX-6-ID06_2_sequence.txt.bz2",
+        "Method": "Raw reads cleaned with Trimmomatic v0.32, using the options ILLUMINACLIP:'costumadapterlist.fa':2:30:10, SLIDINGWINDOW:4:33 and MINLEN:45. Cleaned reads from two females were concatenated and then assembled using Trinity version trinityrnaseq_r20140413p1 using default settings. Assembled transcripts were mapped to the genome using Exonerate-gff3 (https://github.com/hotdogee/exonerate-gff3) with the options: --model est2genome --showtargetgff yes --gff3 yes --showalignment no --showvulgar no --geneseed 250 --bestn 2 --percent 50 --minintron 20 --maxintron 10000. Transcripts mapping to two locations were detected and marked with a note using a custom perl script (available from JP Oeyen (Univ. Bonn/ZFMK, ZMB), janphilipoyen@gmail.com)",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "est_gff"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/atro-females-comb_est2genome/{refseq}/trackData.json"
+    },
+    {
+      "category": "Transcriptome/Assembly",
+      "compress": 0,
+      "key": "A. rosae male-1 Trinity transcriptome",
+      "label": "atro-male-1_est2genome",
+      "metadata": {
+        "Data Source 1": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.sw-1228-WT-63-1_2pA_D191TACXX-6-ID08_D191TACXX-6-ID08_1_sequence.txt.bz2",
+        "Data Source 2": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.sw-1228-WT-63-1_2pA_D191TACXX-6-ID08_D191TACXX-6-ID08_2_sequence.txt.bz2",
+        "Method": "Raw reads cleaned with Trimmomatic v0.32, using the options ILLUMINACLIP:'costumadapterlist.fa':2:30:10, SLIDINGWINDOW:4:33 and MINLEN:45. Cleaned reads were assembled using Trinity version trinityrnaseq_r20140413p1 using default settings. Assembled transcripts were mapped to the genome using Exonerate-gff3 (https://github.com/hotdogee/exonerate-gff3) with the options: --model est2genome --showtargetgff yes --gff3 yes --showalignment no --showvulgar no --geneseed 250 --bestn 2 --percent 50 --minintron 20 --maxintron 10000. Transcripts mapping to two locations were detected and marked with a note using a custom perl script (available from JP Oeyen (Univ. Bonn/ZFMK, ZMB), janphilipoyen@gmail.com)",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "est_gff"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/atro-male-1_est2genome/{refseq}/trackData.json"
+    },
+    {
+      "category": "Transcriptome/Assembly",
+      "compress": 0,
+      "key": "A. rosae male-2 Trinity transcriptome",
+      "label": "atro-male-2_est2genome",
+      "metadata": {
+        "Data Source 1": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-63-1_2pA_D191TACXX-6-ID07_D191TACXX-6-ID07_1_sequence.txt.bz2",
+        "Data Source 2": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-63-1_2pA_D191TACXX-6-ID07_D191TACXX-6-ID07_2_sequence.txt.bz2",
+        "Method": "Raw reads cleaned with Trimmomatic v0.32, using the options ILLUMINACLIP:'costumadapterlist.fa':2:30:10, SLIDINGWINDOW:4:33 and MINLEN:45. Cleaned reads were assembled using Trinity version trinityrnaseq_r20140413p1 using default settings. Assembled transcripts were mapped to the genome using Exonerate-gff3 (https://github.com/hotdogee/exonerate-gff3) with the options: --model est2genome --showtargetgff yes --gff3 yes --showalignment no --showvulgar no --geneseed 250 --bestn 2 --percent 50 --minintron 20 --maxintron 10000. Transcripts mapping to two locations were detected and marked with a note using a custom perl script (available from JP Oeyen (Univ. Bonn/ZFMK, ZMB), janphilipoyen@gmail.com)",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "est_gff"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/atro-male-2_est2genome/{refseq}/trackData.json"
+    },
+    {
+      "category": "Transcriptome/Mapped Reads",
+      "key": "A. rosae male-1 cleaned reads",
+      "label": "aros_male-1_tophat-accepted_hits",
+      "metadata": {
+        "Data Source 1": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.sw-1228-WT-63-1_2pA_D191TACXX-6-ID08_D191TACXX-6-ID08_1_sequence.txt.bz2",
+        "Data Source 2": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.sw-1228-WT-63-1_2pA_D191TACXX-6-ID08_D191TACXX-6-ID08_2_sequence.txt.bz2",
+        "Method": "Raw reads cleaned with Trimmomatic v0.32, using the options ILLUMINACLIP:'costumadapterlist.fa':2:30:10, SLIDINGWINDOW:4:33 and MINLEN:45. Cleaned reads mapped with TopHat v2.0.12 using default settings.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "bam/janphilipoeyen/Athalia_rosae/cleaned-reads-tophat/aros_male-1_tophat-accepted_hits.bam"
+    },
+    {
+      "category": "Transcriptome/Mapped Reads",
+      "key": "A. rosae male-2 cleaned reads",
+      "label": "aros_male-2_tophat-accepted_hits",
+      "metadata": {
+        "Data Source 1": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-63-1_2pA_D191TACXX-6-ID07_D191TACXX-6-ID07_1_sequence.txt.bz2",
+        "Data Source 2": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-63-1_2pA_D191TACXX-6-ID07_D191TACXX-6-ID07_2_sequence.txt.bz2",
+        "Method": "Raw reads cleaned with Trimmomatic v0.32, using the options ILLUMINACLIP:'costumadapterlist.fa':2:30:10, SLIDINGWINDOW:4:33 and MINLEN:45. Cleaned reads mapped with TopHat v2.0.12 using default settings.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "bam/janphilipoeyen/Athalia_rosae/cleaned-reads-tophat/aros_male-2_tophat-accepted_hits.bam"
+    },
+    {
+      "category": "Transcriptome/Mapped Reads",
+      "key": "A. rosae female-1 cleaned reads",
+      "label": "aros_female-1_tophat-accepted_hits",
+      "metadata": {
+        "Data Source 1": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.W-1544-1_2pA_D191TACXX-6-ID05_D191TACXX-6-ID05_1_sequence.txt.bz2",
+        "Data Source 2": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.W-1544-1_2pA_D191TACXX-6-ID05_D191TACXX-6-ID05_2_sequence.txt.bz2",
+        "Method": "Raw reads cleaned with Trimmomatic v0.32, using the options ILLUMINACLIP:'costumadapterlist.fa':2:30:10, SLIDINGWINDOW:4:33 and MINLEN:45. Cleaned reads mapped with TopHat v2.0.12 using default settings.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "bam/janphilipoeyen/Athalia_rosae/cleaned-reads-tophat/aros_female-1_tophat-accepted_hits.bam"
+    },
+    {
+      "category": "Transcriptome/Mapped Reads",
+      "key": "A. rosae female-2 cleaned reads",
+      "label": "aros_female-2_tophat-accepted_hits",
+      "metadata": {
+        "Data Source 1": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-66-1_2pA_D191TACXX-6-ID06_D191TACXX-6-ID06_1_sequence.txt.bz2",
+        "Data Source 2": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-66-1_2pA_D191TACXX-6-ID06_D191TACXX-6-ID06_2_sequence.txt.bz2 ",
+        "Method": "Raw reads cleaned with Trimmomatic v0.32, using the options ILLUMINACLIP:'costumadapterlist.fa':2:30:10, SLIDINGWINDOW:4:33 and MINLEN:45. Cleaned reads mapped with TopHat v2.0.12 using default settings.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "bam/janphilipoeyen/Athalia_rosae/cleaned-reads-tophat/aros_female-2_tophat-accepted_hits.bam"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Transcriptome/Coverage plots (BigWig)",
+      "key": " A. rosae female-1 cleaned reads, XY-plots",
+      "label": "aros_female-1_tophat-accepted_hits_bigwig",
+      "metadata": {
+        "Data Source 1": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.W-1544-1_2pA_D191TACXX-6-ID05_D191TACXX-6-ID05_1_sequence.txt.bz2",
+        "Data Source 2": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.W-1544-1_2pA_D191TACXX-6-ID05_D191TACXX-6-ID05_2_sequence.txt.bz2",
+        "Method": "Raw reads cleaned with Trimmomatic v0.32, using the options ILLUMINACLIP:'costumadapterlist.fa':2:30:10, SLIDINGWINDOW:4:33 and MINLEN:45. Cleaned reads mapped with TopHat v2.0.12 using default settings. Alignment files were converted by the NAL to bigwig format; reads that failed QC, secondary and supplementary alignments, and optical or PCR duplicates were ignored.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "This track represents an X-Y plot of RNA-Seq coverage."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "clip_marker_color": "red",
+        "height": 50,
+        "neg_color": "#005EFF",
+        "pos_color": "#FFA600"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "bigwig/janphilipoeyen/Athalia_rosae/cleaned-reads-tophat/aros_female-1_tophat-accepted_hits.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Transcriptome/Coverage plots (BigWig)",
+      "key": " A. rosae female-2 cleaned reads, XY-plots",
+      "label": "aros_female-2_tophat-accepted_hits_bigwig",
+      "metadata": {
+        "Data Source 1": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-66-1_2pA_D191TACXX-6-ID06_D191TACXX-6-ID06_1_sequence.txt.bz2",
+        "Data Source 2": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-66-1_2pA_D191TACXX-6-ID06_D191TACXX-6-ID06_2_sequence.txt.bz2 ",
+        "Method": "Raw reads cleaned with Trimmomatic v0.32, using the options ILLUMINACLIP:'costumadapterlist.fa':2:30:10, SLIDINGWINDOW:4:33 and MINLEN:45. Cleaned reads mapped with TopHat v2.0.12 using default settings. Alignment files were converted by the NAL to bigwig format; reads that failed QC, secondary and supplementary alignments, and optical or PCR duplicates were ignored.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "This track represents an X-Y plot of RNA-Seq coverage."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "clip_marker_color": "red",
+        "height": 50,
+        "neg_color": "#005EFF",
+        "pos_color": "#FFA600"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "bigwig/janphilipoeyen/Athalia_rosae/cleaned-reads-tophat/aros_female-2_tophat-accepted_hits.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Transcriptome/Coverage plots (BigWig)",
+      "key": " A. rosae male-1 cleaned reads, XY-plots",
+      "label": "aros_male-1_tophat-accepted_hits_bigwig",
+      "metadata": {
+        "Data Source 1": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.sw-1228-WT-63-1_2pA_D191TACXX-6-ID08_D191TACXX-6-ID08_1_sequence.txt.bz2",
+        "Data Source 2": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.sw-1228-WT-63-1_2pA_D191TACXX-6-ID08_D191TACXX-6-ID08_2_sequence.txt.bz2",
+        "Method": "Raw reads cleaned with Trimmomatic v0.32, using the options ILLUMINACLIP:'costumadapterlist.fa':2:30:10, SLIDINGWINDOW:4:33 and MINLEN:45. Cleaned reads mapped with TopHat v2.0.12 using default settings. Alignment files were converted by the NAL to bigwig format; reads that failed QC, secondary and supplementary alignments, and optical or PCR duplicates were ignored.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "This track represents an X-Y plot of RNA-Seq coverage."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "clip_marker_color": "red",
+        "height": 50,
+        "neg_color": "#005EFF",
+        "pos_color": "#FFA600"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "bigwig/janphilipoeyen/Athalia_rosae/cleaned-reads-tophat/aros_male-1_tophat-accepted_hits.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Transcriptome/Coverage plots (BigWig)",
+      "key": " A. rosae male-2 cleaned reads, XY-plots",
+      "label": "aros_male-2_tophat-accepted_hits_bigwig",
+      "metadata": {
+        "Data Source 1": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-63-1_2pA_D191TACXX-6-ID07_D191TACXX-6-ID07_1_sequence.txt.bz2",
+        "Data Source 2": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-63-1_2pA_D191TACXX-6-ID07_D191TACXX-6-ID07_2_sequence.txt.bz2",
+        "Method": "Raw reads cleaned with Trimmomatic v0.32, using the options ILLUMINACLIP:'costumadapterlist.fa':2:30:10, SLIDINGWINDOW:4:33 and MINLEN:45. Cleaned reads mapped with TopHat v2.0.12 using default settings. Alignment files were converted by the NAL to bigwig format; reads that failed QC, secondary and supplementary alignments, and optical or PCR duplicates were ignored.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "This track represents an X-Y plot of RNA-Seq coverage."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "clip_marker_color": "red",
+        "height": 50,
+        "neg_color": "#005EFF",
+        "pos_color": "#FFA600"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "bigwig/janphilipoeyen/Athalia_rosae/cleaned-reads-tophat/aros_male-2_tophat-accepted_hits.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Transcriptome/Coverage plots (BigWig)",
+      "key": "A. rosae male-1 raw reads, XY-plots",
+      "label": "aros_male-1_raw_reads_bigwig",
+      "metadata": {
+        "Alignment method": "TopHat 2.0, default parameters. Alignment files were converted by the NAL to bigwig format; reads that failed QC, secondary and supplementary alignments, and optical or PCR duplicates were ignored.",
+        "Alignment summary": "http://de.iplantcollaborative.org/dl/d/C72E8FAE-2A8F-48CC-8E81-E763757DC126/align_summary.txt",
+        "Data Provider": "Baylor College of Medicine",
+        "Data Source 1": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.sw-1228-WT-63-1_2pA_D191TACXX-6-ID08_D191TACXX-6-ID08_1_sequence.txt.bz2",
+        "Data Source 2": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.sw-1228-WT-63-1_2pA_D191TACXX-6-ID08_D191TACXX-6-ID08_2_sequence.txt.bz2",
+        "File note": "This track replaces the previous track, 'Aros_ID08'.",
+        "Read cleaning method": "None",
+        "Track legend": "This track represents an X-Y plot of RNA-Seq coverage."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "clip_marker_color": "red",
+        "height": 50,
+        "neg_color": "#005EFF",
+        "pos_color": "#FFA600"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "bigwig/Aros_ID08.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Transcriptome/Coverage plots (BigWig)",
+      "key": "A. rosae male-2 raw reads, XY-plots",
+      "label": "aros_male-2_raw_reads_bigwig",
+      "metadata": {
+        "Alignment method": "TopHat 2.0, default parameters. Alignment files were converted by the NAL to bigwig format; reads that failed QC, secondary and supplementary alignments, and optical or PCR duplicates were ignored.",
+        "Alignment summary": "http://de.iplantcollaborative.org/dl/d/DFED2491-A36F-41E0-BE8B-DDEDAE6050FD/align_summary.txt",
+        "Data Provider": "Baylor College of Medicine",
+        "Data Source 1": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-63-1_2pA_D191TACXX-6-ID07_D191TACXX-6-ID07_1_sequence.txt.bz2",
+        "Data Source 2": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-63-1_2pA_D191TACXX-6-ID07_D191TACXX-6-ID07_2_sequence.txt.bz2",
+        "File note": "This track replaces the previous track, 'Aros_ID07'.",
+        "Read cleaning method": "None",
+        "Track legend": "This track represents an X-Y plot of RNA-Seq coverage."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "clip_marker_color": "red",
+        "height": 50,
+        "neg_color": "#005EFF",
+        "pos_color": "#FFA600"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "bigwig/Aros_ID07.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Transcriptome/Coverage plots (BigWig)",
+      "key": "A. rosae female-2 raw reads, XY-plots",
+      "label": "aros_female-2_raw_reads_bigwig",
+      "metadata": {
+        "Alignment method": "TopHat 2.0, default parameters. Alignment files were converted by the NAL to bigwig format; reads that failed QC, secondary and supplementary alignments, and optical or PCR duplicates were ignored.",
+        "Alignment summary": "http://de.iplantcollaborative.org/dl/d/5D8FF6D9-C9E8-43AB-B492-85B96244F147/align_summary.txt",
+        "Data Provider": "Baylor College of Medicine",
+        "Data Source 1": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-66-1_2pA_D191TACXX-6-ID06_D191TACXX-6-ID06_1_sequence.txt.bz2",
+        "Data Source 2": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-66-1_2pA_D191TACXX-6-ID06_D191TACXX-6-ID06_2_sequence.txt.bz2",
+        "File note": "This track replaces the previous track, 'Aros_ID06'.",
+        "Read cleaning method": "None",
+        "Track legend": "This track represents an X-Y plot of RNA-Seq coverage."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "clip_marker_color": "red",
+        "height": 50,
+        "neg_color": "#005EFF",
+        "pos_color": "#FFA600"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "bigwig/Aros_ID06.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Transcriptome/Coverage plots (BigWig)",
+      "key": "A. rosae female-1 raw reads, XY-plots",
+      "label": "aros_female-1_raw_reads_bigwig",
+      "metadata": {
+        "Alignment method": "TopHat 2.0, default parameters. Alignment files were converted by the NAL to bigwig format; reads that failed QC, secondary and supplementary alignments, and optical or PCR duplicates were ignored.",
+        "Alignment summary": "http://de.iplantcollaborative.org/dl/d/14EEEDD5-99A7-4C0E-98F2-2AE508F0ACE3/align_summary.txt",
+        "Data Provider": "Baylor College of Medicine",
+        "Data Source 1": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.W-1544-1_2pA_D191TACXX-6-ID05_D191TACXX-6-ID05_1_sequence.txt.bz2",
+        "Data Source 2": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.W-1544-1_2pA_D191TACXX-6-ID05_D191TACXX-6-ID05_2_sequence.txt.bz2",
+        "File note": "This track replaces the previous track, 'Aros_ID05'.",
+        "Read cleaning method": "None",
+        "Track legend": "This track represents an X-Y plot of RNA-Seq coverage."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "clip_marker_color": "red",
+        "height": 50,
+        "neg_color": "#005EFF",
+        "pos_color": "#FFA600"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "bigwig/Aros_ID05.bigwig"
+    },
+    {
+      "category": "Athalia rosae OGSv1.0/1. Gene Sets/NonCoding",
+      "compress": 0,
+      "key": "Official Gene Set v1.0, miRNA",
+      "label": "OGSv.1.0-miRNA",
+      "metadata": {
+        "Analysis description": "The Official Gene Set OGSv1.0 was generated from the computationally predicted gene set AROS_v0.5.3 and manually curated models.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Official Gene Set OGS_v1.0."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "CDS": "gnomon_CDS",
+          "UTR": "gnomon_UTR",
+          "exon": "container-100pct",
+          "wholeCDS": null
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/OGSv.1.0-miRNA/{refseq}/trackData.json"
+    },
+    {
+      "category": "Athalia rosae OGSv1.0/1. Gene Sets/NonCoding",
+      "compress": 0,
+      "key": "Official Gene Set v1.0, ncRNA",
+      "label": "OGSv.1.0-ncRNA",
+      "metadata": {
+        "Analysis description": "The Official Gene Set OGSv1.0 was generated from the computationally predicted gene set AROS_v0.5.3 and manually curated models.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Official Gene Set OGS_v1.0."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "CDS": "gnomon_CDS",
+          "UTR": "gnomon_UTR",
+          "exon": "container-100pct",
+          "wholeCDS": null
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/OGSv.1.0-ncRNA/{refseq}/trackData.json"
+    },
+    {
+      "category": "Athalia rosae OGSv1.0/1. Gene Sets/NonCoding",
+      "compress": 0,
+      "key": "Official Gene Set v1.0, rRNA",
+      "label": "OGSv.1.0-rRNA",
+      "metadata": {
+        "Analysis description": "The Official Gene Set OGSv1.0 was generated from the computationally predicted gene set AROS_v0.5.3 and manually curated models.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Official Gene Set OGS_v1.0."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "CDS": "gnomon_CDS",
+          "UTR": "gnomon_UTR",
+          "exon": "container-100pct",
+          "wholeCDS": null
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/OGSv.1.0-rRNA/{refseq}/trackData.json"
+    },
+    {
+      "category": "Athalia rosae OGSv1.0/1. Gene Sets/NonCoding",
+      "compress": 0,
+      "key": "Official Gene Set v1.0, snoRNA",
+      "label": "OGSv.1.0-snoRNA",
+      "metadata": {
+        "Analysis description": "The Official Gene Set OGSv1.0 was generated from the computationally predicted gene set AROS_v0.5.3 and manually curated models.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Official Gene Set OGS_v1.0."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "CDS": "gnomon_CDS",
+          "UTR": "gnomon_UTR",
+          "exon": "container-100pct",
+          "wholeCDS": null
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/OGSv.1.0-snoRNA/{refseq}/trackData.json"
+    },
+    {
+      "category": "Athalia rosae OGSv1.0/1. Gene Sets/NonCoding",
+      "compress": 0,
+      "key": "Official Gene Set v1.0, snRNA",
+      "label": "OGSv.1.0-snRNA",
+      "metadata": {
+        "Analysis description": "The Official Gene Set OGSv1.0 was generated from the computationally predicted gene set AROS_v0.5.3 and manually curated models.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Official Gene Set OGS_v1.0."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "CDS": "gnomon_CDS",
+          "UTR": "gnomon_UTR",
+          "exon": "container-100pct",
+          "wholeCDS": null
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/OGSv.1.0-snRNA/{refseq}/trackData.json"
+    },
+    {
+      "category": "Athalia rosae OGSv1.0/1. Gene Sets/NonCoding",
+      "compress": 0,
+      "key": "Official Gene Set v1.0, tRNA",
+      "label": "OGSv.1.0-tRNA",
+      "metadata": {
+        "Analysis description": "The Official Gene Set OGSv1.0 was generated from the computationally predicted gene set AROS_v0.5.3 and manually curated models.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Official Gene Set OGS_v1.0."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "CDS": "gnomon_CDS",
+          "UTR": "gnomon_UTR",
+          "exon": "container-100pct",
+          "wholeCDS": null
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/OGSv.1.0-tRNA/{refseq}/trackData.json"
+    },
+    {
+      "category": "Athalia rosae OGSv1.0/1. Gene Sets/Other features",
+      "compress": 0,
+      "key": "Official Gene Set v1.0, transposable element",
+      "label": "OGSv.1.0-transposable_element",
+      "metadata": {
+        "Analysis description": "The Official Gene Set OGSv1.0 was generated from the computationally predicted gene set AROS_v0.5.3 and manually curated models.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Official Gene Set OGS_v1.0."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": null,
+        "className": "{type}",
+        "renderClassName": "red-100pct"
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/OGSv.1.0-transposable_element/{refseq}/trackData.json"
+    },
+    {
+      "category": "Athalia rosae OGSv1.0/1. Gene Sets/Other features",
+      "compress": 0,
+      "key": "Official Gene Set v1.0, sequence modifications",
+      "label": "OGSv.1.0-sequence",
+      "metadata": {
+        "Analysis description": "The Official Gene Set OGSv1.0 was generated from the computationally predicted gene set AROS_v0.5.3 and manually curated models.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Official Gene Set OGS_v1.0."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "className": "{type}"
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/OGSv.1.0-sequence/{refseq}/trackData.json"
+    }
+  ]
 }
diff --git a/organisms/stage/Bactrocera_cucurbitae/trackList.json b/organisms/stage/Bactrocera_cucurbitae/trackList.json
index d2986e4..e495845 100644
--- a/organisms/stage/Bactrocera_cucurbitae/trackList.json
+++ b/organisms/stage/Bactrocera_cucurbitae/trackList.json
@@ -1,222 +1,275 @@
 {
-   "css" : "./plugins/NAL_CSS/css/contrib_styles.css",
+   "alwaysOnTracks" : "DNA,Annotations",
+   "css" : "./plugins/NAL_CSS/css/main.css",
+   "favicon" : "./plugins/WebApollo/img/webapollo_favicon.ico",
+   "formatVersion" : 1,
    "share_link" : 0,
-   "plugins" : [
-      {
-         "location" : "./plugins/WebApollo",
-         "name" : "WebApollo"
-      }
-   ],
    "tracks" : [
       {
-         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
+         "category" : "Reference sequence",
          "chunkSize" : 20000,
-         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-",
+         "key" : "Reference sequence",
          "label" : "DNA",
+         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
          "type" : "SequenceTrack",
-         "category" : "Reference sequence",
-         "key" : "Reference sequence"
+         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-"
       },
       {
          "autocomplete" : "none",
+         "compress" : 0,
+         "key" : "User-created Annotations",
+         "label" : "Annotations",
+         "phase" : 0,
+         "storeClass" : "WebApollo/Store/SeqFeature/ScratchPad",
          "style" : {
-            "className" : "annot",
-            "renderClassName" : "annot-render",
-            "subfeatureClasses" : {
-               "non_canonical_three_prime_splice_site" : "noncanonical-splice-site",
-               "wholeCDS" : null,
-               "exon" : "container-100pct",
-               "CDS" : "annot-CDS",
-               "non_canonical_five_prime_splice_site" : "noncanonical-splice-site",
-               "UTR" : "annot-UTR"
-            },
-            "arrowheadClass" : "annot-arrowhead",
             "alternateClasses" : {
-               "transposable_element" : {
-                  "renderClassName" : "blue-ibeam-render",
-                  "className" : "blue-ibeam"
+               "miRNA" : {
+                  "className" : "brightgreen-80pct",
+                  "renderClassName" : "gray-center-30pct"
                },
-               "pseudogene" : {
-                  "renderClassName" : "gray-center-30pct",
-                  "className" : "light-purple-80pct"
+               "ncRNA" : {
+                  "className" : "brightgreen-80pct",
+                  "renderClassName" : "gray-center-30pct"
                },
-               "snRNA" : {
-                  "renderClassName" : "gray-center-30pct",
-                  "className" : "brightgreen-80pct"
+               "pseudogene" : {
+                  "className" : "light-purple-80pct",
+                  "renderClassName" : "gray-center-30pct"
                },
                "rRNA" : {
-                  "renderClassName" : "gray-center-30pct",
-                  "className" : "brightgreen-80pct"
-               },
-               "snoRNA" : {
-                  "renderClassName" : "gray-center-30pct",
-                  "className" : "brightgreen-80pct"
+                  "className" : "brightgreen-80pct",
+                  "renderClassName" : "gray-center-30pct"
                },
                "repeat_region" : {
                   "className" : "magenta-80pct"
                },
-               "tRNA" : {
-                  "renderClassName" : "gray-center-30pct",
-                  "className" : "brightgreen-80pct"
+               "snRNA" : {
+                  "className" : "brightgreen-80pct",
+                  "renderClassName" : "gray-center-30pct"
                },
-               "ncRNA" : {
-                  "renderClassName" : "gray-center-30pct",
-                  "className" : "brightgreen-80pct"
+               "snoRNA" : {
+                  "className" : "brightgreen-80pct",
+                  "renderClassName" : "gray-center-30pct"
                },
-               "miRNA" : {
-                  "renderClassName" : "gray-center-30pct",
-                  "className" : "brightgreen-80pct"
+               "tRNA" : {
+                  "className" : "brightgreen-80pct",
+                  "renderClassName" : "gray-center-30pct"
+               },
+               "transposable_element" : {
+                  "className" : "blue-ibeam",
+                  "renderClassName" : "blue-ibeam-render"
                }
             },
-            "uniqueIdField" : "id",
+            "arrowheadClass" : "annot-arrowhead",
             "centerSubFeature" : {
-               "non_canonical_three_prime_splice_site" : false,
-               "non_canonical_five_prime_splice_site" : false
-            }
+               "non_canonical_five_prime_splice_site" : false,
+               "non_canonical_three_prime_splice_site" : false
+            },
+            "className" : "annot",
+            "renderClassName" : "annot-render",
+            "subfeatureClasses" : {
+               "CDS" : "annot-CDS",
+               "UTR" : "annot-UTR",
+               "exon" : "container-100pct",
+               "non_canonical_five_prime_splice_site" : "noncanonical-splice-site",
+               "non_canonical_three_prime_splice_site" : "noncanonical-splice-site",
+               "wholeCDS" : null
+            },
+            "uniqueIdField" : "id"
          },
-         "key" : "User-created Annotations",
-         "storeClass" : "WebApollo/Store/SeqFeature/ScratchPad",
-         "phase" : 0,
-         "compress" : 0,
-         "label" : "Annotations",
-         "type" : "WebApollo/View/Track/AnnotTrack",
-         "subfeatures" : 1
+         "subfeatures" : 1,
+         "type" : "WebApollo/View/Track/AnnotTrack"
       },
       {
-         "style" : {
-            "pos_color" : "black",
-            "neg_color" : "white"
-         },
-         "bicolor_pivot" : "zero",
          "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Reference Assembly",
          "key" : "Gaps in assembly",
+         "label" : "Gaps in assembly",
          "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
-         "urlTemplate" : "bigwig/28588_ref_ASM80634v1_chrUn_refseq_IDS.fa.gaps.bigwig",
+         "style" : {
+            "neg_color" : "white",
+            "pos_color" : "black"
+         },
          "type" : "JBrowse/View/Track/Wiggle/Density",
-         "label" : "Gaps in assembly",
-         "category" : "Reference Assembly"
+         "urlTemplate" : "bigwig/28588_ref_ASM80634v1_chrUn_refseq_IDS.fa.gaps.bigwig"
       },
       {
+         "autoscale" : "local",
+         "bicolor_pivot" : "0.5",
+         "category" : "Reference Assembly",
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+         "label" : "GC Content",
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+         "urlTemplate" : "tracks/RefSeq_Noncoding_RNA/{refseq}/trackData.json"
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+         "type" : "FeatureTrack",
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 }
diff --git a/organisms/stage/Bactrocera_dorsalis/trackList.json b/organisms/stage/Bactrocera_dorsalis/trackList.json
index 7869a19..b0d8d8f 100644
--- a/organisms/stage/Bactrocera_dorsalis/trackList.json
+++ b/organisms/stage/Bactrocera_dorsalis/trackList.json
@@ -1,582 +1,635 @@
 {
-   "css" : "./plugins/NAL_CSS/css/contrib_styles.css",
+   "alwaysOnTracks" : "DNA,Annotations",
+   "css" : "./plugins/NAL_CSS/css/main.css",
+   "favicon" : "./plugins/WebApollo/img/webapollo_favicon.ico",
+   "formatVersion" : 1,
    "share_link" : 0,
    "tracks" : [
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          "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
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-         "category" : "Reference sequence",
          "type" : "SequenceTrack",
-         "label" : "DNA",
-         "key" : "Reference sequence"
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       {
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+         "key" : "User-created Annotations",
+         "label" : "Annotations",
+         "phase" : 0,
+         "storeClass" : "WebApollo/Store/SeqFeature/ScratchPad",
          "style" : {
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-            "className" : "annot",
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-                  "renderClassName" : "blue-ibeam-render"
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-               "pseudogene" : {
-                  "className" : "light-purple-80pct",
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                   "renderClassName" : "gray-center-30pct"
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                   "renderClassName" : "gray-center-30pct"
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                "repeat_region" : {
                   "className" : "magenta-80pct"
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-               "ncRNA" : {
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                   "renderClassName" : "gray-center-30pct"
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                   "renderClassName" : "gray-center-30pct"
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                "tRNA" : {
                   "className" : "brightgreen-80pct",
                   "renderClassName" : "gray-center-30pct"
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             "arrowheadClass" : "annot-arrowhead",
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             "centerSubFeature" : {
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+               "exon" : "container-100pct",
+               "non_canonical_five_prime_splice_site" : "noncanonical-splice-site",
+               "non_canonical_three_prime_splice_site" : "noncanonical-splice-site",
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-         "storeClass" : "WebApollo/Store/SeqFeature/ScratchPad",
-         "phase" : 0,
-         "compress" : 0,
-         "label" : "Annotations",
-         "type" : "WebApollo/View/Track/AnnotTrack",
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          "autoscale" : "local",
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-         "urlTemplate" : "bigwig/27457_ref_ASM78921v2_chrUn_refseq_IDS.fa.gaps.bigwig",
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          "label" : "Gaps in assembly",
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          "metadata" : {
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             "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
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          "style" : {
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+            "Sequencing platform and version " : "Illumina GAIIx, 2x100 bp PE",
+            "Sex" : "Pool",
+            "Strain" : "Punador",
+            "Tissue/lifestage" : "Pooled Eggs"
          },
-         "label" : "Punador_egg, XY Plot",
-         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
-         "category" : "Transcriptome/Coverage plots (BigWig)"
-      },
-      {
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          "style" : {
-            "neg_color" : "#0086B3",
-            "pos_color" : "#00BFFF",
             "bg_color" : "rgba(230,230,230,0.6)",
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+            "neg_color" : "#0086B3",
+            "pos_color" : "#00BFFF"
          },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "bam/GEIB_FilesforI5k/egg_accepted_hits.bigwig"
+      },
+      {
+         "autoscale" : "local",
          "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage plots (BigWig)",
          "key" : "Punador_unmatedFemale, XY Plot",
-         "autoscale" : "local",
-         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
-         "urlTemplate" : "bam/GEIB_FilesforI5k/female_accepted_hits.bigwig",
+         "label" : "Punador_unmatedFemale, XY Plot",
          "metadata" : {
-            "Publication Status" : "Published - Geib et al.: Characterizing the developmental transcriptome of the oriental fruit fly, Bactrocera dorsalis (Diptera: Tephritidae) through comparative genomic analysis with Drosophila melanogaster utilizing modENCODE datasets. BMC Genomics 2014 15:942",
             "Analysis method" : "TopHat v2.0.13",
-            "Tissue/lifestage" : "Pooled Unmated Adult Female",
-            "Sequencing platform and version " : "Illumina GAIIx, 2x100 bp PE",
-            "Sex" : "Female ",
-            "Other notes" : "See publication and NCBI Bioproject PRJNA167923 for sample details",
-            "Geographical location of specimen collection" : "Punador Lab colony, USDA-ARS Pacific Basin Agricultural Research Center, Hilo, HI",
             "DOI" : "doi:10.1186/1471-2164-15-942",
             "Data provider" : "Scott Geib, USDA-ARS-PBARC",
-            "Date completed" : "6/28/15",
             "Data source URL" : "http://www.ncbi.nlm.nih.gov/bioproject/167923",
+            "Date completed" : "6/28/15",
+            "Geographical location of specimen collection" : "Punador Lab colony, USDA-ARS Pacific Basin Agricultural Research Center, Hilo, HI",
             "NCBI SRA accession" : "SRX261511",
-            "Strain" : "Punador"
+            "Other notes" : "See publication and NCBI Bioproject PRJNA167923 for sample details",
+            "Publication Status" : "Published - Geib et al.: Characterizing the developmental transcriptome of the oriental fruit fly, Bactrocera dorsalis (Diptera: Tephritidae) through comparative genomic analysis with Drosophila melanogaster utilizing modENCODE datasets. BMC Genomics 2014 15:942",
+            "Sequencing platform and version " : "Illumina GAIIx, 2x100 bp PE",
+            "Sex" : "Female ",
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          },
-         "label" : "Punador_unmatedFemale, XY Plot",
-         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
-         "category" : "Transcriptome/Coverage plots (BigWig)"
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-      {
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          },
-         "bicolor_pivot" : "zero",
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "bam/GEIB_FilesforI5k/female_accepted_hits.bigwig"
+      },
+      {
          "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage plots (BigWig)",
          "key" : "Punador_larvae, XY Plot",
-         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
-         "urlTemplate" : "bam/GEIB_FilesforI5k/larvae_accepted_hits.bigwig",
+         "label" : "Punador_larvae, XY Plot",
          "metadata" : {
-            "Publication Status" : "Published - Geib et al.: Characterizing the developmental transcriptome of the oriental fruit fly, Bactrocera dorsalis (Diptera: Tephritidae) through comparative genomic analysis with Drosophila melanogaster utilizing modENCODE datasets. BMC Genomics 2014 15:942",
             "Analysis method" : "TopHat v2.0.13",
-            "Tissue/lifestage" : "Pooled Larvae",
-            "Sequencing platform and version " : "Illumina GAIIx, 2x100 bp PE",
-            "Sex" : "Pool",
-            "Other notes" : "See publication and NCBI Bioproject PRJNA167923 for sample details",
-            "Geographical location of specimen collection" : "Punador Lab colony, USDA-ARS Pacific Basin Agricultural Research Center, Hilo, HI",
             "DOI" : "doi:10.1186/1471-2164-15-942",
             "Data provider" : "Scott Geib, USDA-ARS-PBARC",
-            "Date completed" : "6/28/15",
             "Data source URL" : "http://www.ncbi.nlm.nih.gov/bioproject/167923",
+            "Date completed" : "6/28/15",
+            "Geographical location of specimen collection" : "Punador Lab colony, USDA-ARS Pacific Basin Agricultural Research Center, Hilo, HI",
             "NCBI SRA accession" : "SRX261508",
-            "Strain" : "Punador"
+            "Other notes" : "See publication and NCBI Bioproject PRJNA167923 for sample details",
+            "Publication Status" : "Published - Geib et al.: Characterizing the developmental transcriptome of the oriental fruit fly, Bactrocera dorsalis (Diptera: Tephritidae) through comparative genomic analysis with Drosophila melanogaster utilizing modENCODE datasets. BMC Genomics 2014 15:942",
+            "Sequencing platform and version " : "Illumina GAIIx, 2x100 bp PE",
+            "Sex" : "Pool",
+            "Strain" : "Punador",
+            "Tissue/lifestage" : "Pooled Larvae"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "bg_color" : "rgba(230,230,230,0.6)",
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          },
-         "label" : "Punador_larvae, XY Plot",
          "type" : "JBrowse/View/Track/Wiggle/XYPlot",
-         "category" : "Transcriptome/Coverage plots (BigWig)"
+         "urlTemplate" : "bam/GEIB_FilesforI5k/larvae_accepted_hits.bigwig"
       },
       {
-         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
-         "urlTemplate" : "bam/GEIB_FilesforI5k/egg_accepted_hits.bam",
-         "type" : "WebApollo/View/Track/DraggableAlignments",
-        "metadata": {
-                "Geographical location of specimen collection": "Punador Lab colony, USDA-ARS Pacific Basin Agricultural Research Center, Hilo, HI",
-                "Tissue/lifestage": "Pooled Eggs",
-                "Sex": "Pool",
-                "Strain": "Punador",
-                "Other notes": "See publication and NCBI Bioproject PRJNA167923 for sample details",
-                "NCBI SRA accession": "SRX261507",
-                "Sequencing platform and version ": "Illumina GAIIx, 2x100 bp PE",
-                "Data source URL": "http://www.ncbi.nlm.nih.gov/bioproject/167923",
-                "Publication Status": "Published - Geib et al.: Characterizing the developmental transcriptome of the oriental fruit fly, Bactrocera dorsalis (Diptera: Tephritidae) through comparative genomic analysis with Drosophila melanogaster utilizing modENCODE datasets. BMC Genomics 2014 15:942",
-                "DOI": "doi:10.1186/1471-2164-15-942",
-                "Data provider": "Scott Geib, USDA-ARS-PBARC",
-                "Analysis method": "TopHat v2.0.13",
-                "Date completed": "6/28/15"
-                },
          "category" : "Transcriptome/Mapped Reads",
+         "key" : "Punador_egg",
          "label" : "Punador_egg",
-         "key" : "Punador_egg"
-      },
-      {
+         "metadata" : {
+            "Analysis method" : "TopHat v2.0.13",
+            "DOI" : "doi:10.1186/1471-2164-15-942",
+            "Data provider" : "Scott Geib, USDA-ARS-PBARC",
+            "Data source URL" : "http://www.ncbi.nlm.nih.gov/bioproject/167923",
+            "Date completed" : "6/28/15",
+            "Geographical location of specimen collection" : "Punador Lab colony, USDA-ARS Pacific Basin Agricultural Research Center, Hilo, HI",
+            "NCBI SRA accession" : "SRX261507",
+            "Other notes" : "See publication and NCBI Bioproject PRJNA167923 for sample details",
+            "Publication Status" : "Published - Geib et al.: Characterizing the developmental transcriptome of the oriental fruit fly, Bactrocera dorsalis (Diptera: Tephritidae) through comparative genomic analysis with Drosophila melanogaster utilizing modENCODE datasets. BMC Genomics 2014 15:942",
+            "Sequencing platform and version " : "Illumina GAIIx, 2x100 bp PE",
+            "Sex" : "Pool",
+            "Strain" : "Punador",
+            "Tissue/lifestage" : "Pooled Eggs"
+         },
          "storeClass" : "JBrowse/Store/SeqFeature/BAM",
-         "urlTemplate" : "bam/GEIB_FilesforI5k/female_accepted_hits.bam",
-         "label" : "Punador_unmatedFemale",
-         "metadata": {
-                     "Geographical location of specimen collection": "Punador Lab colony, USDA-ARS Pacific Basin Agricultural Research Center, Hilo, HI",
-                     "Tissue/lifestage": "Pooled Unmated Adult Female",
-                     "Sex": "Female ",
-                     "Strain": "Punador",
-                     "Other notes": "See publication and NCBI Bioproject PRJNA167923 for sample details",
-                     "NCBI SRA accession": "SRX261511",
-                     "Sequencing platform and version ": "Illumina GAIIx, 2x100 bp PE",
-                     "Data source URL": "http://www.ncbi.nlm.nih.gov/bioproject/167923",
-                     "Publication Status": "Published - Geib et al.: Characterizing the developmental transcriptome of the oriental fruit fly, Bactrocera dorsalis (Diptera: Tephritidae) through comparative genomic analysis with Drosophila melanogaster utilizing modENCODE datasets. BMC Genomics 2014 15:942",
-                     "DOI": "doi:10.1186/1471-2164-15-942",
-                     "Data provider": "Scott Geib, USDA-ARS-PBARC",
-                     "Analysis method": "TopHat v2.0.13",
-                     "Date completed": "6/28/15"
-                     },
-         "category" : "Transcriptome/Mapped Reads",
          "type" : "WebApollo/View/Track/DraggableAlignments",
-         "key" : "Punador_unmatedFemale"
+         "urlTemplate" : "bam/GEIB_FilesforI5k/egg_accepted_hits.bam"
       },
       {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "Punador_unmatedFemale",
+         "label" : "Punador_unmatedFemale",
+         "metadata" : {
+            "Analysis method" : "TopHat v2.0.13",
+            "DOI" : "doi:10.1186/1471-2164-15-942",
+            "Data provider" : "Scott Geib, USDA-ARS-PBARC",
+            "Data source URL" : "http://www.ncbi.nlm.nih.gov/bioproject/167923",
+            "Date completed" : "6/28/15",
+            "Geographical location of specimen collection" : "Punador Lab colony, USDA-ARS Pacific Basin Agricultural Research Center, Hilo, HI",
+            "NCBI SRA accession" : "SRX261511",
+            "Other notes" : "See publication and NCBI Bioproject PRJNA167923 for sample details",
+            "Publication Status" : "Published - Geib et al.: Characterizing the developmental transcriptome of the oriental fruit fly, Bactrocera dorsalis (Diptera: Tephritidae) through comparative genomic analysis with Drosophila melanogaster utilizing modENCODE datasets. BMC Genomics 2014 15:942",
+            "Sequencing platform and version " : "Illumina GAIIx, 2x100 bp PE",
+            "Sex" : "Female ",
+            "Strain" : "Punador",
+            "Tissue/lifestage" : "Pooled Unmated Adult Female"
+         },
          "storeClass" : "JBrowse/Store/SeqFeature/BAM",
-         "urlTemplate" : "bam/GEIB_FilesforI5k/larvae_accepted_hits.bam",
          "type" : "WebApollo/View/Track/DraggableAlignments",
-         "metadata": {
-                     "Geographical location of specimen collection": "Punador Lab colony, USDA-ARS Pacific Basin Agricultural Research Center, Hilo, HI",
-                     "Tissue/lifestage": "Pooled Larvae",
-                     "Sex": "Pool",
-                     "Strain": "Punador",
-                     "Other notes": "See publication and NCBI Bioproject PRJNA167923 for sample details",
-                     "NCBI SRA accession": "SRX261508",
-                     "Sequencing platform and version ": "Illumina GAIIx, 2x100 bp PE",
-                     "Data source URL": "http://www.ncbi.nlm.nih.gov/bioproject/167923",
-                     "Publication Status": "Published - Geib et al.: Characterizing the developmental transcriptome of the oriental fruit fly, Bactrocera dorsalis (Diptera: Tephritidae) through comparative genomic analysis with Drosophila melanogaster utilizing modENCODE datasets. BMC Genomics 2014 15:942",
-                     "DOI": "doi:10.1186/1471-2164-15-942",
-                     "Data provider": "Scott Geib, USDA-ARS-PBARC",
-                     "Analysis method": "TopHat v2.0.13",
-                     "Date completed": "6/28/15"
-                     },
+         "urlTemplate" : "bam/GEIB_FilesforI5k/female_accepted_hits.bam"
+      },
+      {
          "category" : "Transcriptome/Mapped Reads",
+         "key" : "Punador_larvae",
          "label" : "Punador_larvae",
-         "key" : "Punador_larvae"
+         "metadata" : {
+            "Analysis method" : "TopHat v2.0.13",
+            "DOI" : "doi:10.1186/1471-2164-15-942",
+            "Data provider" : "Scott Geib, USDA-ARS-PBARC",
+            "Data source URL" : "http://www.ncbi.nlm.nih.gov/bioproject/167923",
+            "Date completed" : "6/28/15",
+            "Geographical location of specimen collection" : "Punador Lab colony, USDA-ARS Pacific Basin Agricultural Research Center, Hilo, HI",
+            "NCBI SRA accession" : "SRX261508",
+            "Other notes" : "See publication and NCBI Bioproject PRJNA167923 for sample details",
+            "Publication Status" : "Published - Geib et al.: Characterizing the developmental transcriptome of the oriental fruit fly, Bactrocera dorsalis (Diptera: Tephritidae) through comparative genomic analysis with Drosophila melanogaster utilizing modENCODE datasets. BMC Genomics 2014 15:942",
+            "Sequencing platform and version " : "Illumina GAIIx, 2x100 bp PE",
+            "Sex" : "Pool",
+            "Strain" : "Punador",
+            "Tissue/lifestage" : "Pooled Larvae"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "bam/GEIB_FilesforI5k/larvae_accepted_hits.bam"
       },
       {
-         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
-         "urlTemplate" : "bam/GEIB_FilesforI5k/male_accepted_hits.bam",
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "Punador_male",
          "label" : "Punador_male",
+         "metadata" : {
+            "Analysis method" : "TopHat v2.0.13",
+            "DOI" : "doi:10.1186/1471-2164-15-942",
+            "Data provider" : "Scott Geib, USDA-ARS-PBARC",
+            "Data source URL" : "http://www.ncbi.nlm.nih.gov/bioproject/167923",
+            "Date completed" : "6/28/15",
+            "Geographical location of specimen collection" : "Punador Lab colony, USDA-ARS Pacific Basin Agricultural Research Center, Hilo, HI",
+            "NCBI SRA accession" : "SRX261510",
+            "Other notes" : "See publication and NCBI Bioproject PRJNA167923 for sample details",
+            "Publication Status" : "Published - Geib et al.: Characterizing the developmental transcriptome of the oriental fruit fly, Bactrocera dorsalis (Diptera: Tephritidae) through comparative genomic analysis with Drosophila melanogaster utilizing modENCODE datasets. BMC Genomics 2014 15:942",
+            "Sequencing platform and version " : "Illumina GAIIx, 2x100 bp PE",
+            "Sex" : "Male",
+            "Strain" : "Punador",
+            "Tissue/lifestage" : "Pooled Adult Male "
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
          "type" : "WebApollo/View/Track/DraggableAlignments",
-         "metadata": {
-                     "Geographical location of specimen collection": "Punador Lab colony, USDA-ARS Pacific Basin Agricultural Research Center, Hilo, HI",
-                     "Tissue/lifestage": "Pooled Adult Male ",
-                     "Sex": "Male",
-                     "Strain": "Punador",
-                     "Other notes": "See publication and NCBI Bioproject PRJNA167923 for sample details",
-                     "NCBI SRA accession": "SRX261510",
-                     "Sequencing platform and version ": "Illumina GAIIx, 2x100 bp PE",
-                     "Data source URL": "http://www.ncbi.nlm.nih.gov/bioproject/167923",
-                     "Publication Status": "Published - Geib et al.: Characterizing the developmental transcriptome of the oriental fruit fly, Bactrocera dorsalis (Diptera: Tephritidae) through comparative genomic analysis with Drosophila melanogaster utilizing modENCODE datasets. BMC Genomics 2014 15:942",
-                     "DOI": "doi:10.1186/1471-2164-15-942",
-                     "Data provider": "Scott Geib, USDA-ARS-PBARC",
-                     "Analysis method": "TopHat v2.0.13",
-                     "Date completed": "6/28/15"
-                     },
-         "category" : "Transcriptome/Mapped Reads",
-         "key" : "Punador_male"
+         "urlTemplate" : "bam/GEIB_FilesforI5k/male_accepted_hits.bam"
       },
       {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "Punador_matedFemale",
+         "label" : "Punador_matedFemale",
+         "metadata" : {
+            "Analysis method" : "TopHat v2.0.13",
+            "DOI" : "doi:10.1186/1471-2164-15-942",
+            "Data provider" : "Scott Geib, USDA-ARS-PBARC",
+            "Data source URL" : "http://www.ncbi.nlm.nih.gov/bioproject/167923",
+            "Date completed" : "6/28/15",
+            "Geographical location of specimen collection" : "Punador Lab colony, USDA-ARS Pacific Basin Agricultural Research Center, Hilo, HI",
+            "NCBI SRA accession" : "SRX261512",
+            "Other notes" : "See publication and NCBI Bioproject PRJNA167923 for sample details",
+            "Publication Status" : "Published - Geib et al.: Characterizing the developmental transcriptome of the oriental fruit fly, Bactrocera dorsalis (Diptera: Tephritidae) through comparative genomic analysis with Drosophila melanogaster utilizing modENCODE datasets. BMC Genomics 2014 15:942",
+            "Sequencing platform and version " : "Illumina GAIIx, 2x100 bp PE",
+            "Sex" : "Female",
+            "Strain" : "Punador",
+            "Tissue/lifestage" : "Pooled Mated Adult Female"
+         },
          "storeClass" : "JBrowse/Store/SeqFeature/BAM",
-         "urlTemplate" : "bam/GEIB_FilesforI5k/mated_accepted_hits.bam",
          "type" : "WebApollo/View/Track/DraggableAlignments",
-         "metadata": {
-                     "Geographical location of specimen collection": "Punador Lab colony, USDA-ARS Pacific Basin Agricultural Research Center, Hilo, HI",
-                     "Tissue/lifestage": "Pooled Mated Adult Female",
-                     "Sex": "Female",
-                     "Strain": "Punador",
-                     "Other notes": "See publication and NCBI Bioproject PRJNA167923 for sample details",
-                     "NCBI SRA accession": "SRX261512",
-                     "Sequencing platform and version ": "Illumina GAIIx, 2x100 bp PE",
-                     "Data source URL": "http://www.ncbi.nlm.nih.gov/bioproject/167923",
-                     "Publication Status": "Published - Geib et al.: Characterizing the developmental transcriptome of the oriental fruit fly, Bactrocera dorsalis (Diptera: Tephritidae) through comparative genomic analysis with Drosophila melanogaster utilizing modENCODE datasets. BMC Genomics 2014 15:942",
-                     "DOI": "doi:10.1186/1471-2164-15-942",
-                     "Data provider": "Scott Geib, USDA-ARS-PBARC",
-                     "Analysis method": "TopHat v2.0.13",
-                     "Date completed": "6/28/15"
-                     },
+         "urlTemplate" : "bam/GEIB_FilesforI5k/mated_accepted_hits.bam"
+      },
+      {
          "category" : "Transcriptome/Mapped Reads",
-         "label" : "Punador_matedFemale",
-         "key" : "Punador_matedFemale"
+         "key" : "Punador_pupae",
+         "label" : "Punador_pupae",
+         "metadata" : {
+            "Analysis method" : "TopHat v2.0.13",
+            "DOI" : "doi:10.1186/1471-2164-15-942",
+            "Data provider" : "Scott Geib, USDA-ARS-PBARC",
+            "Data source URL" : "http://www.ncbi.nlm.nih.gov/bioproject/167923",
+            "Date completed" : "6/28/15",
+            "Geographical location of specimen collection" : "Punador Lab colony, USDA-ARS Pacific Basin Agricultural Research Center, Hilo, HI",
+            "NCBI SRA accession" : "SRX261509",
+            "Other notes" : "See publication and NCBI Bioproject PRJNA167923 for sample details",
+            "Publication Status" : "Published - Geib et al.: Characterizing the developmental transcriptome of the oriental fruit fly, Bactrocera dorsalis (Diptera: Tephritidae) through comparative genomic analysis with Drosophila melanogaster utilizing modENCODE datasets. BMC Genomics 2014 15:942",
+            "Sequencing platform and version " : "Illumina GAIIx, 2x100 bp PE",
+            "Sex" : "Pool",
+            "Strain" : "Punador",
+            "Tissue/lifestage" : "Pooled Pupae"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "bam/GEIB_FilesforI5k/pupae_accepted_hits.bam"
       },
       {
+         "category" : "RNA-Seq/Mapped Reads",
+         "key" : "Bacdor_ASM78921v2_RNA-Seq-alignments_2021-06-01",
+         "label" : "Bacdor_ASM78921v2_RNA-Seq-alignments_2021-06-01",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR1979675'>SRR1979675</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=DRR126149'>DRR126149</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR9945682'>SRR9945682</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR1646840'>SRR1646840</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=ERR4026397'>ERR4026397</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR13518309'>SRR13518309</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=ERR4026396'>ERR4026396</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR1646839'>SRR1646839</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR5092564'>SRR5092564</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR6981547'>SRR6981547</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Dark red alignments: Mapped portion of read aligned to forward strand<br>Light red alignments: Spliced portion of read aligned to forward strand<br>Dark blue alignments: Mapped portion of read aligned to reverse strand<br>Light blue alignments: Spliced portion of read aligned to reverse strand<br>Red marking - deletion in the read relative to the reference<br>Green marking - insertion in the read relative to the reference<br>Yellow marking  - mismatch (hover over the mismatch to see what the snp is)"
+         },
          "storeClass" : "JBrowse/Store/SeqFeature/BAM",
-         "urlTemplate" : "bam/GEIB_FilesforI5k/pupae_accepted_hits.bam",
-         "label" : "Punador_pupae",
          "type" : "WebApollo/View/Track/DraggableAlignments",
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diff --git a/organisms/stage/Bactrocera_oleae/trackList.json b/organisms/stage/Bactrocera_oleae/trackList.json
index 52399f3..bdfce96 100644
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+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "exon": "container-100pct",
+          "match_part": "repeat"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/Simple repeats/{refseq}/trackData.json"
+    },
+    {
+      "category": "JAMg/3. Other features",
+      "compress": 0,
+      "key": "Known Insecta Repeats",
+      "label": "Known Insecta Repeats",
+      "metadata": {
+        "Analysis method": "RepeatMasker-open-4-0-6",
+        "Date completed": "1/3/16",
+        "Descriptive track name": "Known Insecta Repeats",
+        "File provider": "Alexie Papanicolaou; Hawkesbury Institute for the Environment",
+        "File type": "GFF3",
+        "Publication Status": "Unpublished - released under Creative License Attribution"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "exon": "container-100pct",
+          "match_part": "repeat"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/Known Insecta Repeats/{refseq}/trackData.json"
+    },
+    {
+      "category": "JAMg/3. Other features",
+      "compress": 0,
+      "key": "tRNAScan predictions (mtDNA eukaryotic)",
+      "label": "tRNAScan predictions (mtDNA eukaryotic)",
+      "metadata": {
+        "Analysis method": "TRNAscan-SE-1.3.1",
+        "Date completed": "1/3/16",
+        "Descriptive track name": "tRNAScan predictions (mtDNA eukaryotic)",
+        "File provider": "Alexie Papanicolaou; Hawkesbury Institute for the Environment",
+        "File type": "GFF3",
+        "Publication Status": "Unpublished - released under Creative License Attribution"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "CDS": "gnomon_CDS",
+          "UTR": "gnomon_UTR",
+          "exon": "container-100pct",
+          "match_part": "protein2genome",
+          "wholeCDS": null
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/tRNAScan predictions (mtDNA eukaryotic)/{refseq}/trackData.json"
+    },
+    {
+      "category": "JAMg/3. Other features",
+      "compress": 0,
+      "key": "tRNAScan predictions (general eukaryotic)",
+      "label": "tRNAScan predictions (general eukaryotic)",
+      "metadata": {
+        "Analysis method": "TRNAscan-SE-1.3.1",
+        "Date completed": "1/3/16",
+        "Descriptive track name": "tRNAScan predictions (general eukaryotic)",
+        "File provider": "Alexie Papanicolaou; Hawkesbury Institute for the Environment",
+        "File type": "GFF3",
+        "Publication Status": "Unpublished - released under Creative License Attribution"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "CDS": "gnomon_CDS",
+          "UTR": "gnomon_UTR",
+          "exon": "container-100pct",
+          "match_part": "protein2genome",
+          "wholeCDS": null
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/tRNAScan predictions (general eukaryotic)/{refseq}/trackData.json"
+    },
+    {
+      "category": "JAMg/3. Other features",
+      "compress": 0,
+      "key": "tRNA aragorn predictions (mtDNA eukaryotic)",
+      "label": "tRNA aragorn predictions (mtDNA eukaryotic)",
+      "metadata": {
+        "Analysis method": "aragorn1.2.36/",
+        "Date completed": "1/3/16",
+        "Descriptive track name": "tRNA aragorn predictions (mtDNA eukaryotic)",
+        "File provider": "Alexie Papanicolaou; Hawkesbury Institute for the Environment",
+        "File type": "GFF3",
+        "Publication Status": "Unpublished - released under Creative License Attribution"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "exon": "container-100pct",
+          "match_part": "protein2genome",
+          "wholeCDS": null
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/tRNA aragorn predictions (mtDNA eukaryotic)/{refseq}/trackData.json"
+    }
+  ]
 }
diff --git a/organisms/stage/Bemisia_tabaci/trackList.json b/organisms/stage/Bemisia_tabaci/trackList.json
index 313bc71..64f7a8a 100644
--- a/organisms/stage/Bemisia_tabaci/trackList.json
+++ b/organisms/stage/Bemisia_tabaci/trackList.json
@@ -1,1280 +1,1293 @@
 {
-   "css" : "./plugins/NAL_CSS/css/contrib_styles.css",
+   "alwaysOnTracks" : "DNA,Annotations",
+   "css" : "./plugins/NAL_CSS/css/main.css",
+   "favicon" : "./plugins/WebApollo/img/webapollo_favicon.ico",
+   "formatVersion" : 1,
+   "names" : {
+      "type" : "Hash",
+      "url" : "names/"
+   },
    "share_link" : 0,
-   "plugins" : [
-      {
-         "location" : "./plugins/WebApollo",
-         "name" : "WebApollo"
-      }
-   ],
    "tracks" : [
       {
-         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
+         "category" : "Reference sequence",
          "chunkSize" : 20000,
-         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-",
+         "key" : "Reference sequence",
          "label" : "DNA",
+         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
          "type" : "SequenceTrack",
-         "category" : "Reference sequence",
-         "key" : "Reference sequence"
+         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-"
       },
       {
          "autocomplete" : "none",
+         "compress" : 0,
+         "key" : "User-created Annotations",
+         "label" : "Annotations",
+         "phase" : 0,
+         "storeClass" : "WebApollo/Store/SeqFeature/ScratchPad",
          "style" : {
-            "className" : "annot",
-            "renderClassName" : "annot-render",
-            "subfeatureClasses" : {
-               "non_canonical_three_prime_splice_site" : "noncanonical-splice-site",
-               "wholeCDS" : null,
-               "exon" : "container-100pct",
-               "CDS" : "annot-CDS",
-               "non_canonical_five_prime_splice_site" : "noncanonical-splice-site",
-               "UTR" : "annot-UTR"
-            },
-            "arrowheadClass" : "annot-arrowhead",
             "alternateClasses" : {
-               "transposable_element" : {
-                  "renderClassName" : "blue-ibeam-render",
-                  "className" : "blue-ibeam"
+               "miRNA" : {
+                  "className" : "brightgreen-80pct",
+                  "renderClassName" : "gray-center-30pct"
                },
-               "pseudogene" : {
-                  "renderClassName" : "gray-center-30pct",
-                  "className" : "light-purple-80pct"
+               "ncRNA" : {
+                  "className" : "brightgreen-80pct",
+                  "renderClassName" : "gray-center-30pct"
                },
-               "snRNA" : {
-                  "renderClassName" : "gray-center-30pct",
-                  "className" : "brightgreen-80pct"
+               "pseudogene" : {
+                  "className" : "light-purple-80pct",
+                  "renderClassName" : "gray-center-30pct"
                },
                "rRNA" : {
-                  "renderClassName" : "gray-center-30pct",
-                  "className" : "brightgreen-80pct"
-               },
-               "snoRNA" : {
-                  "renderClassName" : "gray-center-30pct",
-                  "className" : "brightgreen-80pct"
+                  "className" : "brightgreen-80pct",
+                  "renderClassName" : "gray-center-30pct"
                },
                "repeat_region" : {
                   "className" : "magenta-80pct"
                },
-               "miRNA" : {
-                  "renderClassName" : "gray-center-30pct",
-                  "className" : "brightgreen-80pct"
+               "snRNA" : {
+                  "className" : "brightgreen-80pct",
+                  "renderClassName" : "gray-center-30pct"
+               },
+               "snoRNA" : {
+                  "className" : "brightgreen-80pct",
+                  "renderClassName" : "gray-center-30pct"
                },
                "tRNA" : {
-                  "renderClassName" : "gray-center-30pct",
-                  "className" : "brightgreen-80pct"
+                  "className" : "brightgreen-80pct",
+                  "renderClassName" : "gray-center-30pct"
                },
-               "ncRNA" : {
-                  "renderClassName" : "gray-center-30pct",
-                  "className" : "brightgreen-80pct"
+               "transposable_element" : {
+                  "className" : "blue-ibeam",
+                  "renderClassName" : "blue-ibeam-render"
                }
             },
-            "uniqueIdField" : "id",
+            "arrowheadClass" : "annot-arrowhead",
             "centerSubFeature" : {
-               "non_canonical_three_prime_splice_site" : false,
-               "non_canonical_five_prime_splice_site" : false
-            }
+               "non_canonical_five_prime_splice_site" : false,
+               "non_canonical_three_prime_splice_site" : false
+            },
+            "className" : "annot",
+            "renderClassName" : "annot-render",
+            "subfeatureClasses" : {
+               "CDS" : "annot-CDS",
+               "UTR" : "annot-UTR",
+               "exon" : "container-100pct",
+               "non_canonical_five_prime_splice_site" : "noncanonical-splice-site",
+               "non_canonical_three_prime_splice_site" : "noncanonical-splice-site",
+               "wholeCDS" : null
+            },
+            "uniqueIdField" : "id"
          },
-         "key" : "User-created Annotations",
-         "storeClass" : "WebApollo/Store/SeqFeature/ScratchPad",
-         "phase" : 0,
-         "compress" : 0,
-         "label" : "Annotations",
-         "type" : "WebApollo/View/Track/AnnotTrack",
-         "subfeatures" : 1
+         "subfeatures" : 1,
+         "type" : "WebApollo/View/Track/AnnotTrack"
       },
       {
-         "style" : {
-            "pos_color" : "black",
-            "neg_color" : "white"
-         },
-         "bicolor_pivot" : "zero",
          "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Reference Assembly",
          "key" : "Gaps in assembly",
-         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
-         "urlTemplate" : "bigwig/GCF_001854935.1_ASM185493v1_genomic.fna.gaps.bigwig",
-         "type" : "JBrowse/View/Track/Wiggle/Density",
          "label" : "Gaps in assembly",
          "metadata" : {
-            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank",
+            "Track contact" : "The i5k workspace@NAL",
             "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
-            "Track contact" : "The i5k workspace@NAL"
+            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
          },
-         "category" : "Reference Assembly"
-      },
-      {
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
          "style" : {
-            "neg_color" : "rgba(255,255,0,50)",
-            "pos_color" : "rgba(0,0,255,50)"
+            "neg_color" : "white",
+            "pos_color" : "black"
          },
+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/GCF_001854935.1_ASM185493v1_genomic.fna.gaps.bigwig"
+      },
+      {
+         "autoscale" : "local",
          "bicolor_pivot" : "0.5",
+         "category" : "Reference Assembly",
          "key" : "GC Content",
-         "scoreType": "avgScore",
-         "autoscale" : "local",
-         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
-         "urlTemplate" : "bigwig/GCF_001854935.1_ASM185493v1_genomic.fna.gc.bigwig",
-         "type" : "JBrowse/View/Track/Wiggle/Density",
          "label" : "GC Content",
-         "category" : "Reference Assembly",
          "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
             "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
-            "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track.",
-            "Track contact" : "The i5k workspace@NAL"
-         }
-      },
-      {
+            "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+         },
+         "scoreType" : "avgScore",
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
          "style" : {
-            "className" : "container-16px",
-            "subfeatureClasses" : {
-               "wholeCDS" : null,
-               "exon" : "container-100pct",
-               "CDS" : "primary_gene_set-cds",
-               "UTR" : "primary_gene_set-utr"
-            },
-            "arrowheadClass" : "trellis-arrowhead"
+            "neg_color" : "rgba(255,255,0,50)",
+            "pos_color" : "rgba(0,0,255,50)"
          },
-         "key" : "NCBI Predicted protein coding genes, Annotation Release 100",
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
-         "trackType" : null,
-         "urlTemplate" : "tracks/NCBI_Annotation_Release_100_protein-coding/{refseq}/trackData.json",
+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/GCF_001854935.1_ASM185493v1_genomic.fna.gc.bigwig"
+      },
+      {
+         "category" : "NCBI Annotation Release 100/1. Gene Sets/Protein Coding",
          "compress" : 0,
+         "key" : "NCBI Predicted protein coding genes, Annotation Release 100",
+         "label" : "NCBI_Annotation_Release_100_protein-coding",
          "metadata" : {
+            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Bemisia_tabaci/README_CURRENT_RELEASE",
+            "Data provider" : "NCBI",
             "Data source" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/854/935/GCF_001854935.1_ASM185493v1/GCF_001854935.1_ASM185493v1_genomic.gff.gz",
             "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/",
-            "Data provider" : "NCBI",
-            "Note" : "Some genes may have non-coding transcripts",
-            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Bemisia_tabaci/README_CURRENT_RELEASE"
+            "Note" : "Some genes may have non-coding transcripts"
          },
-         "type" : "FeatureTrack",
-         "category" : "NCBI Annotation Release 100/1. Gene Sets/Protein Coding",
-         "label" : "NCBI_Annotation_Release_100_protein-coding"
-      },
-      {
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "className" : "container-16px",
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "{type}",
             "subfeatureClasses" : {
-               "wholeCDS" : null,
+               "CDS" : "primary_gene_set-cds",
+               "UTR" : "primary_gene_set-utr",
                "exon" : "container-100pct",
-               "CDS" : "gnomon_CDS",
-               "UTR" : "gnomon_UTR"
-            },
-            "arrowheadClass" : "trellis-arrowhead"
+               "wholeCDS" : null
+            }
          },
-         "key" : "NCBI Predicted pseudogenes, Annotation Release 100",
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "trackType" : null,
-         "urlTemplate" : "tracks/NCBI_Annotation_Release_100_Pseudogene/{refseq}/trackData.json",
-         "compress" : 0,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/NCBI_Annotation_Release_100_protein-coding/{refseq}/trackData.json"
+      },
+      {
          "category" : "NCBI Annotation Release 100/1. Gene Sets/Pseudogenes",
+         "compress" : 0,
+         "key" : "NCBI Predicted pseudogenes, Annotation Release 100",
          "label" : "NCBI_Annotation_Release_100_Pseudogene",
-         "type" : "FeatureTrack",
          "metadata" : {
-            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/",
-            "Data source" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/854/935/GCF_001854935.1_ASM185493v1/GCF_001854935.1_ASM185493v1_genomic.gff.gz",
+            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Bemisia_tabaci/README_CURRENT_RELEASE",
             "Data provider" : "NCBI",
-            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Bemisia_tabaci/README_CURRENT_RELEASE"
-         }
-      },
-      {
+            "Data source" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/854/935/GCF_001854935.1_ASM185493v1/GCF_001854935.1_ASM185493v1_genomic.gff.gz",
+            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "className" : "container-16px",
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "{type}",
             "subfeatureClasses" : {
-               "wholeCDS" : null,
-               "exon" : "container-100pct",
                "CDS" : "gnomon_CDS",
-               "UTR" : null
-            },
-            "arrowheadClass" : "trellis-arrowhead"
+               "UTR" : "gnomon_UTR",
+               "exon" : "container-100pct",
+               "wholeCDS" : null
+            }
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-         "key" : "NCBI Predicted mtDNA protein coding genes, Annotation Release 100",
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "trackType" : null,
-         "urlTemplate" : "tracks/NCBI Predicted mtDNA protein coding genes, Annotation Release 100/{refseq}/trackData.json",
-         "compress" : 0,
          "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/NCBI_Annotation_Release_100_Pseudogene/{refseq}/trackData.json"
+      },
+      {
+         "category" : "NCBI Annotation Release 100/1. Gene Sets/Protein Coding",
+         "compress" : 0,
+         "key" : "NCBI Predicted mtDNA protein coding genes, Annotation Release 100",
+         "label" : "NCBI Predicted mtDNA protein coding genes, Annotation Release 100",
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-            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/",
+            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Bemisia_tabaci/README_CURRENT_RELEASE",
             "Data provider" : "NCBI",
-            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Bemisia_tabaci/README_CURRENT_RELEASE"
+            "Data source" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/854/935/GCF_001854935.1_ASM185493v1/GCF_001854935.1_ASM185493v1_genomic.gff.gz",
+            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
          },
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-         "category" : "NCBI Annotation Release 100/1. Gene Sets/Protein Coding"
-      },
-      {
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "className" : "container-16px",
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "{type}",
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-               "UTR" : "gnomon_UTR"
-            },
-            "arrowheadClass" : "trellis-arrowhead"
+               "UTR" : null,
+               "exon" : "container-100pct",
+               "wholeCDS" : null
+            }
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-         "key" : "NCBI Predicted lncRNA, Annotation Release 100",
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "trackType" : null,
-         "urlTemplate" : "tracks/NCBI_Annotation_Release_100_lncRNA/{refseq}/trackData.json",
-         "compress" : 0,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/NCBI Predicted mtDNA protein coding genes, Annotation Release 100/{refseq}/trackData.json"
+      },
+      {
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+         "compress" : 0,
+         "key" : "NCBI Predicted lncRNA, Annotation Release 100",
          "label" : "NCBI_Annotation_Release_100_lncRNA",
-         "type" : "FeatureTrack",
          "metadata" : {
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+            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Bemisia_tabaci/README_CURRENT_RELEASE",
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-         }
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+            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "className" : "container-16px",
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "{type}",
             "subfeatureClasses" : {
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                "CDS" : "gnomon_CDS",
-               "UTR" : "gnomon_UTR"
-            },
-            "arrowheadClass" : "trellis-arrowhead"
+               "UTR" : "gnomon_UTR",
+               "exon" : "container-100pct",
+               "wholeCDS" : null
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-         "key" : "NCBI Predicted tRNAs, Annotation Release 100",
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          "trackType" : null,
-         "urlTemplate" : "tracks/NCBI_Annotation_Release_100_tRNA/{refseq}/trackData.json",
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-	"Publication status":"Published: Please cite https://doi.org/10.1186/s12915-016-0321-y",
-	"Tissues/Life stage included":"adults",
-	"isolate":"MEAM17"
-},
          "type" : "WebApollo/View/Track/DraggableAlignments",
-         "label" : "TYLCV_72h_rep2",
-         "key" : "TYLCV_72h_rep2"
+         "urlTemplate" : "user_contributed_data/ARS_11_2017/Bemisia_tabaci_Nov_29__2017/Bemisia_tabaci_Bam_Files/WF-35.bam.sorted"
       },
       {
-         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
-         "urlTemplate" : "user_contributed_data/ARS_11_2017/Bemisia_tabaci_Nov_29__2017/Bemisia_tabaci_Bam_Files/WF-26.bam.sorted",
-
-"category" : "Transcriptome/Mapped Reads",
-"metadata" : {
-	"Track legend":"Mapped RNA-Seq reads:<br>Aligned regions: blue<br>Spanned regions (possible splice junctions): light blue<br>Deletions in the read relative to the reference: red<br>Insertions in the read relative to the reference: green<br>Mismatch: yellow (hover over the mismatch to see what the snp is)",
-	"Geographic location (latitude and longitude)":"Charleston, SC, USA",
-	"Data description":"RNA derived from adults fed on uninfected tomato cuttings for 48 h",
-	"Data source":"PRJNA312467",
-	"Data provider":"Kai-Shu Ling, USDA-ARS",
-	"Method":"Illumina HiSeq 2507",
-	"Publication status":"Published: Please cite https://doi.org/10.1186/s12915-016-0321-y",
-	"Tissues/Life stage included":"adults",
-	"isolate":"MEAM8"
-},
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "healthy_48h_rep2",
          "label" : "healthy_48h_rep2",
+         "metadata" : {
+            "Data description" : "RNA derived from adults fed on uninfected tomato cuttings for 48 h",
+            "Data provider" : "Kai-Shu Ling, USDA-ARS",
+            "Data source" : "PRJNA312467",
+            "Geographic location (latitude and longitude)" : "Charleston, SC, USA",
+            "Method" : "Illumina HiSeq 2507",
+            "Publication status" : "Published: Please cite https://doi.org/10.1186/s12915-016-0321-y",
+            "Tissues/Life stage included" : "adults",
+            "Track legend" : "Mapped RNA-Seq reads:<br>Aligned regions: blue<br>Spanned regions (possible splice junctions): light blue<br>Deletions in the read relative to the reference: red<br>Insertions in the read relative to the reference: green<br>Mismatch: yellow (hover over the mismatch to see what the snp is)",
+            "isolate" : "MEAM8"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
          "type" : "WebApollo/View/Track/DraggableAlignments",
-         "key" : "healthy_48h_rep2"
+         "urlTemplate" : "user_contributed_data/ARS_11_2017/Bemisia_tabaci_Nov_29__2017/Bemisia_tabaci_Bam_Files/WF-26.bam.sorted"
       },
       {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "healthy_72h_rep3",
+         "label" : "healthy_72h_rep3",
+         "metadata" : {
+            "Data description" : "RNA derived from adults fed on uninfected tomato cuttings for 72 h",
+            "Data provider" : "Kai-Shu Ling, USDA-ARS",
+            "Data source" : "PRJNA312467",
+            "Geographic location (latitude and longitude)" : "Charleston, SC, USA",
+            "Method" : "Illumina HiSeq 2514",
+            "Publication status" : "Published: Please cite https://doi.org/10.1186/s12915-016-0321-y",
+            "Tissues/Life stage included" : "adults",
+            "Track legend" : "Mapped RNA-Seq reads:<br>Aligned regions: blue<br>Spanned regions (possible splice junctions): light blue<br>Deletions in the read relative to the reference: red<br>Insertions in the read relative to the reference: green<br>Mismatch: yellow (hover over the mismatch to see what the snp is)",
+            "isolate" : "MEAM15"
+         },
          "storeClass" : "JBrowse/Store/SeqFeature/BAM",
-         "urlTemplate" : "user_contributed_data/ARS_11_2017/Bemisia_tabaci_Nov_29__2017/Bemisia_tabaci_Bam_Files/WF-33.bam.sorted",
-
-"category" : "Transcriptome/Mapped Reads",
-"metadata" : {
-	"Track legend":"Mapped RNA-Seq reads:<br>Aligned regions: blue<br>Spanned regions (possible splice junctions): light blue<br>Deletions in the read relative to the reference: red<br>Insertions in the read relative to the reference: green<br>Mismatch: yellow (hover over the mismatch to see what the snp is)",
-	"Geographic location (latitude and longitude)":"Charleston, SC, USA",
-	"Data description":"RNA derived from adults fed on uninfected tomato cuttings for 72 h",
-	"Data source":"PRJNA312467",
-	"Data provider":"Kai-Shu Ling, USDA-ARS",
-	"Method":"Illumina HiSeq 2514",
-	"Publication status":"Published: Please cite https://doi.org/10.1186/s12915-016-0321-y",
-	"Tissues/Life stage included":"adults",
-	"isolate":"MEAM15"
-},
          "type" : "WebApollo/View/Track/DraggableAlignments",
-         "label" : "healthy_72h_rep3",
-         "key" : "healthy_72h_rep3"
+         "urlTemplate" : "user_contributed_data/ARS_11_2017/Bemisia_tabaci_Nov_29__2017/Bemisia_tabaci_Bam_Files/WF-33.bam.sorted"
       },
       {
-         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
-         "urlTemplate" : "user_contributed_data/ARS_11_2017/Bemisia_tabaci_Nov_29__2017/Bemisia_tabaci_Bam_Files/WF-37.bam.sorted",
-
-"category" : "Transcriptome/Mapped Reads",
-"metadata" : {
-	"Track legend":"Mapped RNA-Seq reads:<br>Aligned regions: blue<br>Spanned regions (possible splice junctions): light blue<br>Deletions in the read relative to the reference: red<br>Insertions in the read relative to the reference: green<br>Mismatch: yellow (hover over the mismatch to see what the snp is)",
-	"Geographic location (latitude and longitude)":"Charleston, SC, USA",
-	"Data description":"RNA derived from eggs",
-	"Data source":"PRJNA312467",
-	"Data provider":"Kai-Shu Ling, USDA-ARS",
-	"Method":"Illumina HiSeq 2518",
-	"Publication status":"Published: Please cite https://doi.org/10.1186/s12915-016-0321-y",
-	"Tissues/Life stage included":"Eggs",
-	"isolate":"MEAM19"
-},
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "Eggs_rep1",
          "label" : "Eggs_rep1",
+         "metadata" : {
+            "Data description" : "RNA derived from eggs",
+            "Data provider" : "Kai-Shu Ling, USDA-ARS",
+            "Data source" : "PRJNA312467",
+            "Geographic location (latitude and longitude)" : "Charleston, SC, USA",
+            "Method" : "Illumina HiSeq 2518",
+            "Publication status" : "Published: Please cite https://doi.org/10.1186/s12915-016-0321-y",
+            "Tissues/Life stage included" : "Eggs",
+            "Track legend" : "Mapped RNA-Seq reads:<br>Aligned regions: blue<br>Spanned regions (possible splice junctions): light blue<br>Deletions in the read relative to the reference: red<br>Insertions in the read relative to the reference: green<br>Mismatch: yellow (hover over the mismatch to see what the snp is)",
+            "isolate" : "MEAM19"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
          "type" : "WebApollo/View/Track/DraggableAlignments",
-         "key" : "Eggs_rep1"
+         "urlTemplate" : "user_contributed_data/ARS_11_2017/Bemisia_tabaci_Nov_29__2017/Bemisia_tabaci_Bam_Files/WF-37.bam.sorted"
       },
       {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "TYLCV_24h_rep1",
+         "label" : "TYLCV_24h_rep1",
+         "metadata" : {
+            "Data description" : "RNA derived from adults fed on TYLCV-infected tomato cuttings for 24 h",
+            "Data provider" : "Kai-Shu Ling, USDA-ARS",
+            "Data source" : "PRJNA312467",
+            "Geographic location (latitude and longitude)" : "Charleston, SC, USA",
+            "Method" : "Illumina HiSeq 2503",
+            "Publication status" : "Published: Please cite https://doi.org/10.1186/s12915-016-0321-y",
+            "Tissues/Life stage included" : "adults",
+            "Track legend" : "Mapped RNA-Seq reads:<br>Aligned regions: blue<br>Spanned regions (possible splice junctions): light blue<br>Deletions in the read relative to the reference: red<br>Insertions in the read relative to the reference: green<br>Mismatch: yellow (hover over the mismatch to see what the snp is)",
+            "isolate" : "MEAM4"
+         },
          "storeClass" : "JBrowse/Store/SeqFeature/BAM",
-         "urlTemplate" : "user_contributed_data/ARS_11_2017/Bemisia_tabaci_Nov_29__2017/Bemisia_tabaci_Bam_Files/WF-22.bam.sorted",
-
-"category" : "Transcriptome/Mapped Reads",
-"metadata" : {
-	"Track legend":"Mapped RNA-Seq reads:<br>Aligned regions: blue<br>Spanned regions (possible splice junctions): light blue<br>Deletions in the read relative to the reference: red<br>Insertions in the read relative to the reference: green<br>Mismatch: yellow (hover over the mismatch to see what the snp is)",
-	"Geographic location (latitude and longitude)":"Charleston, SC, USA",
-	"Data description":"RNA derived from adults fed on TYLCV-infected tomato cuttings for 24 h",
-	"Data source":"PRJNA312467",
-	"Data provider":"Kai-Shu Ling, USDA-ARS",
-	"Method":"Illumina HiSeq 2503",
-	"Publication status":"Published: Please cite https://doi.org/10.1186/s12915-016-0321-y",
-	"Tissues/Life stage included":"adults",
-	"isolate":"MEAM4"
-},
          "type" : "WebApollo/View/Track/DraggableAlignments",
-         "label" : "TYLCV_24h_rep1",
-         "key" : "TYLCV_24h_rep1"
+         "urlTemplate" : "user_contributed_data/ARS_11_2017/Bemisia_tabaci_Nov_29__2017/Bemisia_tabaci_Bam_Files/WF-22.bam.sorted"
       },
       {
-         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
-         "urlTemplate" : "user_contributed_data/ARS_11_2017/Bemisia_tabaci_Nov_29__2017/Bemisia_tabaci_Bam_Files/WF-21.bam.sorted",
-
-"category" : "Transcriptome/Mapped Reads",
-"metadata" : {
-	"Track legend":"Mapped RNA-Seq reads:<br>Aligned regions: blue<br>Spanned regions (possible splice junctions): light blue<br>Deletions in the read relative to the reference: red<br>Insertions in the read relative to the reference: green<br>Mismatch: yellow (hover over the mismatch to see what the snp is)",
-	"Geographic location (latitude and longitude)":"Charleston, SC, USA",
-	"Data description":"RNA derived from adults fed on uninfected tomato cuttings for 24 h",
-	"Data source":"PRJNA312467",
-	"Data provider":"Kai-Shu Ling, USDA-ARS",
-	"Method":"Illumina HiSeq 2502",
-	"Publication status":"Published: Please cite https://doi.org/10.1186/s12915-016-0321-y",
-	"Tissues/Life stage included":"adults",
-	"isolate":"MEAM3"
-},
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "healthy_24h_rep3",
          "label" : "healthy_24h_rep3",
+         "metadata" : {
+            "Data description" : "RNA derived from adults fed on uninfected tomato cuttings for 24 h",
+            "Data provider" : "Kai-Shu Ling, USDA-ARS",
+            "Data source" : "PRJNA312467",
+            "Geographic location (latitude and longitude)" : "Charleston, SC, USA",
+            "Method" : "Illumina HiSeq 2502",
+            "Publication status" : "Published: Please cite https://doi.org/10.1186/s12915-016-0321-y",
+            "Tissues/Life stage included" : "adults",
+            "Track legend" : "Mapped RNA-Seq reads:<br>Aligned regions: blue<br>Spanned regions (possible splice junctions): light blue<br>Deletions in the read relative to the reference: red<br>Insertions in the read relative to the reference: green<br>Mismatch: yellow (hover over the mismatch to see what the snp is)",
+            "isolate" : "MEAM3"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
          "type" : "WebApollo/View/Track/DraggableAlignments",
-         "key" : "healthy_24h_rep3"
+         "urlTemplate" : "user_contributed_data/ARS_11_2017/Bemisia_tabaci_Nov_29__2017/Bemisia_tabaci_Bam_Files/WF-21.bam.sorted"
       },
       {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "healthy_72h_rep2",
+         "label" : "healthy_72h_rep2",
+         "metadata" : {
+            "Data description" : "RNA derived from adults fed on uninfected tomato cuttings for 72 h",
+            "Data provider" : "Kai-Shu Ling, USDA-ARS",
+            "Data source" : "PRJNA312467",
+            "Geographic location (latitude and longitude)" : "Charleston, SC, USA",
+            "Method" : "Illumina HiSeq 2513",
+            "Publication status" : "Published: Please cite https://doi.org/10.1186/s12915-016-0321-y",
+            "Tissues/Life stage included" : "adults",
+            "Track legend" : "Mapped RNA-Seq reads:<br>Aligned regions: blue<br>Spanned regions (possible splice junctions): light blue<br>Deletions in the read relative to the reference: red<br>Insertions in the read relative to the reference: green<br>Mismatch: yellow (hover over the mismatch to see what the snp is)",
+            "isolate" : "MEAM14"
+         },
          "storeClass" : "JBrowse/Store/SeqFeature/BAM",
-         "urlTemplate" : "user_contributed_data/ARS_11_2017/Bemisia_tabaci_Nov_29__2017/Bemisia_tabaci_Bam_Files/WF-32.bam.sorted",
-
-"category" : "Transcriptome/Mapped Reads",
-"metadata" : {
-	"Track legend":"Mapped RNA-Seq reads:<br>Aligned regions: blue<br>Spanned regions (possible splice junctions): light blue<br>Deletions in the read relative to the reference: red<br>Insertions in the read relative to the reference: green<br>Mismatch: yellow (hover over the mismatch to see what the snp is)",
-	"Geographic location (latitude and longitude)":"Charleston, SC, USA",
-	"Data description":"RNA derived from adults fed on uninfected tomato cuttings for 72 h",
-	"Data source":"PRJNA312467",
-	"Data provider":"Kai-Shu Ling, USDA-ARS",
-	"Method":"Illumina HiSeq 2513",
-	"Publication status":"Published: Please cite https://doi.org/10.1186/s12915-016-0321-y",
-	"Tissues/Life stage included":"adults",
-	"isolate":"MEAM14"
-},
          "type" : "WebApollo/View/Track/DraggableAlignments",
-         "label" : "healthy_72h_rep2",
-         "key" : "healthy_72h_rep2"
+         "urlTemplate" : "user_contributed_data/ARS_11_2017/Bemisia_tabaci_Nov_29__2017/Bemisia_tabaci_Bam_Files/WF-32.bam.sorted"
       },
       {
-         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
-         "urlTemplate" : "user_contributed_data/ARS_11_2017/Bemisia_tabaci_Nov_29__2017/Bemisia_tabaci_Bam_Files/WF-36.bam.sorted",
-
-"category" : "Transcriptome/Mapped Reads",
-"metadata" : {
-	"Track legend":"Mapped RNA-Seq reads:<br>Aligned regions: blue<br>Spanned regions (possible splice junctions): light blue<br>Deletions in the read relative to the reference: red<br>Insertions in the read relative to the reference: green<br>Mismatch: yellow (hover over the mismatch to see what the snp is)",
-	"Geographic location (latitude and longitude)":"Charleston, SC, USA",
-	"Data description":"RNA derived from adults fed on TYLCV-infected tomato cuttings for 72 h",
-	"Data source":"PRJNA312467",
-	"Data provider":"Kai-Shu Ling, USDA-ARS",
-	"Method":"Illumina HiSeq 2517",
-	"Publication status":"Published: Please cite https://doi.org/10.1186/s12915-016-0321-y",
-	"Tissues/Life stage included":"adults",
-	"isolate":"MEAM18"
-},
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "TYLCV_72h_rep3",
          "label" : "TYLCV_72h_rep3",
+         "metadata" : {
+            "Data description" : "RNA derived from adults fed on TYLCV-infected tomato cuttings for 72 h",
+            "Data provider" : "Kai-Shu Ling, USDA-ARS",
+            "Data source" : "PRJNA312467",
+            "Geographic location (latitude and longitude)" : "Charleston, SC, USA",
+            "Method" : "Illumina HiSeq 2517",
+            "Publication status" : "Published: Please cite https://doi.org/10.1186/s12915-016-0321-y",
+            "Tissues/Life stage included" : "adults",
+            "Track legend" : "Mapped RNA-Seq reads:<br>Aligned regions: blue<br>Spanned regions (possible splice junctions): light blue<br>Deletions in the read relative to the reference: red<br>Insertions in the read relative to the reference: green<br>Mismatch: yellow (hover over the mismatch to see what the snp is)",
+            "isolate" : "MEAM18"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
          "type" : "WebApollo/View/Track/DraggableAlignments",
-         "key" : "TYLCV_72h_rep3"
+         "urlTemplate" : "user_contributed_data/ARS_11_2017/Bemisia_tabaci_Nov_29__2017/Bemisia_tabaci_Bam_Files/WF-36.bam.sorted"
       },
       {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "TYLCV_48h_rep2",
+         "label" : "TYLCV_48h_rep2",
+         "metadata" : {
+            "Data description" : "RNA derived from adults fed on TYLCV-infected tomato cuttings for 48 h",
+            "Data provider" : "Kai-Shu Ling, USDA-ARS",
+            "Data source" : "PRJNA312467",
+            "Geographic location (latitude and longitude)" : "Charleston, SC, USA",
+            "Method" : "Illumina HiSeq 2510",
+            "Publication status" : "Published: Please cite https://doi.org/10.1186/s12915-016-0321-y",
+            "Tissues/Life stage included" : "adults",
+            "Track legend" : "Mapped RNA-Seq reads:<br>Aligned regions: blue<br>Spanned regions (possible splice junctions): light blue<br>Deletions in the read relative to the reference: red<br>Insertions in the read relative to the reference: green<br>Mismatch: yellow (hover over the mismatch to see what the snp is)",
+            "isolate" : "MEAM11"
+         },
          "storeClass" : "JBrowse/Store/SeqFeature/BAM",
-         "urlTemplate" : "user_contributed_data/ARS_11_2017/Bemisia_tabaci_Nov_29__2017/Bemisia_tabaci_Bam_Files/WF-29.bam.sorted",
-
-"category" : "Transcriptome/Mapped Reads",
-"metadata" : {
-	"Track legend":"Mapped RNA-Seq reads:<br>Aligned regions: blue<br>Spanned regions (possible splice junctions): light blue<br>Deletions in the read relative to the reference: red<br>Insertions in the read relative to the reference: green<br>Mismatch: yellow (hover over the mismatch to see what the snp is)",
-	"Geographic location (latitude and longitude)":"Charleston, SC, USA",
-	"Data description":"RNA derived from adults fed on TYLCV-infected tomato cuttings for 48 h",
-	"Data source":"PRJNA312467",
-	"Data provider":"Kai-Shu Ling, USDA-ARS",
-	"Method":"Illumina HiSeq 2510",
-	"Publication status":"Published: Please cite https://doi.org/10.1186/s12915-016-0321-y",
-	"Tissues/Life stage included":"adults",
-	"isolate":"MEAM11"
-},
          "type" : "WebApollo/View/Track/DraggableAlignments",
-         "label" : "TYLCV_48h_rep2",
-         "key" : "TYLCV_48h_rep2"
+         "urlTemplate" : "user_contributed_data/ARS_11_2017/Bemisia_tabaci_Nov_29__2017/Bemisia_tabaci_Bam_Files/WF-29.bam.sorted"
       },
       {
-         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
-         "urlTemplate" : "user_contributed_data/ARS_11_2017/Bemisia_tabaci_Nov_29__2017/Bemisia_tabaci_Bam_Files/WF-28.bam.sorted",
-
-"category" : "Transcriptome/Mapped Reads",
-"metadata" : {
-	"Track legend":"Mapped RNA-Seq reads:<br>Aligned regions: blue<br>Spanned regions (possible splice junctions): light blue<br>Deletions in the read relative to the reference: red<br>Insertions in the read relative to the reference: green<br>Mismatch: yellow (hover over the mismatch to see what the snp is)",
-	"Geographic location (latitude and longitude)":"Charleston, SC, USA",
-	"Data description":"RNA derived from adults fed on TYLCV-infected tomato cuttings for 48 h",
-	"Data source":"PRJNA312467",
-	"Data provider":"Kai-Shu Ling, USDA-ARS",
-	"Method":"Illumina HiSeq 2509",
-	"Publication status":"Published: Please cite https://doi.org/10.1186/s12915-016-0321-y",
-	"Tissues/Life stage included":"adults",
-	"isolate":"MEAM10"
-},
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "TYLCV_48h_rep1",
          "label" : "TYLCV_48h_rep1",
+         "metadata" : {
+            "Data description" : "RNA derived from adults fed on TYLCV-infected tomato cuttings for 48 h",
+            "Data provider" : "Kai-Shu Ling, USDA-ARS",
+            "Data source" : "PRJNA312467",
+            "Geographic location (latitude and longitude)" : "Charleston, SC, USA",
+            "Method" : "Illumina HiSeq 2509",
+            "Publication status" : "Published: Please cite https://doi.org/10.1186/s12915-016-0321-y",
+            "Tissues/Life stage included" : "adults",
+            "Track legend" : "Mapped RNA-Seq reads:<br>Aligned regions: blue<br>Spanned regions (possible splice junctions): light blue<br>Deletions in the read relative to the reference: red<br>Insertions in the read relative to the reference: green<br>Mismatch: yellow (hover over the mismatch to see what the snp is)",
+            "isolate" : "MEAM10"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
          "type" : "WebApollo/View/Track/DraggableAlignments",
-         "key" : "TYLCV_48h_rep1"
+         "urlTemplate" : "user_contributed_data/ARS_11_2017/Bemisia_tabaci_Nov_29__2017/Bemisia_tabaci_Bam_Files/WF-28.bam.sorted"
       },
       {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "TYLCV_72h_rep1",
+         "label" : "TYLCV_72h_rep1",
+         "metadata" : {
+            "Data description" : "RNA derived from adults fed on TYLCV-infected tomato cuttings for 72 h",
+            "Data provider" : "Kai-Shu Ling, USDA-ARS",
+            "Data source" : "PRJNA312467",
+            "Geographic location (latitude and longitude)" : "Charleston, SC, USA",
+            "Method" : "Illumina HiSeq 2515",
+            "Publication status" : "Published: Please cite https://doi.org/10.1186/s12915-016-0321-y",
+            "Tissues/Life stage included" : "adults",
+            "Track legend" : "Mapped RNA-Seq reads:<br>Aligned regions: blue<br>Spanned regions (possible splice junctions): light blue<br>Deletions in the read relative to the reference: red<br>Insertions in the read relative to the reference: green<br>Mismatch: yellow (hover over the mismatch to see what the snp is)",
+            "isolate" : "MEAM16"
+         },
          "storeClass" : "JBrowse/Store/SeqFeature/BAM",
-         "urlTemplate" : "user_contributed_data/ARS_11_2017/Bemisia_tabaci_Nov_29__2017/Bemisia_tabaci_Bam_Files/WF-34.bam.sorted",
-
-"category" : "Transcriptome/Mapped Reads",
-"metadata" : {
-	"Track legend":"Mapped RNA-Seq reads:<br>Aligned regions: blue<br>Spanned regions (possible splice junctions): light blue<br>Deletions in the read relative to the reference: red<br>Insertions in the read relative to the reference: green<br>Mismatch: yellow (hover over the mismatch to see what the snp is)",
-	"Geographic location (latitude and longitude)":"Charleston, SC, USA",
-	"Data description":"RNA derived from adults fed on TYLCV-infected tomato cuttings for 72 h",
-	"Data source":"PRJNA312467",
-	"Data provider":"Kai-Shu Ling, USDA-ARS",
-	"Method":"Illumina HiSeq 2515",
-	"Publication status":"Published: Please cite https://doi.org/10.1186/s12915-016-0321-y",
-	"Tissues/Life stage included":"adults",
-	"isolate":"MEAM16"
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          "type" : "WebApollo/View/Track/DraggableAlignments",
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          "label" : "healthy_48h_rep3",
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diff --git a/organisms/stage/Blattella_germanica/trackList.json b/organisms/stage/Blattella_germanica/trackList.json
index 2ea652a..1878a2c 100644
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-         "category" : "Transcriptome/Mapped Reads",
-         "metadata" : {
-            "Data URL" : "http://www.ncbi.nlm.nih.gov/Traces/sra/?run=SRR1552487; http://www.ncbi.nlm.nih.gov/Traces/sra/?run=SRR1552488",
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+      "key": "cegma",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
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+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
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+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Annelida proteins as part of the MAKER automated annotation pipeline."
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+        "Track legend": "Results from Protein2genome alignments of a set of Arthropoda proteins as part of the MAKER automated annotation pipeline."
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+      "key": "protein2genome_Cephalochordata",
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+        "Track legend": "Results from Protein2genome alignments of a set of Chelicerata proteins as part of the MAKER automated annotation pipeline."
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+        "Track legend": "Results from Protein2genome alignments of a set of Cnidaria proteins as part of the MAKER automated annotation pipeline."
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+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
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+        "Track legend": "Results from Protein2genome alignments of a set of Craniata proteins as part of the MAKER automated annotation pipeline."
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+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
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+        "Track legend": "Results from Protein2genome alignments of a set of Crustacea proteins as part of the MAKER automated annotation pipeline."
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+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Echinodermata proteins as part of the MAKER automated annotation pipeline."
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+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
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+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline."
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+        "Track legend": "Results from Protein2genome alignments of a set of Nematomorpha proteins as part of the MAKER automated annotation pipeline."
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+      "key": "protein2genome_Placozoa",
+      "label": "protein2genome_Placozoa",
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+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline."
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+      "urlTemplate": "tracks/protein2genome_Placozoa/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+      "key": "protein2genome_Platyhelminthes",
+      "label": "protein2genome_Platyhelminthes",
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+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline."
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+      "urlTemplate": "tracks/protein2genome_Platyhelminthes/{refseq}/trackData.json"
+    },
+    {
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+      "key": "protein2genome_Priapulida",
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+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline."
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+      "urlTemplate": "tracks/protein2genome_Priapulida/{refseq}/trackData.json"
+    },
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+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline."
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+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
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+      "urlTemplate": "tracks/protein2genome_Tardigrada/{refseq}/trackData.json"
+    },
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+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline."
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+    },
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
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+      "key": "repeatmasker",
+      "label": "repeatmasker",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from RepeatMasker as part of the MAKER automated annotation pipeline."
+      },
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+      "key": "repeatrunner",
+      "label": "repeatrunner",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
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+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Repeatrunner as part of the MAKER automated annotation pipeline."
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+      "key": "Gaps in assembly",
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+      "metadata": {
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+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
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+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+      },
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+      "urlTemplate": "bigwig/Bgermanica.scaffolds.gc.bigwig"
+    },
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+      "label": "BG_RNAseq_heads_NCSU",
+      "metadata": {
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+        "Data Source 4 Alignment Summary": "http://de.iplantcollaborative.org/dl/d/DAA3D4D7-4D22-451D-9914-EAD37D2E0A5B/align_summary.txt",
+        "Note": "This is merged dataset from four separate sources",
+        "RNA dataset name": "BG_RNAseq_heads_NCSU",
+        "Species name": "Blattella germanica"
+      },
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+      "urlTemplate": "user_contributed_data/Blatella_transcriptome/TopHat2-SE_Lane1_2_Sample3_4_merged-2015-09-01-21-37-00.7/TopHat2-SE_Lane1_2_Sample3_4_merged.bam"
+    },
+    {
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+      "category": "Transcriptome/Coverage Plots (BigWig)",
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+      "label": "BG_RNAseq_heads_NCSU (Coverage Plot)",
+      "metadata": {
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+        "Data Source 4 Alignment Summary": "http://de.iplantcollaborative.org/dl/d/DAA3D4D7-4D22-451D-9914-EAD37D2E0A5B/align_summary.txt",
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+        "RNA dataset name": "BG_RNAseq_heads_NCSU",
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+      },
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+    },
+    {
+      "category": "Transcriptome/Mapped Reads",
+      "key": "BG_RNAseq_heads_UW",
+      "label": "BG_RNAseq_heads_UW",
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+        "Alignment summary": "PE_SRR1552487: http://de.iplantcollaborative.org/dl/d/C663364F-AAA3-427F-8DFD-27772ED2BDCB/align_summary.txt; PE_SRR1552488: http://de.iplantcollaborative.org/dl/d/908426A6-7915-4CB4-9EA7-ABDA19590C4F/align_summary.txt",
+        "Citation": "Recurrent loss of CenH3 is associated with independent transitions to holocentricity in insects. Drinnenberg IA, deYoung D, Henikoff S, Malik HS. Elife. 2014 Sep 23;3. doi: 10.7554/eLife.03676.PMID:25247700",
+        "Data URL": "http://www.ncbi.nlm.nih.gov/Traces/sra/?run=SRR1552487; http://www.ncbi.nlm.nih.gov/Traces/sra/?run=SRR1552488",
+        "Data provider": "Inez Anna Drinnenberg",
+        "File provider": "Kim Walden, UIUC",
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+        "Citation": "Recurrent loss of CenH3 is associated with independent transitions to holocentricity in insects. Drinnenberg IA, deYoung D, Henikoff S, Malik HS. Elife. 2014 Sep 23;3. doi: 10.7554/eLife.03676.PMID:25247700",
+        "Data URL": "http://www.ncbi.nlm.nih.gov/Traces/sra/?run=SRR1552487; http://www.ncbi.nlm.nih.gov/Traces/sra/?run=SRR1552488",
+        "Data provider": "Inez Anna Drinnenberg",
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+        "Publication": "Dong-Juan Niu, Yan Liu, Xiao-Tong Dong, Shuang-Lin Dong. 2016. Transcriptome based identification and tissue expression profiles of chemosensory genes in Blattella germanica (Blattaria: Blattidae). http://dx.doi.org/10.1016/j.cbd.2016.03.002",
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+      "urlTemplate": "tracks/BGER_v0.6.2_repeatmasker/{refseq}/trackData.json"
+    },
+    {
+      "category": "BGER_v0.6.2/1. Gene Sets/Manually annotated genes",
+      "compress": 0,
+      "key": "Manual annotations for gene set BGERv0.6.2, v1",
+      "label": "BGERv0.6.2_manual_annotations_v1",
+      "metadata": {
+        "Data provider": "Evelien Jongepier, Westfaelische Wilhelms-University - Institute for Evolution and Biodiversity - Evolutionary Bioinformatics Group",
+        "Method": "Manual annotation (Exonerate/Augustus)",
+        "Note": "Track contains protein-coding and non-coding features, as well as two models with stop_codon_read_through features.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Manual annotations of the computationally predicted gene set BGERv0.6.2. Note that stop codon read-through features are visualized as a purple box on the CDS feature."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "CDS": "alt_gene_set-cds",
+          "UTR": "alt_gene_set-utr",
+          "exon": "container-100pct",
+          "wholeCDS": null
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/BGERv0.6.2_manual_annotations_v1/{refseq}/trackData.json"
+    }
+  ]
 }
diff --git a/organisms/stage/Bombus_impatiens/trackList.json b/organisms/stage/Bombus_impatiens/trackList.json
index 9fb8450..18291c7 100644
--- a/organisms/stage/Bombus_impatiens/trackList.json
+++ b/organisms/stage/Bombus_impatiens/trackList.json
@@ -1,184 +1,177 @@
 {
-   "formatVersion" : 1,
-   "names" : {
-      "type" : "Hash",
-      "url" : "names/"
-   },
-   "tracks" : [
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-         "faiUrlTemplate" : "seq/GCF_000188095.2_BIMP_2.1_genomic.fna.fai",
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-         "storeClass" : "JBrowse/Store/Sequence/IndexedFasta",
-         "type" : "SequenceTrack",
-         "urlTemplate" : "seq/GCF_000188095.2_BIMP_2.1_genomic.fna",
-         "useAsRefSeqStore" : 1
+  "formatVersion": 1,
+  "names": {
+    "type": "Hash",
+    "url": "names/"
+  },
+  "tracks": [
+    {
+      "category": "Reference sequence",
+      "faiUrlTemplate": "seq/GCF_000188095.2_BIMP_2.1_genomic.fna.fai",
+      "key": "Reference sequence",
+      "label": "DNA",
+      "seqType": "dna",
+      "storeClass": "JBrowse/Store/Sequence/IndexedFasta",
+      "type": "SequenceTrack",
+      "urlTemplate": "seq/GCF_000188095.2_BIMP_2.1_genomic.fna",
+      "useAsRefSeqStore": 1
+    },
+    {
+      "category": "Official Gene Set",
+      "compress": 0,
+      "fmtDetailValue_Id": "function (id, feature) {  var name2 = id.replace(/-R./, '');  if(feature.get('type')=='mRNA') {    return '<a target=_blank href=https://i5k.nal.usda.gov/'+name2+'>'+id+'</a>';} else { return id}}",
+      "key": "OGSv1.1 Gene",
+      "label": "bomimp_current_models",
+      "menuTemplate": [
+        {
+          "label": "View details"
+        },
+        {
+          "action": "newWindow",
+          "iconClass": "dijitIconDatabase",
+          "label": "function(track,feature){ return 'Search HymenopteraMine for '+feature.get('id')}",
+          "title": "function(track,feature){ return 'Search HymenopteraMine for '+feature.get('id')}",
+          "url": "function(track,feature){ return 'https://hymenopteramine.rnet.missouri.edu/hymenopteramine/keywordSearchResults.do?searchTerm='+feature.get('id')+'&searchSubmit=Search'}"
+        }
+      ],
+      "metadata": {
+        "Data description": "Sadd et al. 2015, doi:10.1186/s13059-015-0623-3",
+        "Data provider": "BeeBase, http://hymenopteragenome.org/beebase/?q=consortium_datasets",
+        "Data source": "BeeBase, http://hymenopteragenome.org/beebase/?q=consortium_datasets",
+        "Method": "Sadd et al. 2015, doi:10.1186/s13059-015-0623-3",
+        "Publication status": "Published, doi:10.1186/s13059-015-0623-3"
       },
-      {
-         "compress" : 0,
-         "fmtDetailValue_Id" : "function(id, feature) { var name2 = id.replace(/-R./, ''); if(feature.get('type')=='mRNA') { return ''+id+' (Click for Gene pag          e)';} else {return id}}",
-         "key" : "OGSv1.1 Gene",
-         "category" : "Official Gene Set",
-         "label" : "bomimp_current_models",
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
-         "fmtDetailValue_Id": "function (id, feature) {  var name2 = id.replace(/\-R./, '');  if(feature.get('type')=='mRNA') {    return '<a target=_blank href=https://i5k.nal.usda.gov/'+name2+'>'+id+'</a>';} else { return id;}}",
-         "menuTemplate" : [
-             {
-                "label" : "View details",
-             },
-             {
-              "label": "function(track,feature){ return 'Open gene page for '+feature.get('id').replace(/\-R./, '')}",
-              "title": "function(track,feature){ return 'Open gene page for '+feature.get('id').replace(/\-R./, '')}",
-              "iconClass" : "dijitIconDatabase",
-              "action": "newWindow",
-              "url" : "function(track,feature){ return 'https://i5k.nal.usda.gov/'+feature.get('id').replace(/\-R./, '')}",
-              },
-             {
-              "label": "function(track,feature){ return 'Search HymenopteraMine for '+feature.get('id')}",
-              "title": "function(track,feature){ return 'Search HymenopteraMine for '+feature.get('id')}",
-              "iconClass" : "dijitIconDatabase",
-              "action": "newWindow",
-              "url" : "function(track,feature){ return 'http://128.206.116.3:8080/hymenopteramine/keywordSearchResults.do?searchTerm='+feature.get('id')+'&searchSubmit=Search'}",
-              },
-        ],
-	"metadata" : {
-		   "Data description":"Sadd et al. 2015, doi:10.1186/s13059-015-0623-3",
-		   "Data source":"BeeBase, http://hymenopteragenome.org/beebase/?q=consortium_datasets",
-		   "Data provider":"BeeBase, http://hymenopteragenome.org/beebase/?q=consortium_datasets",
-		   "Method":"Sadd et al. 2015, doi:10.1186/s13059-015-0623-3",
-		   "Publication status":"Published, doi:10.1186/s13059-015-0623-3"
-	},
-         "style" : {
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-            "className" : "container-16px",
-            "subfeatureClasses" : {
-               "CDS" : "primary_gene_set-cds",
-               "UTR" : "primary_gene_set-utr",
-               "exon" : "container-100pct",
-               "wholeCDS" : null
-            }
-         },
-         "trackType" : null,
-         "type" : "ColorByType/View/Track/ColorByTypeDraggable",
-         "urlTemplate" : "tracks/bomimp_current_models/{refseq}/trackData.json"
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "CDS": "primary_gene_set-cds",
+          "UTR": "primary_gene_set-utr",
+          "exon": "container-100pct",
+          "wholeCDS": null
+        }
       },
-      {
-         "autoscale" : "local",
-         "bicolor_pivot" : "zero",
-         "category" : "Reference Assembly",
-         "key" : "Gaps in assembly",
-         "label" : "Gaps in assembly",
-         "metadata" : {
-            "Track contact" : "The i5k workspace@NAL",
-            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
-            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
-         },
-         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
-         "style" : {
-            "neg_color" : "white",
-            "pos_color" : "black"
-         },
-         "type" : "JBrowse/View/Track/Wiggle/Density",
-         "urlTemplate" : "bigwig/GCF_000188095.2_BIMP_2.1_genomic.fna.gaps.bigwig"
+      "trackType": null,
+      "type": "HTMLFeatures",
+      "urlTemplate": "tracks/bomimp_current_models/{refseq}/trackData.json"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Reference Assembly",
+      "key": "Gaps in assembly",
+      "label": "Gaps in assembly",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
       },
-      {
-         "autoscale" : "local",
-         "bicolor_pivot" : "0.5",
-         "category" : "Reference Assembly",
-         "key" : "GC Content",
-         "label" : "GC Content",
-         "metadata" : {
-            "Track contact" : "The i5k workspace@NAL",
-            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
-            "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
-         },
-         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
-         "style" : {
-            "neg_color" : "rgba(255,255,0,50)",
-            "pos_color" : "rgba(0,0,255,50)"
-         },
-         "type" : "JBrowse/View/Track/Wiggle/Density",
-         "urlTemplate" : "bigwig/GCF_000188095.2_BIMP_2.1_genomic.fna.gc.bigwig"
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "white",
+        "pos_color": "black"
       },
-      {
-         "category" : "NCBI Annotation Release 102",
-         "compress" : 0,
-         "key" : "NCBI_Annotation_Release_102_Pseudogene",
-         "label" : "NCBI_Annotation_Release_102_Pseudogene",
-         "menuTemplate" : [
-             {
-                "label" : "View details",
-             },
-             {
-              "label": "function(track,feature){ return 'Open GenBank page for '+feature.get('name')}",
-              "title": "function(track,feature){ return 'Open GenBank page for '+feature.get('name')}",
-              "iconClass" : "dijitIconDatabase",
-              "action": "newWindow",
-              "url" : "function(track,feature){ return 'https://www.ncbi.nlm.nih.gov/nuccore/'+feature.get('name')}",
-              },
-        ],
-         "metadata" : {
-            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Bombus_impatiens/README_CURRENT_RELEASE",
-            "Data provider" : "NCBI",
-            "Data source" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/188/095/GCF_000188095.2_BIMP_2.1/GCF_000188095.2_BIMP_2.1_genomic.gff.gz",
-            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
-         },
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
-         "style" : {
-            "arrowheadClass" : "trellis-arrowhead",
-            "className" : "container-16px",
-            "description" : "product, note, description",
-            "subfeatureClasses" : {
-               "CDS" : "gnomon_CDS",
-               "UTR" : "gnomon_UTR",
-               "exon" : "container-100pct",
-               "wholeCDS" : null
-            }
-         },
-         "trackType" : "HTMLFeatures",
-         "type" : "HTMLFeatures",
-         "urlTemplate" : "tracks/NCBI_Annotation_Release_102_Pseudogene/{refseq}/trackData.json"
+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "bigwig/GCF_000188095.2_BIMP_2.1_genomic.fna.gaps.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "0.5",
+      "category": "Reference Assembly",
+      "key": "GC Content",
+      "label": "GC Content",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
       },
-      {
-         "category" : "NCBI Annotation Release 102",
-         "compress" : 0,
-         "key" : "NCBI_Annotation_Release_102_Gene",
-         "label" : "NCBI_Annotation_Release_102_Gene",
-         "menuTemplate" : [
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-             },
-             {
-              "label": "function(track,feature){ return 'Open GenBank page for '+feature.get('name')}",
-              "title": "function(track,feature){ return 'Open GenBank page for '+feature.get('name')}",
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-              "action": "newWindow",
-              "url" : "function(track,feature){ return 'https://www.ncbi.nlm.nih.gov/nuccore/'+feature.get('name')}",
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-        ],
-         "metadata" : {
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-            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
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-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
-         "style" : {
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-            "className" : "container-16px",
-            "description" : "product, note, description",
-            "subfeatureClasses" : {
-               "CDS" : "gnomon_CDS",
-               "UTR" : "gnomon_UTR",
-               "exon" : "container-100pct",
-               "wholeCDS" : null
-            }
-         },
-         "trackType" : "ColorByType/View/Track/ColorByTypeDraggable",
-         "type" : "ColorByType/View/Track/ColorByTypeDraggable",
-         "urlTemplate" : "tracks/NCBI_Annotation_Release_102_Gene/{refseq}/trackData.json"
-      }
-   ]
+      "scoreType": "avgScore",
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "rgba(255,255,0,50)",
+        "pos_color": "rgba(0,0,255,50)"
+      },
+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "bigwig/GCF_000188095.2_BIMP_2.1_genomic.fna.gc.bigwig"
+    },
+    {
+      "category": "NCBI Annotation Release 102",
+      "compress": 0,
+      "key": "NCBI_Annotation_Release_102_Pseudogene",
+      "label": "NCBI_Annotation_Release_102_Pseudogene",
+      "menuTemplate": [
+        {
+          "label": "View details"
+        },
+        {
+          "action": "newWindow",
+          "iconClass": "dijitIconDatabase",
+          "label": "function(track,feature){ return 'Open GenBank page for '+feature.get('name')}",
+          "title": "function(track,feature){ return 'Open GenBank page for '+feature.get('name')}",
+          "url": "function(track,feature){ return 'https://www.ncbi.nlm.nih.gov/nuccore/'+feature.get('name')}"
+        }
+      ],
+      "metadata": {
+        "Data description": "ftp://ftp.ncbi.nlm.nih.gov/genomes/Bombus_impatiens/README_CURRENT_RELEASE",
+        "Data provider": "NCBI",
+        "Data source": "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/188/095/GCF_000188095.2_BIMP_2.1/GCF_000188095.2_BIMP_2.1_genomic.gff.gz",
+        "Method": "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "description": "product, note, description",
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+          "CDS": "gnomon_CDS",
+          "UTR": "gnomon_UTR",
+          "exon": "container-100pct",
+          "wholeCDS": null
+        }
+      },
+      "trackType": "HTMLFeatures",
+      "type": "HTMLFeatures",
+      "urlTemplate": "tracks/NCBI_Annotation_Release_102_Pseudogene/{refseq}/trackData.json"
+    },
+    {
+      "category": "NCBI Annotation Release 102",
+      "compress": 0,
+      "key": "NCBI_Annotation_Release_102_Gene",
+      "label": "NCBI_Annotation_Release_102_Gene",
+      "menuTemplate": [
+        {
+          "label": "View details"
+        },
+        {
+          "action": "newWindow",
+          "iconClass": "dijitIconDatabase",
+          "label": "function(track,feature){ return 'Open GenBank page for '+feature.get('name')}",
+          "title": "function(track,feature){ return 'Open GenBank page for '+feature.get('name')}",
+          "url": "function(track,feature){ return 'https://www.ncbi.nlm.nih.gov/nuccore/'+feature.get('name')}"
+        }
+      ],
+      "metadata": {
+        "Data description": "ftp://ftp.ncbi.nlm.nih.gov/genomes/Bombus_impatiens/README_CURRENT_RELEASE",
+        "Data provider": "NCBI",
+        "Data source": "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/188/095/GCF_000188095.2_BIMP_2.1/GCF_000188095.2_BIMP_2.1_genomic.gff.gz",
+        "Method": "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "description": "product, note, description",
+        "subfeatureClasses": {
+          "CDS": "gnomon_CDS",
+          "UTR": "gnomon_UTR",
+          "exon": "container-100pct",
+          "wholeCDS": null
+        }
+      },
+      "trackType": "HTMLFeatures",
+      "type": "HTMLFeatures",
+      "urlTemplate": "tracks/NCBI_Annotation_Release_102_Gene/{refseq}/trackData.json"
+    }
+  ]
 }
diff --git a/organisms/stage/Bombus_terrestris/trackList.json b/organisms/stage/Bombus_terrestris/trackList.json
index 34fdfaf..2d308c5 100644
--- a/organisms/stage/Bombus_terrestris/trackList.json
+++ b/organisms/stage/Bombus_terrestris/trackList.json
@@ -1,151 +1,211 @@
 {
-    "formatVersion": 1,
-    "names": {
-        "type": "Hash",
-        "url": "names/"
-    },
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-        },
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-            "compress": 0,
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-                }
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-            "trackType": null,
-            "type": "ColorByType/View/Track/ColorByTypeDraggable",
-            "urlTemplate": "tracks/bomter_current_models/{refseq}/trackData.json"
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-            "bicolor_pivot": "zero",
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-            "key": "Gaps in assembly",
-            "label": "Gaps in assembly",
-            "metadata": {
-                "Track contact": "The i5k workspace@NAL",
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-                "Track legend": "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
-            },
-            "storeClass": "JBrowse/Store/SeqFeature/BigWig",
-            "style": {
-                "neg_color": "white",
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-            "category": "Reference Assembly",
-            "key": "GC Content",
-            "label": "GC Content",
-            "metadata": {
-                "Track contact": "The i5k workspace@NAL",
-                "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
-                "Track legend": "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
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+   "names" : {
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+         "key" : "Gaps in assembly",
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+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
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+         },
+         "scoreType" : "avgScore",
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
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+         },
+         "trackType" : "HTMLFeatures",
+         "type" : "HTMLFeatures",
+         "urlTemplate" : "tracks/NCBI_Annotation_Release_102_Pseudogene/{refseq}/trackData.json"
+      },
+      {
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          "menuTemplate" : [
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+            {
+               "label" : "View details"
             },
-            "trackType": "ColorByType/View/Track/ColorByTypeDraggable",
-            "type": "ColorByType/View/Track/ColorByTypeDraggable",
-            "urlTemplate": "tracks/NCBI_Annotation_Release_102_Gene/{refseq}/trackData.json"
-        }
-    ]
+            {
+               "action" : "newWindow",
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+         "type" : "HTMLFeatures",
+         "urlTemplate" : "tracks/NCBI_Annotation_Release_102_Gene/{refseq}/trackData.json"
+      },
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+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
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+         },
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+         "unsafePopup" : true,
+         "urlTemplate" : "analyses/Bombus-terrestris-RNA-Seq_2021-06-08_v1.0/Bomter_Bter_1.0_RNA-Seq-alignments_2021-06-08.bam"
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+         "label" : "Bomter_Bter_1.0_RNA-Seq-alignments_2021-06-08_coverage",
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+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "unsafePopup" : true,
+         "urlTemplate" : "analyses/Bombus-terrestris-RNA-Seq_2021-06-08_v1.0/Bomter_Bter_1.0_RNA-Seq-alignments_2021-06-08.bigwig"
+      },
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+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR1734824'>SRR1734824</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR3879962'>SRR3879962</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR2396648'>SRR2396648</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR12587877'>SRR12587877</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR8085481'>SRR8085481</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR1169738'>SRR1169738</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR1169744'>SRR1169744</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR8085459'>SRR8085459</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR5125112'>SRR5125112</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR8936121'>SRR8936121</a>",
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+            "Track legend" : "Junction reads generated by Hisat2 aligner and regtools. The number of alignments supporting the junction read is listed in blue."
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+         "urlTemplate" : "tracks/Bomter_Bter_1.0_RNA-Seq-alignments_2021-06-08_junctions/{refseq}/trackData.json"
+      }
+   ]
 }
diff --git a/organisms/stage/Bradysia_coprophila/trackList.json b/organisms/stage/Bradysia_coprophila/trackList.json
index e8f58d8..876e791 100644
--- a/organisms/stage/Bradysia_coprophila/trackList.json
+++ b/organisms/stage/Bradysia_coprophila/trackList.json
@@ -1,261 +1,261 @@
 {
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-         "category" : "NCBI Annotation Release 100",
-         "compress" : 0,
-         "key" : "NCBI_Annotation_Release_100_Gene",
-         "label" : "bracop_current_models",
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+  "names": {
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+    "url": "names/"
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-               "iconClass" : "dijitIconDatabase",
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-               "title" : "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
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-            }
-         },
-         "trackType" : "HTMLFeatures",
-         "type" : "HTMLFeatures",
-         "urlTemplate" : "tracks/bracop_current_models/{refseq}/trackData.json"
+             {
+                "label" : "View details"
+             },
+             {
+              "label": "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
+              "title": "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
+              "iconClass" : "dijitIconDatabase",
+              "action": "newWindow",
+              "url" : "function(track,feature){ return 'https://www.ncbi.nlm.nih.gov/nuccore/'+feature.get('name')}"
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+        "Data provider": "NCBI",
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+        "Method": "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
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+      "style": {
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+      "type": "HTMLFeatures",
+      "urlTemplate": "tracks/bracop_current_models/{refseq}/trackData.json"
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+      "compress": 0,
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+      "metadata": {
+        "Data description": "ftp://ftp.ncbi.nlm.nih.gov/genomes/Bradysia_coprophila/README_CURRENT_RELEASE",
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+        "Method": "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
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+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
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+          "exon": "container-100pct",
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+      "trackType": "HTMLFeatures",
+      "type": "HTMLFeatures",
+      "urlTemplate": "tracks/NCBI_Annotation_Release_100_Pseudogene/{refseq}/trackData.json"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Reference Assembly",
+      "key": "Gaps in assembly",
+      "label": "Gaps in assembly",
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 }
diff --git a/organisms/stage/Catajapyx_aquilonaris/trackList.json b/organisms/stage/Catajapyx_aquilonaris/trackList.json
index bbb6210..e23b689 100644
--- a/organisms/stage/Catajapyx_aquilonaris/trackList.json
+++ b/organisms/stage/Catajapyx_aquilonaris/trackList.json
@@ -1,1234 +1,1228 @@
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+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Cnidaria proteins as part of the MAKER automated annotation pipeline."
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+      "compress": 0,
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+      "label": "protein2genome_Craniata",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Craniata proteins as part of the MAKER automated annotation pipeline."
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+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
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+          "match_part": "protein2genome"
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Craniata/{refseq}/trackData.json"
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+      "compress": 0,
+      "key": "protein2genome_Crustacea",
+      "label": "protein2genome_Crustacea",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Crustacea proteins as part of the MAKER automated annotation pipeline."
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+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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+        "subfeatureClasses": {
+          "match_part": "protein2genome"
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+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Crustacea/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Echinodermata",
+      "label": "protein2genome_Echinodermata",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Echinodermata proteins as part of the MAKER automated annotation pipeline."
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+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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+        "subfeatureClasses": {
+          "match_part": "protein2genome"
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+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Echinodermata/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Mollusca",
+      "label": "protein2genome_Mollusca",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Mollusca proteins as part of the MAKER automated annotation pipeline."
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+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
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+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Mollusca/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Nemata",
+      "label": "protein2genome_Nemata",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline."
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+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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+          "match_part": "protein2genome"
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+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Nemata/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Nematomorpha",
+      "label": "protein2genome_Nematomorpha",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Nematomorpha proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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+          "match_part": "protein2genome"
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+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Nematomorpha/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Onychophora",
+      "label": "protein2genome_Onychophora",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Onychophora proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
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+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Onychophora/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Parazoa",
+      "label": "protein2genome_Parazoa",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
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+          "match_part": "protein2genome"
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+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Parazoa/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Placozoa",
+      "label": "protein2genome_Placozoa",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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+        "subfeatureClasses": {
+          "match_part": "protein2genome"
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+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Placozoa/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Platyhelminthes",
+      "label": "protein2genome_Platyhelminthes",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
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+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Platyhelminthes/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Priapulida",
+      "label": "protein2genome_Priapulida",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Priapulida/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Tardigrada",
+      "label": "protein2genome_Tardigrada",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Tardigrada/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Tunicata",
+      "label": "protein2genome_Tunicata",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Tunicata/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_UNCATEGORISED",
+      "label": "protein2genome_UNCATEGORISED",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
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+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_UNCATEGORISED/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/2. Evidence/Repeats",
+      "compress": 0,
+      "key": "repeatmasker",
+      "label": "repeatmasker",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from RepeatMasker as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "repeat"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/repeatmasker/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/2. Evidence/Repeats",
+      "compress": 0,
+      "key": "repeatrunner",
+      "label": "repeatrunner",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Repeatrunner as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "repeat"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/repeatrunner/{refseq}/trackData.json"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Reference Assembly",
+      "key": "Gaps in assembly",
+      "label": "Gaps in assembly",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "white",
+        "pos_color": "black"
+      },
+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "bigwig/forcepstail.scaffolds_NALmod.fa.gaps.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "0.5",
+      "category": "Reference Assembly",
+      "key": "GC Content",
+      "label": "GC Content",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+      },
+      "scoreType": "avgScore",
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "rgba(255,255,0,50)",
+        "pos_color": "rgba(0,0,255,50)"
+      },
+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "bigwig/forcepstail.scaffolds_NALmod.fa.gc.bigwig"
+    },
+    {
+      "category": "Transcriptome/Mapped Reads",
+      "key": "Catajapyx aquilonaris RNAseq reads",
+      "label": "Catajapyx aquilonaris RNAseq reads",
+      "metadata": {
+        "Data Source": "Raw data available from 1kite upon request (http://www.1kite.org/)",
+        "Data Submitter": "Jan Philip",
+        "Methods": "Raw reads cleaned with Trimmomatic v0.32. Cleaned reads mapped with TopHat v2.0.12 using default settings.",
+        "Track description": "Catajapyx aquilonaris RNAseq reads"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "bam/accepted_hits_sorted.bam"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Transcriptome/Coverage plots (BigWig)",
+      "clip_marker_color": "red",
+      "height": 50,
+      "key": "Catajapyx aquilonaris RNAseq coverage",
+      "label": "catajapyx aquilonaris RNAseq coverage",
+      "metadata": {
+        "Data Source": "Raw data available from 1kite upon request (http://www.1kite.org/)",
+        "Data Submitter": "Jan Philip",
+        "Methods": "Raw reads cleaned with Trimmomatic v0.32. Cleaned reads mapped with TopHat v2.0.12 using default settings.",
+        "Track description": "Catajapyx aquilonaris RNAseq, converted to BigWig"
+      },
+      "origin_color": "#888",
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "#0086B3",
+        "pos_color": "#00BFFF"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "bigwig/accepted_hits_sorted.bigwig",
+      "variance_band_color": "rgba(0,0,0,0.3)"
+    },
+    {
+      "category": "Transcriptome/Assembly",
+      "compress": 0,
+      "key": "Catajapyx aquilonaris 1kite transcriptome",
+      "label": "Catajapyx aquilonaris 1kite transcriptome",
+      "metadata": {
+        "Data Source": "Raw data available from 1kite upon request (http://www.1kite.org/)",
+        "Data description": "Transcripts were mapped to the genome using Exonerate-gff3 (https://github.com/hotdogee/exonerate-gff3) with the options: --model est2genome --showtargetgff yes --gff3 yes --showalignment no --showvulgar no --geneseed 250 --bestn 2 --percent 50 --minintron 20 --maxintron 10000. Transcripts mapping to multiple locations were detected and marked with a note using a custom perl script (available from JP Oeyen (Univ. Bonn/ZFMK, ZMB), janphilipoyen@gmail.com)",
+        "Data provider": "Jan Philip"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "CDS": "transcriptome-cds",
+          "UTR": "transcriptome-utr",
+          "exon": "container-100pct",
+          "match_part": "transcriptome-match_part",
+          "wholeCDS": null
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/Catajapyx aquilonaris 1kite transcriptome/{refseq}/trackData.json"
+    }
+  ]
 }
diff --git a/organisms/stage/Centruroides_sculpturatus/trackList.json b/organisms/stage/Centruroides_sculpturatus/trackList.json
index e70dd6b..639826b 100644
--- a/organisms/stage/Centruroides_sculpturatus/trackList.json
+++ b/organisms/stage/Centruroides_sculpturatus/trackList.json
@@ -1,1218 +1,1210 @@
 {
-   "css" : "./plugins/NAL_CSS/css/contrib_styles.css",
-   "share_link" : 0,
-   "plugins" : [
-      {
-         "location" : "./plugins/WebApollo",
-         "name" : "WebApollo"
-      }
-   ],
-   "tracks" : [
-      {
-         "chunkSize" : 20000,
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+      "key": "blastx_Platyhelminthes",
+      "label": "blastx_Platyhelminthes",
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+        "Track legend": "Results from Blastx alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline."
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+      "label": "blastx_Priapulida",
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+      "key": "cegma",
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+        "Track legend": "Results from Protein2genome alignments of a set of Chelicerata proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Chelicerata/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Cnidaria",
+      "label": "protein2genome_Cnidaria",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research",
+        "Track legend": "Results from Protein2genome alignments of a set of Cnidaria proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Cnidaria/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Craniata",
+      "label": "protein2genome_Craniata",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research",
+        "Track legend": "Results from Protein2genome alignments of a set of Craniata proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Craniata/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Crustacea",
+      "label": "protein2genome_Crustacea",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research",
+        "Track legend": "Results from Protein2genome alignments of a set of Crustacea proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Crustacea/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Echinodermata",
+      "label": "protein2genome_Echinodermata",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research",
+        "Track legend": "Results from Protein2genome alignments of a set of Echinodermata proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Echinodermata/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Mollusca",
+      "label": "protein2genome_Mollusca",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research",
+        "Track legend": "Results from Protein2genome alignments of a set of Mollusca proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Mollusca/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Nemata",
+      "label": "protein2genome_Nemata",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research",
+        "Track legend": "Results from Protein2genome alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Nemata/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Nematomorpha",
+      "label": "protein2genome_Nematomorpha",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research",
+        "Track legend": "Results from Protein2genome alignments of a set of Nematomorpha proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Nematomorpha/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Onychophora",
+      "label": "protein2genome_Onychophora",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research",
+        "Track legend": "Results from Protein2genome alignments of a set of Onychophora proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Onychophora/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Parazoa",
+      "label": "protein2genome_Parazoa",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research",
+        "Track legend": "Results from Protein2genome alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Parazoa/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Placozoa",
+      "label": "protein2genome_Placozoa",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research",
+        "Track legend": "Results from Protein2genome alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Placozoa/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Platyhelminthes",
+      "label": "protein2genome_Platyhelminthes",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research",
+        "Track legend": "Results from Protein2genome alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Platyhelminthes/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Priapulida",
+      "label": "protein2genome_Priapulida",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research",
+        "Track legend": "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Priapulida/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Tardigrada",
+      "label": "protein2genome_Tardigrada",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research",
+        "Track legend": "Results from Protein2genome alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Tardigrada/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Tunicata",
+      "label": "protein2genome_Tunicata",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research",
+        "Track legend": "Results from Protein2genome alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Tunicata/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_UNCATEGORISED",
+      "label": "protein2genome_UNCATEGORISED",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research",
+        "Track legend": "Results from Protein2genome alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_UNCATEGORISED/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/2. Evidence/Repeats",
+      "compress": 0,
+      "key": "repeatmasker",
+      "label": "repeatmasker",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research",
+        "Track legend": "Results from RepeatMasker as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "repeat"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/repeatmasker/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/2. Evidence/Repeats",
+      "compress": 0,
+      "key": "repeatrunner",
+      "label": "repeatrunner",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research",
+        "Track legend": "Results from Repeatrunner as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "repeat"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/repeatrunner/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/1. Gene Sets/Supplementary Gene Predictions",
+      "compress": 0,
+      "key": "snap_masked",
+      "label": "snap_masked",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research",
+        "Track legend": "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "snap"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/snap_masked/{refseq}/trackData.json"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "0.5",
+      "category": "Reference Assembly",
+      "key": "GC Content",
+      "label": "GC Content",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+      },
+      "scoreType": "avgScore",
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "rgba(255,255,0,50)",
+        "pos_color": "rgba(0,0,255,50)"
+      },
+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "bigwig/Cscul.scaffolds.50.fa.gc.bigwig"
+    }
+  ]
 }
diff --git a/organisms/stage/Cephus_cinctus/trackList.json b/organisms/stage/Cephus_cinctus/trackList.json
index 140af89..dc18d0c 100644
--- a/organisms/stage/Cephus_cinctus/trackList.json
+++ b/organisms/stage/Cephus_cinctus/trackList.json
@@ -45,6 +45,7 @@
             "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
             "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
          },
+         "scoreType" : "avgScore",
          "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
          "style" : {
             "neg_color" : "rgba(255,255,0,50)",
@@ -67,7 +68,7 @@
          "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
             "arrowheadClass" : "webapollo-arrowhead",
-            "className" : "container-10px",
+            "className" : "{type}",
             "subfeatureClasses" : {
                "match_part" : "protein_domains"
             }
@@ -928,21 +929,21 @@
             {
                "action" : "newWindow",
                "iconClass" : "dijitIconDatabase",
-               "label" : "function(track,feature){ return 'Find gene page for '+feature.get('id')}",
-               "title" : "function(track,feature){ return 'Find gene page for '+feature.get('id')}",
-               "url" : "function(track,feature){ return 'https://i5k.nal.usda.gov/search/site/'+feature.get('id')}"
+               "label" : "function(track,feature){ return 'Find gene page at NCBI for '+feature.get('id')}",
+               "title" : "function(track,feature){ return 'Find gene page at NCBI for '+feature.get('id')}",
+               "url" : "function(track,feature){ return 'https://www.ncbi.nlm.nih.gov/protein/'+feature.get('id')}"
             }
          ],
+         "metadata" : {
+            "Data provider" : "National Agricultural Library; Cephus cinctus annotation community; NCBI",
+            "Data source" : "https://doi.org/10.15482/USDA.ADC/1484022; https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/341/935/GCF_000341935.1_Ccin1/",
+            "Materials and Methods" : "https://doi.org/10.15482/USDA.ADC/1484022",
+            "Publication status" : "Published, please cite https://doi.org/10.1093/gbe/evy232"
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- metadata: {
-"Data source":"https://doi.org/10.15482/USDA.ADC/1484022; https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/341/935/GCF_000341935.1_Ccin1/",
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-"Publication status":"Published, please cite https://doi.org/10.1093/gbe/evy232",
-"Data provider":"National Agricultural Library; Cephus cinctus annotation community; NCBI"
-},
-        "style" : {
+         "style" : {
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-            "className" : "container-16px",
+            "className" : "{type}",
             "description" : "product, note, description",
             "subfeatureClasses" : {
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@@ -951,8 +952,8 @@
                "wholeCDS" : null
             }
          },
-         "trackType" : "ColorByType/View/Track/ColorByTypeDraggable",
-         "type" : "ColorByType/View/Track/ColorByTypeDraggable",
+         "trackType" : "HTMLFeatures",
+         "type" : "HTMLFeatures",
          "urlTemplate" : "tracks/cepcin_current_models/{refseq}/trackData.json"
       },
       {
@@ -960,12 +961,6 @@
          "compress" : 0,
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@@ -973,15 +968,21 @@ metadata: {
             {
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-               "label" : "function(track,feature){ return 'Find gene page for '+feature.get('id')}",
-               "title" : "function(track,feature){ return 'Find gene page for '+feature.get('id')}",
-               "url" : "function(track,feature){ return 'https://i5k.nal.usda.gov/search/site/'+feature.get('id')}"
+               "label" : "function(track,feature){ return 'Find gene page at NCBI for '+feature.get('id')}",
+               "title" : "function(track,feature){ return 'Find gene page at NCBI for '+feature.get('id')}",
+               "url" : "function(track,feature){ return 'https://www.ncbi.nlm.nih.gov/nuccore/'+feature.get('id')}"
             }
          ],
+         "metadata" : {
+            "Data provider" : "National Agricultural Library; Cephus cinctus annotation community; NCBI",
+            "Data source" : "https://doi.org/10.15482/USDA.ADC/1484022; https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/341/935/GCF_000341935.1_Ccin1/",
+            "Materials and Methods" : "https://doi.org/10.15482/USDA.ADC/1484022",
+            "Publication status" : "Published, please cite https://doi.org/10.1093/gbe/evy232"
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          "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
             "arrowheadClass" : "trellis-arrowhead",
-            "className" : "container-16px",
+            "className" : "{type}",
             "description" : "product, note, description",
             "subfeatureClasses" : {
                "CDS" : "gnomon_CDS",
@@ -999,16 +1000,16 @@ metadata: {
          "compress" : 0,
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             "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
          },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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             "arrowheadClass" : "trellis-arrowhead",
-            "className" : "container-16px",
+            "className" : "{type}",
             "description" : "product, note, description",
             "subfeatureClasses" : {
                "CDS" : "gnomon_CDS",
@@ -1017,9 +1018,68 @@ metadata: {
                "wholeCDS" : null
             }
          },
-         "trackType" : "ColorByType/View/Track/ColorByTypeDraggable",
-         "type" : "ColorByType/View/Track/ColorByTypeDraggable",
+         "trackType" : "HTMLFeatures",
+         "type" : "HTMLFeatures",
          "urlTemplate" : "tracks/NCBI_Cephus_cinctus_Annotation_Release_101-tRNAs-and-rRNAs/{refseq}/trackData.json"
+      },
+      {
+         "category" : "RNA-Seq/Mapped Reads",
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+         "label" : "Cepcin_Ccin1_RNA-Seq-alignments_2021-07-03",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
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+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Dark red alignments: Mapped portion of read aligned to forward strand<br>Light red alignments: Spliced portion of read aligned to forward strand<br>Dark blue alignments: Mapped portion of read aligned to reverse strand<br>Light blue alignments: Spliced portion of read aligned to reverse strand<br>Red marking - deletion in the read relative to the reference<br>Green marking - insertion in the read relative to the reference<br>Yellow marking  - mismatch (hover over the mismatch to see what the snp is)"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "unsafePopup" : true,
+         "urlTemplate" : "analyses/Cephus-cinctus-RNA-Seq_2021-07-03_v1.0/Cepcin_Ccin1_RNA-Seq-alignments_2021-07-03.bam"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "RNA-Seq/Coverage Plots",
+         "key" : "Cepcin_Ccin1_RNA-Seq-alignments_2021-07-03_coverage",
+         "label" : "Cepcin_Ccin1_RNA-Seq-alignments_2021-07-03_coverage",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR4298847'>SRR4298847</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR3048750'>SRR3048750</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR3051636'>SRR3051636</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR3051777'>SRR3051777</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR4298768'>SRR4298768</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR4298774'>SRR4298774</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR3052011'>SRR3052011</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR3048775'>SRR3048775</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR4298845'>SRR4298845</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR3052016'>SRR3052016</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "unsafePopup" : true,
+         "urlTemplate" : "analyses/Cephus-cinctus-RNA-Seq_2021-07-03_v1.0/Cepcin_Ccin1_RNA-Seq-alignments_2021-07-03.bigwig"
+      },
+      {
+         "category" : "RNA-Seq/Splice junctions",
+         "compress" : 0,
+         "key" : "Cepcin_Ccin1_RNA-Seq-alignments_2021-07-03_junctions",
+         "label" : "Cepcin_Ccin1_RNA-Seq-alignments_2021-07-03_junctions",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR4298847'>SRR4298847</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR3048750'>SRR3048750</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR3051636'>SRR3051636</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR3051777'>SRR3051777</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR4298768'>SRR4298768</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR4298774'>SRR4298774</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR3052011'>SRR3052011</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR3048775'>SRR3048775</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR4298845'>SRR4298845</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR3052016'>SRR3052016</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Junction reads generated by Hisat2 aligner and regtools. The number of alignments supporting the junction read is listed in blue."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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+            "description" : "score"
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "unsafePopup" : true,
+         "urlTemplate" : "tracks/Cepcin_Ccin1_RNA-Seq-alignments_2021-07-03_junctions/{refseq}/trackData.json"
       }
    ]
 }
diff --git a/organisms/stage/Ceratitis_capitata/trackList.json b/organisms/stage/Ceratitis_capitata/trackList.json
index b63559d..4b89da3 100644
--- a/organisms/stage/Ceratitis_capitata/trackList.json
+++ b/organisms/stage/Ceratitis_capitata/trackList.json
@@ -1,1857 +1,1851 @@
 {
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+        "Data provider": "Alexie Papanicolaou",
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+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "pos_color": "#00BFFF"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "user_contributed_files/papanicolaou/ceratitis/RNASEQ_BAM/PE/gsnap.ViFe96_sample7_vs_Ccap01172013.concordant_uniq.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Transcriptome/Coverage Plots (BigWig)",
+      "key": "Pooled Adult Gastrointestinal tract, Female, Egypt II wild type, CoFe6uts_sample1 (Coverage Plots)",
+      "label": "Pooled Adult Gastrointestinal tract, Female, Egypt II wild type, CoFe6uts_sample1 (Coverage Plots)",
+      "metadata": {
+        "Analysis method (program and version)": "GSNAP v2014-12-28",
+        "Date completed": "JUNE 2014",
+        "File provider (name and affiliation)": "Alexie Papanicolaou, Hawkesbury Institute for the Environment",
+        "Geographical location of specimen collection (Country, Site, Latitude, Longitude)": "Egypt II wild type strain",
+        "NCBI BioSample": "NA",
+        "NCBI SRA accession #": "NA",
+        "Other methods": "justpreprocessmyreads",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Sequencing platform and version (Illumina Hi-Seq 200 bp)": "Illumina HiSeq 2000",
+        "Sex (male/female/pooled/other/unknown)": "Female",
+        "Strain": "Egypt II wild type",
+        "TaxID": "7213",
+        "Tissues included (Whole individual/ antenna / pooled larva / pooled adult female/ etc.)": "Pooled Adult Gastrointestinal tract"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "pos_color": "#00BFFF"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "user_contributed_files/papanicolaou/ceratitis/RNASEQ_BAM/PE/gsnap.CoFe6uts_sample1_vs_Ccap01172013.concordant_uniq.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Transcriptome/Coverage Plots (BigWig)",
+      "key": "Pooled Lower Reproductive tract (spermatheca, female accessory glands and uterus) from Mated-adult (4 days after mating), Female, Egypt II wild type (Coverage Plots)",
+      "label": "Pooled Lower Reproductive tract (spermatheca, female accessory glands and uterus) from Mated-adult (4 days after mating), Female, Egypt II wild type (Coverage Plots)",
+      "metadata": {
+        "Analysis method (program and version)": "GSNAP v2014-12-28",
+        "Date completed": "JUNE 2014",
+        "File provider (name and affiliation)": "Alexie Papanicolaou, Hawkesbury Institute for the Environment",
+        "Geographical location of specimen collection (Country, Site, Latitude, Longitude)": "Egypt II wild type strain",
+        "NCBI BioSample": "NA",
+        "NCBI SRA accession #": "NA",
+        "Other methods": "justpreprocessmyreads",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Sequencing platform and version (Illumina Hi-Seq 200 bp)": "Illumina HiSeq 2000",
+        "Sex (male/female/pooled/other/unknown)": "Female",
+        "Strain": "Egypt II wild type",
+        "TaxID": "7213",
+        "Tissues included (Whole individual/ antenna / pooled larva / pooled adult female/ etc.)": "Pooled Lower Reproductive tract (spermatheca, female accessory glands and uterus) from Mated-adult (4 days after mating)"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "pos_color": "#00BFFF"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "user_contributed_files/papanicolaou/ceratitis/RNASEQ_BAM/PE/gsnap.MoFe96_sample3_vs_Ccap01172013.concordant_uniq.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Transcriptome/Coverage Plots (BigWig)",
+      "key": "embryo, pooled, Ispra (Coverage Plots)",
+      "label": "embryo, pooled, Ispra (Coverage Plots)",
+      "metadata": {
+        "Analysis method (program and version)": "GSNAP v2014-12-28",
+        "Date completed": "JUNE 2014",
+        "File provider (name and affiliation)": "Alexie Papanicolaou, Hawkesbury Institute for the Environment",
+        "Geographical location of specimen collection (Country, Site, Latitude, Longitude)": "colony",
+        "NCBI BioSample": "SAMN02055687",
+        "NCBI SRA accession #": "SRR836188",
+        "Other methods": "justpreprocessmyreads",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Sequencing platform and version (Illumina Hi-Seq 200 bp)": "Illumina Genome Analyzer IIx",
+        "Sex (male/female/pooled/other/unknown)": "pooled",
+        "Strain": "Ispra",
+        "TaxID": "7213",
+        "Tissues included (Whole individual/ antenna / pooled larva / pooled adult female/ etc.)": "embryo"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "pos_color": "#00BFFF"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "user_contributed_files/papanicolaou/ceratitis/RNASEQ_BAM/PE/gsnap.SRR836188_vs_Ccap01172013-genome.concordant_uniq.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Transcriptome/Coverage Plots (BigWig)",
+      "key": "Pooled Adult Gastrointestinal tract, Female, Egypt II wild type, sample 10 (Coverage Plots)",
+      "label": "Pooled Adult Gastrointestinal tract, Female, Egypt II wild type, sample 10 (Coverage Plots)",
+      "metadata": {
+        "Analysis method (program and version)": "GSNAP v2014-12-28",
+        "Date completed": "JUNE 2014",
+        "File provider (name and affiliation)": "Alexie Papanicolaou, Hawkesbury Institute for the Environment",
+        "Geographical location of specimen collection (Country, Site, Latitude, Longitude)": "Egypt II wild type strain",
+        "NCBI BioSample": "NA",
+        "NCBI SRA accession #": "NA",
+        "Other methods": "justpreprocessmyreads",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Sequencing platform and version (Illumina Hi-Seq 200 bp)": "Illumina HiSeq 2000",
+        "Sex (male/female/pooled/other/unknown)": "Female",
+        "Strain": "Egypt II wild type",
+        "TaxID": "7213",
+        "Tissues included (Whole individual/ antenna / pooled larva / pooled adult female/ etc.)": "Pooled Adult Gastrointestinal tract"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "pos_color": "#00BFFF"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "user_contributed_files/papanicolaou/ceratitis/RNASEQ_BAM/SE/gsnap.sample10.fastq.trimmomatic_vs_Ccap01172013.unpaired_uniq.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Transcriptome/Coverage Plots (BigWig)",
+      "key": "Pooled Lower Reproductive tract from Mated-adult (spermatheca, female accessory glands and uterus), Female, Egypt II wild type, sample 4 (Coverage Plots)",
+      "label": "Pooled Lower Reproductive tract from Mated-adult (spermatheca, female accessory glands and uterus), Female, Egypt II wild type, sample 4 (Coverage Plots)",
+      "metadata": {
+        "Analysis method (program and version)": "GSNAP v2014-12-28",
+        "Date completed": "JUNE 2014",
+        "File provider (name and affiliation)": "Alexie Papanicolaou, Hawkesbury Institute for the Environment",
+        "Geographical location of specimen collection (Country, Site, Latitude, Longitude)": "Egypt II wild type strain",
+        "NCBI BioSample": "NA",
+        "NCBI SRA accession #": "NA",
+        "Other methods": "justpreprocessmyreads",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Sequencing platform and version (Illumina Hi-Seq 200 bp)": "Illumina HiSeq 2000",
+        "Sex (male/female/pooled/other/unknown)": "Female",
+        "Strain": "Egypt II wild type",
+        "TaxID": "7213",
+        "Tissues included (Whole individual/ antenna / pooled larva / pooled adult female/ etc.)": "Pooled Lower Reproductive tract from Mated-adult (spermatheca, female accessory glands and uterus)"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "pos_color": "#00BFFF"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "user_contributed_files/papanicolaou/ceratitis/RNASEQ_BAM/SE/gsnap.sample4.fastq.trimmomatic_vs_Ccap01172013.unpaired_uniq.bigwig"
+    },
+    {
+      "category": "OGSv1.1/1. Gene Sets/Pseudogenes",
+      "compress": 0,
+      "key": "Published OGS v1.1, pseudogenes",
+      "label": "OGSv1-1_pseudogene",
+      "metadata": {
+        "Data description": "06 Dec 2015: This track reconciles the two OGS tracks produced by JAMg (v1) and NCBI (v2) and bring in the manual curation track. For every locus, a 2-2 comparison was made and then one gene was kept in that order: manual curation that have been approved, NCBI and JAMg. No alternative splice genes were kept.",
+        "Data provider": "Alexie Papanicolaou, Hawkesbury Institute for the Environment",
+        "Method": "reconsile_OGSs_to_master_OGS and AEGeAn parseval 64f3e0f924",
+        "Publication Status": "Published, please cite Genome Biology DOI: 10.1186/s13059-016-1049-2"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "UTR": "ogs-utr",
+          "exon": "container-100pct",
+          "pseudogenic_exon": "ogs-utr",
+          "wholeCDS": null
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/OGSv1-1_pseudogene/{refseq}/trackData.json"
+    },
+    {
+      "category": "OGSv1.1/1. Gene Sets/Protein Coding",
+      "compress": 0,
+      "key": "Published OGS v1.1, protein-coding genes",
+      "label": "cercap_current_models",
+      "metadata": {
+        "Data description": "06 Dec 2015: This track reconciles the two OGS tracks produced by JAMg (v1) and NCBI (v2) and bring in the manual curation track. For every locus, a 2-2 comparison was made and then one gene was kept in that order: manual curation that have been approved, NCBI and JAMg. No alternative splice genes were kept.",
+        "Data provider": "Alexie Papanicolaou, Hawkesbury Institute for the Environment",
+        "Method": "reconsile_OGSs_to_master_OGS and AEGeAn parseval 64f3e0f924",
+        "Publication Status": "Published, please cite Genome Biology DOI: 10.1186/s13059-016-1049-2"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "CDS": "ogs-cds",
+          "UTR": "ogs-utr",
+          "exon": "container-100pct",
+          "five_prime_cis_splice_site": null,
+          "five_prime_utr": null,
+          "intron": null,
+          "three_prime_cis_splice_site": null,
+          "three_prime_utr": null,
+          "wholeCDS": null
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/cercap_current_models/{refseq}/trackData.json"
+    }
+  ]
 }
diff --git a/organisms/stage/Chelonus_insularis/trackList.json b/organisms/stage/Chelonus_insularis/trackList.json
index ec7ee96..c4969d4 100644
--- a/organisms/stage/Chelonus_insularis/trackList.json
+++ b/organisms/stage/Chelonus_insularis/trackList.json
@@ -45,6 +45,7 @@
             "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
             "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
          },
+         "scoreType" : "avgScore",
          "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
          "style" : {
             "neg_color" : "rgba(255,255,0,50)",
@@ -67,7 +68,7 @@
                "iconClass" : "dijitIconDatabase",
                "label" : "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
                "title" : "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
-               "url" : "function(track,feature){ return 'https://i5k.nal.usda.gov/search/site/'+feature.get('name')}"
+               "url" : "function(track,feature){ return 'https://www.ncbi.nlm.nih.gov/nuccore/'+feature.get('name')}"
             }
          ],
          "metadata" : {
@@ -79,7 +80,7 @@
          "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
             "arrowheadClass" : "trellis-arrowhead",
-            "className" : "container-16px",
+            "className" : "{type}",
             "description" : "product, note, description",
             "subfeatureClasses" : {
                "CDS" : "gnomon_CDS",
@@ -88,8 +89,8 @@
                "wholeCDS" : null
             }
          },
-         "trackType" : "ColorByType/View/Track/ColorByTypeDraggable",
-         "type" : "ColorByType/View/Track/ColorByTypeDraggable",
+         "trackType" : "HTMLFeatures",
+         "type" : "HTMLFeatures",
          "urlTemplate" : "tracks/cheins_current_models/{refseq}/trackData.json"
       },
       {
@@ -106,7 +107,7 @@
          "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
             "arrowheadClass" : "trellis-arrowhead",
-            "className" : "container-16px",
+            "className" : "{type}",
             "description" : "product, note, description",
             "subfeatureClasses" : {
                "CDS" : "gnomon_CDS",
@@ -558,6 +559,65 @@
          "trackType" : null,
          "type" : "FeatureTrack",
          "urlTemplate" : "tracks/Cheins_ASM1335770v1_RNA-Seq-alignments_2020-07-17_junctions/{refseq}/trackData.json"
+      },
+      {
+         "category" : "RNA-Seq/Mapped Reads",
+         "key" : "Cheins_ASM1335770v1_RNA-Seq-alignments_2021-06-09",
+         "label" : "Cheins_ASM1335770v1_RNA-Seq-alignments_2021-06-09",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11845186'>SRR11845186</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11845185'>SRR11845185</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11845184'>SRR11845184</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11845190'>SRR11845190</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11845189'>SRR11845189</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Dark red alignments: Mapped portion of read aligned to forward strand<br>Light red alignments: Spliced portion of read aligned to forward strand<br>Dark blue alignments: Mapped portion of read aligned to reverse strand<br>Light blue alignments: Spliced portion of read aligned to reverse strand<br>Red marking - deletion in the read relative to the reference<br>Green marking - insertion in the read relative to the reference<br>Yellow marking  - mismatch (hover over the mismatch to see what the snp is)"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "unsafePopup" : true,
+         "urlTemplate" : "analyses/Chelonus-insularis-RNA-Seq_2021-06-09_v1.0/Cheins_ASM1335770v1_RNA-Seq-alignments_2021-06-09.bam"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "RNA-Seq/Coverage Plots",
+         "key" : "Cheins_ASM1335770v1_RNA-Seq-alignments_2021-06-09_coverage",
+         "label" : "Cheins_ASM1335770v1_RNA-Seq-alignments_2021-06-09_coverage",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11845186'>SRR11845186</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11845185'>SRR11845185</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11845184'>SRR11845184</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11845190'>SRR11845190</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11845189'>SRR11845189</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "unsafePopup" : true,
+         "urlTemplate" : "analyses/Chelonus-insularis-RNA-Seq_2021-06-09_v1.0/Cheins_ASM1335770v1_RNA-Seq-alignments_2021-06-09.bigwig"
+      },
+      {
+         "category" : "RNA-Seq/Splice junctions",
+         "compress" : 0,
+         "key" : "Cheins_ASM1335770v1_RNA-Seq-alignments_2021-06-09_junctions",
+         "label" : "Cheins_ASM1335770v1_RNA-Seq-alignments_2021-06-09_junctions",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11845186'>SRR11845186</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11845185'>SRR11845185</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11845184'>SRR11845184</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11845190'>SRR11845190</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11845189'>SRR11845189</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Junction reads generated by Hisat2 aligner and regtools. The number of alignments supporting the junction read is listed in blue."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "className" : "feature",
+            "description" : "score"
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "unsafePopup" : true,
+         "urlTemplate" : "tracks/Cheins_ASM1335770v1_RNA-Seq-alignments_2021-06-09_junctions/{refseq}/trackData.json"
       }
    ]
 }
diff --git a/organisms/stage/Cimex_lectularius/trackList.json b/organisms/stage/Cimex_lectularius/trackList.json
index 11cc0a4..bb70f7a 100644
--- a/organisms/stage/Cimex_lectularius/trackList.json
+++ b/organisms/stage/Cimex_lectularius/trackList.json
@@ -1,1445 +1,1438 @@
 {
-   "defaultTracks":"Contamination,cimlec_current_models",
-   "css" : "./plugins/NAL_CSS/css/contrib_styles.css",
-   "share_link" : 0,
-   "plugins" : [
-      {
-         "location" : "./plugins/WebApollo",
-         "name" : "WebApollo"
-      }
-   ],
-   "tracks" : [
-      {
-         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
-         "chunkSize" : 20000,
-         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-",
-         "label" : "DNA",
-         "type" : "SequenceTrack",
-         "key" : "Reference sequence"
-      },
-      {
-         "autocomplete" : "none",
-         "style" : {
-            "className" : "annot",
-            "renderClassName" : "annot-render",
-            "subfeatureClasses" : {
-               "non_canonical_three_prime_splice_site" : "noncanonical-splice-site",
-               "wholeCDS" : null,
-               "exon" : "container-100pct",
-               "CDS" : "annot-CDS",
-               "non_canonical_five_prime_splice_site" : "noncanonical-splice-site",
-               "UTR" : "annot-UTR"
-            },
-            "arrowheadClass" : "annot-arrowhead",
-            "alternateClasses" : {
-               "transposable_element" : {
-                  "renderClassName" : "blue-ibeam-render",
-                  "className" : "blue-ibeam"
-               },
-               "pseudogene" : {
-                  "renderClassName" : "gray-center-30pct",
-                  "className" : "light-purple-80pct"
-               },
-               "snRNA" : {
-                  "renderClassName" : "gray-center-30pct",
-                  "className" : "brightgreen-80pct"
-               },
-               "rRNA" : {
-                  "renderClassName" : "gray-center-30pct",
-                  "className" : "brightgreen-80pct"
-               },
-               "snoRNA" : {
-                  "renderClassName" : "gray-center-30pct",
-                  "className" : "brightgreen-80pct"
-               },
-               "repeat_region" : {
-                  "className" : "magenta-80pct"
-               },
-               "tRNA" : {
-                  "renderClassName" : "gray-center-30pct",
-                  "className" : "brightgreen-80pct"
-               },
-               "ncRNA" : {
-                  "renderClassName" : "gray-center-30pct",
-                  "className" : "brightgreen-80pct"
-               },
-               "miRNA" : {
-                  "renderClassName" : "gray-center-30pct",
-                  "className" : "brightgreen-80pct"
-               }
-            },
-            "uniqueIdField" : "id",
-            "centerSubFeature" : {
-               "non_canonical_three_prime_splice_site" : false,
-               "non_canonical_five_prime_splice_site" : false
-            }
-         },
-         "key" : "User-created Annotations",
-         "storeClass" : "WebApollo/Store/SeqFeature/ScratchPad",
-         "phase" : 0,
-         "compress" : 0,
-         "label" : "Annotations",
-         "type" : "WebApollo/View/Track/AnnotTrack",
-         "subfeatures" : 1
-      },
-      {
-         "style" : {
-            "className" : "container-16px",
-            "subfeatureClasses" : {
-               "wholeCDS" : null,
-               "exon" : "container-100pct",
-               "CDS" : "primary_gene_set-cds",
-               "UTR" : "primary_gene_set-utr"
-            },
-            "arrowheadClass" : "trellis-arrowhead"
-         },
-         "key" : "CLEC_v0.5.3-Models",
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
-         "trackType" : null,
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+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
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+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
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+      "label": "protein2genome_Chelicerata",
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+      "label": "protein2genome_Cnidaria",
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+      "key": "protein2genome_Craniata",
+      "label": "protein2genome_Craniata",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
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+      "key": "protein2genome_Crustacea",
+      "label": "protein2genome_Crustacea",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
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+      "key": "protein2genome_Echinodermata",
+      "label": "protein2genome_Echinodermata",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
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+      "label": "protein2genome_Mollusca",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
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+      "key": "protein2genome_Nemata",
+      "label": "protein2genome_Nemata",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
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+        "Publication status": "Published, if using please cite: doi:10.1038/ncomms10165.",
+        "Track legend": "Results from Protein2genome alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline."
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+      "type": "FeatureTrack",
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+      "key": "protein2genome_Nematomorpha",
+      "label": "protein2genome_Nematomorpha",
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+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published, if using please cite: doi:10.1038/ncomms10165.",
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+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
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+        "arrowheadClass": "webapollo-arrowhead",
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+          "match_part": "protein2genome"
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Nematomorpha/{refseq}/trackData.json"
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+      "key": "protein2genome_Onychophora",
+      "label": "protein2genome_Onychophora",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published, if using please cite: doi:10.1038/ncomms10165.",
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+        "arrowheadClass": "webapollo-arrowhead",
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+          "match_part": "protein2genome"
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+      "key": "protein2genome_Parazoa",
+      "label": "protein2genome_Parazoa",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
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+        "Publication status": "Published, if using please cite: doi:10.1038/ncomms10165.",
+        "Track legend": "Results from Protein2genome alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline."
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+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
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+        "arrowheadClass": "webapollo-arrowhead",
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+      "type": "FeatureTrack",
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+      "key": "protein2genome_Placozoa",
+      "label": "protein2genome_Placozoa",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
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+        "Track legend": "Results from Protein2genome alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline."
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+        "arrowheadClass": "webapollo-arrowhead",
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+      "urlTemplate": "tracks/protein2genome_Placozoa/{refseq}/trackData.json"
+    },
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+      "key": "protein2genome_Platyhelminthes",
+      "label": "protein2genome_Platyhelminthes",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
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+        "Track legend": "Results from Protein2genome alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline."
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+        "arrowheadClass": "webapollo-arrowhead",
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+          "match_part": "protein2genome"
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Platyhelminthes/{refseq}/trackData.json"
+    },
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+      "key": "protein2genome_Priapulida",
+      "label": "protein2genome_Priapulida",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
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+        "Track legend": "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline."
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+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
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+        "arrowheadClass": "webapollo-arrowhead",
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Priapulida/{refseq}/trackData.json"
+    },
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+      "key": "protein2genome_Tardigrada",
+      "label": "protein2genome_Tardigrada",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
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+        "Track legend": "Results from Protein2genome alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline."
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+        "arrowheadClass": "webapollo-arrowhead",
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+      "urlTemplate": "tracks/protein2genome_Tardigrada/{refseq}/trackData.json"
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+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+      "key": "protein2genome_Tunicata",
+      "label": "protein2genome_Tunicata",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
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+        "Track legend": "Results from Protein2genome alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline."
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+        "arrowheadClass": "webapollo-arrowhead",
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Tunicata/{refseq}/trackData.json"
+    },
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+      "key": "protein2genome_UNCATEGORISED",
+      "label": "protein2genome_UNCATEGORISED",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published, if using please cite: doi:10.1038/ncomms10165.",
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+      "key": "repeatmasker",
+      "label": "repeatmasker",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published, if using please cite: doi:10.1038/ncomms10165.",
+        "Track legend": "Results from RepeatMasker as part of the MAKER automated annotation pipeline."
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+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
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+        "arrowheadClass": "webapollo-arrowhead",
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+      "category": "BCM_v0.5.3/2. Evidence/Repeats",
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+      "key": "repeatrunner",
+      "label": "repeatrunner",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published, if using please cite: doi:10.1038/ncomms10165.",
+        "Track legend": "Results from Repeatrunner as part of the MAKER automated annotation pipeline."
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+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/repeatrunner/{refseq}/trackData.json"
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+      "key": "snap_masked",
+      "label": "snap_masked",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published, if using please cite: doi:10.1038/ncomms10165.",
+        "Track legend": "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "snap"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/snap_masked/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/1. Gene Sets/Primary Gene Sets: Protein Coding",
+      "compress": 0,
+      "key": "CLEC_v0.5.2-Models-DEPRECATED",
+      "label": "cimlec_deprecated_models",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published, if using please cite: doi:10.1038/ncomms10165.",
+        "Track legend": "Consensus gene models from the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "CDS": "deprecated_gene_set-cds",
+          "UTR": "deprecated_gene_set-utr",
+          "exon": "container-100pct",
+          "wholeCDS": null
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/CLEC_v0.5.2-Models/{refseq}/trackData.json"
+    },
+    {
+      "category": "Transcriptome/Mapped Reads",
+      "chunkSizeLimit": 35000000,
+      "key": "female RNA-Seq",
+      "label": "cimlec_RNA_female",
+      "metadata": {
+        "Alignment method": "TopHat 2.0, default parameters",
+        "Alignment summary": "http://de.iplantcollaborative.org/dl/d/D0300D5C-7D1B-4208-890D-67C1A90B2F23/align_summary.txt",
+        "Data Provider": "Baylor College of Medicine",
+        "Data Source 1": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Bed_bug/RNA_sequence/Clec_RNA-Adult-Female_300Bp_ICD_CLI5RP.A7MX-F-1_1pA_D16AUACXX-4-ID03_1_sequence.txt.bz2",
+        "Data Source 2": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Bed_bug/RNA_sequence/Clec_RNA-Adult-Female_300Bp_ICD_CLI5RP.A7MX-F-1_1pA_D16AUACXX-4-ID03_2_sequence.txt.bz2",
+        "Read cleaning method": "None"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "bam/Clec_RNA-Adult-Female_300Bp_ICD_CLI5RP.bam"
+    },
+    {
+      "category": "Transcriptome/Mapped Reads",
+      "key": "male RNA-Seq",
+      "label": "cimlec_RNA_male",
+      "metadata": {
+        "Alignment method": "TopHat 2.0, default parameters",
+        "Alignment summary": "http://de.iplantcollaborative.org/dl/d/48B9A48D-1A7D-4314-9F00-0B8FC73485DB/align_summary.txt",
+        "Data Provider": "Baylor College of Medicine",
+        "Data Source 1": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Bed_bug/RNA_sequence/Clec_RNA-Adult-Male_300Bp_ICD_CLI5RP.A7MX-M-1_1pA_D16AUACXX-4-ID04_1_sequence.txt",
+        "Data Source 2": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Bed_bug/RNA_sequence/Clec_RNA-Adult-Male_300Bp_ICD_CLI5RP.A7MX-M-1_1pA_D16AUACXX-4-ID04_2_sequence.txt",
+        "Read cleaning method": "None"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "bam/Clec_RNA-Adult-Male_300Bp_ICD_CLI5RP.bam"
+    },
+    {
+      "category": "Transcriptome/Assembly",
+      "compress": 0,
+      "key": "Koganemaru et al. 2013 transcriptome assembly",
+      "label": "Transcriptome models",
+      "metadata": {
+        "Assembly methods": "http://dx.doi.org/10.1016/j.pestbp.2013.01.001",
+        "Publication status": "Published, if using please cite http://dx.doi.org/10.1016/j.pestbp.2013.01.001",
+        "Raw data source": "GEO accession # GSE31823"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "CDS": "transcriptome-cds",
+          "UTR": "transcriptome-utr",
+          "exon": "container-100pct",
+          "wholeCDS": null
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/Transcriptome models/{refseq}/trackData.json"
+    },
+    {
+      "category": "Transcriptome/Mapped Reads",
+      "key": "3-day-old embryo RNA-Seq, combined",
+      "label": "Harlan_RNASeq_combined",
+      "metadata": {
+        "Data Source": "Zach Adelman, Brittany Delong, Dini Miller (Virginia Tech)",
+        "Mapping parameters": "tophat -a 20 -i 30 -p 8 --no-discordant --no-mixed --microexon-search",
+        "Mapping program": "Tophat v2.0.10",
+        "Sequencing platform": "Illumina Hi-Seq 200 bp PE",
+        "Sex": "Mixed",
+        "Source of materials": "3 day old embryos (both male and female) from Harlan strain bed bugs",
+        "Status": "unpublished - please follow Ft. Lauderdale and Toronto agreements",
+        "Track legend": "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "user_files/zadel/Harlan_combined_NALmod.bam.sorted.bam"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Transcriptome/Coverage plots (BigWig)",
+      "key": "3-day-old embryo RNA-Seq, combined-density plots",
+      "label": "Harlan_RNASeq_combined-density",
+      "metadata": {
+        "Data Source": "Zach Adelman, Brittany Delong, Dini Miller (Virginia Tech)",
+        "Mapping parameters": "tophat -a 20 -i 30 -p 8 --no-discordant --no-mixed --microexon-search",
+        "Mapping program": "Tophat v2.0.10",
+        "Sequencing platform": "Illumina Hi-Seq 200 bp PE",
+        "Sex": "Mixed",
+        "Source of materials": "3 day old embryos (both male and female) from Harlan strain bed bugs",
+        "Status": "unpublished - please follow Ft. Lauderdale and Toronto agreements",
+        "Track legend": "This track represents a density plot of RNA-Seq coverage. Darker blue represents higher coverage, and lighter blue lower coverage."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "user_files/zadel/Harlan_combined_NALmod.bam.sorted_2.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "category": "Transcriptome/Coverage plots (BigWig)",
+      "key": "3-day-old embryo RNA-Seq, combined-XYplots",
+      "label": "Harlan_RNASeq_combined-XYplots",
+      "metadata": {
+        "Data Source": "Zach Adelman, Brittany Delong, Dini Miller (Virginia Tech)",
+        "Mapping parameters": "tophat -a 20 -i 30 -p 8 --no-discordant --no-mixed --microexon-search",
+        "Mapping program": "Tophat v2.0.10",
+        "Sequencing platform": "Illumina Hi-Seq 200 bp PE",
+        "Sex": "Mixed",
+        "Source of materials": "3 day old embryos (both male and female) from Harlan strain bed bugs",
+        "Status": "unpublished - please follow Ft. Lauderdale and Toronto agreements",
+        "Track legend": "This track represents an X-Y plot of RNA-Seq coverage. The y-axis has a minimum value of abs(2000); areas with higher coverage are indicated by a red clip."
+      },
+      "min_score": 0,
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "clip_marker_color": "red",
+        "height": 50,
+        "neg_color": "#005EFF",
+        "pos_color": "#FFA600"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "user_files/zadel/Harlan_combined_NALmod.bam.sorted_2.bigwig",
+      "variance_band": false
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Reference Assembly",
+      "key": "Gaps in assembly",
+      "label": "Gaps in assembly",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "white",
+        "pos_color": "black"
+      },
+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "bigwig/Clec_Bbug02212013.GAPS.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "0.5",
+      "category": "Reference Assembly",
+      "key": "GC Content",
+      "label": "GC Content",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+      },
+      "scoreType": "avgScore",
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "rgba(255,255,0,50)",
+        "pos_color": "rgba(0,0,255,50)"
+      },
+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "bigwig/Clec_Bbug02212013.genome_GC.bigwig"
+    },
+    {
+      "category": "Official Gene Set/2. Noncoding Genes",
+      "compress": 0,
+      "key": "C. lectularius OGS_v1.2 - pseudogenes",
+      "label": "clec_OGS_v1.2_pseudogene",
+      "metadata": {
+        "Analysis description": "The Official Gene Set OGS_v1.2 was generated from the computationally predicted gene set CLEC_v0.5.3 and manually curated models.",
+        "Description": "Published, if using please cite: doi:10.1038/ncomms10165",
+        "Publication status": "Published, if using please cite: doi:10.1038/ncomms10165",
+        "Track legend": "Official Gene Set OGS_v1.2"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "CDS": "ogs-cds",
+          "UTR": "ogs-utr",
+          "pseudogenic_exon": "ogs-utr",
+          "wholeCDS": null
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/clec_OGS_v1.2_pseudogene/{refseq}/trackData.json"
+    },
+    {
+      "category": "Official Gene Set/1. Protein Coding Genes",
+      "compress": 0,
+      "fmtDetailValue_Id": "function(id, feature) { var name2 = id.replace(/-R./, ''); if(feature.get('type')=='mRNA') { return '<a href=\"https://i5k.nal.usda.gov/'+name2+'\" target=\"_blank\"><b>'+id+'</a> (Click for Gene page)</b>';} else {return id}}",
+      "key": "C. lectularius OGS_v1.2",
+      "label": "cimlec_current_models",
+      "menuTemplate": [
+        {
+          "label": "View details"
+        },
+        {
+          "action": "newWindow",
+          "iconClass": "dijitIconDatabase",
+          "label": "function(track,feature){ return 'Find gene page at VEuPathDB for '+feature.get('id').replace(/-R./, '')}",
+          "title": "function(track,feature){ return 'Find gene page at VEuPathDB for '+feature.get('id').replace(/-R./, '')}",
+          "url": "function(track,feature){ return 'https://veupathdb.org/veupathdb/app/search?q='+feature.get('id').replace(/-R./, '')}"
+        }
+      ],
+      "metadata": {
+        "Analysis description": "The Official Gene Set OGS_v1.2 was generated from the computationally predicted gene set CLEC_v0.5.3 and manually curated models.",
+        "Description": "Published, if using please cite: doi:10.1038/ncomms10165",
+        "Publication status": "Published, if using please cite: doi:10.1038/ncomms10165",
+        "Track legend": "Official Gene Set OGS_v1.2. Note that stop codon read-through features are visualized as red bars above and below the CDS."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "description": "method, source",
+        "subfeatureClasses": {
+          "CDS": "ogs-cds",
+          "UTR": "ogs-utr",
+          "exon": "container-100pct",
+          "five_prime_utr": "ogs-utr",
+          "stop_codon_read_through": "red-100pct",
+          "three_prime_utr": "ogs-utr",
+          "wholeCDS": null
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/clec_OGS_v1.2/{refseq}/trackData.json"
+    },
+    {
+      "category": "Reference Assembly",
+      "compress": 0,
+      "key": "Contamination",
+      "label": "Contamination",
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": null,
+        "className": "{type}",
+        "renderClassName": "red-100pct"
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/Contamination/{refseq}/trackData.json"
+    }
+  ]
 }
diff --git a/organisms/stage/Clitarchus_hookeri/trackList.json b/organisms/stage/Clitarchus_hookeri/trackList.json
index afac14f..a1e4d6e 100644
--- a/organisms/stage/Clitarchus_hookeri/trackList.json
+++ b/organisms/stage/Clitarchus_hookeri/trackList.json
@@ -1 +1,105 @@
-{"formatVersion":1,"names":{"type":"Hash","url":"names/"},"tracks":[{"category":"Reference sequence","faiUrlTemplate":"seq/GCA_002778355.1_ASM277835v1_genomic_over_1000.fna.fai","key":"Reference sequence","label":"DNA","seqType":"dna","storeClass":"JBrowse/Store/Sequence/IndexedFasta","type":"SequenceTrack","urlTemplate":"seq/GCA_002778355.1_ASM277835v1_genomic_over_1000.fna","useAsRefSeqStore":1},{"category":"1. Clitarchus hookeri Maker annotations/1. Gene Sets/Protein Coding","compress":0,"key":"Clitarchus hookeri Maker annotations","label":"clihoo_current_models","metadata":{"Data description":"https://doi.org/10.1186/s12864-017-4245-x","Data provider":"Chen Wu, Plant and Food New Zealand","Data source":"https://i5k.nal.usda.gov/annotations/739260/","Method":"https://i5k.nal.usda.gov/annotations/739260/"},"storeClass":"JBrowse/Store/SeqFeature/NCList","style":{"arrowheadClass":"trellis-arrowhead","className":"container-16px","subfeatureClasses":{"CDS":"primary_gene_set-cds","UTR":"primary_gene_set-utr","exon":"container-100pct","wholeCDS":null}},"trackType":null,"type":"FeatureTrack","urlTemplate":"tracks/clihoo_current_models/{refseq}/trackData.json"},{"autoscale":"local","bicolor_pivot":"zero","category":"Reference Assembly - only scaffolds over 1000 bp","key":"Gaps in assembly","label":"Gaps in assembly","metadata":{"Track contact":"The i5k workspace@NAL","Track description":"This track was created as part of the data proccessing workflow used to create the Web Apollo instance.","Track legend":"Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"},"storeClass":"JBrowse/Store/SeqFeature/BigWig","style":{"neg_color":"white","pos_color":"black"},"type":"JBrowse/View/Track/Wiggle/Density","urlTemplate":"bigwig/GCA_002778355.1_ASM277835v1_genomic_over_1000.fna.gap.bigwig"},{"autoscale":"local","bicolor_pivot":"0.5","category":"Reference Assembly - only scaffolds over 1000 bp","key":"GC Content","label":"GC Content","metadata":{"Track contact":"The i5k workspace@NAL","Track description":"This track was created as part of the data proccessing workflow used to create the Web Apollo instance.","Track legend":"Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."},"storeClass":"JBrowse/Store/SeqFeature/BigWig","style":{"neg_color":"rgba(255,255,0,50)","pos_color":"rgba(0,0,255,50)"},"type":"JBrowse/View/Track/Wiggle/Density","urlTemplate":"bigwig/GCA_002778355.1_ASM277835v1_genomic_over_1000.fna.gc"},{"category":"2. Transcriptome","compress":0,"key":"Ovariolar Tips RNA-Seq, Cufflinks analysis","label":"OvariolarTips_Cufflinks","metadata":{"Data provider":"Chen Wu, Plant and Food Research, NZ","Data source":"PRJNA429033","Geographic location":"Herekino (35 9.373 S, 173 17.155 E), Bream Head (35 50.479 S, 174 34.485 E), Lake Karapiro (37 56.445 S, 175 35.672 E), Cape Kidnappers (39 40.000 S, 177 46.000 E), Okuti Valley (43 47.390 S, 172 50.248 E)","Method":"https://i5k.nal.usda.gov/node/739289","Publication status":"Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use","Sequencing method":"Illumina HiSeq2000","Tissues/Life stage":"Adult ovariolar tips"},"storeClass":"JBrowse/Store/SeqFeature/NCList","style":{"arrowheadClass":"trellis-arrowhead","className":"container-16px","subfeatureClasses":{"CDS":"primary_gene_set-cds","UTR":"primary_gene_set-utr","exon":"transcriptome-cds","wholeCDS":null}},"trackType":null,"type":"FeatureTrack","urlTemplate":"tracks/OvariolarTips_Cufflinks/{refseq}/trackData.json"},{"category":"2. Transcriptome","compress":0,"key":"Ovary and Testis RNA-Seq, Cufflinks analysis","label":"OvaryAndTestis_Cufflinks_Cufflinks","metadata":{"Data provider":"Chen Wu, Plant and Food Research, NZ","Data source":"SRX3055387; SRX3055384; SRX3055383; SRX3055382; SRX3055381; SRX3055380","Geographic location":"37°0.111 S, 174° 55.039 E","Method":"https://i5k.nal.usda.gov/node/739288/","Publication status":"Published - please cite https://doi.org/10.1186/s12864-017-4245-x","Sequencing method":"Illumina HiSeq2000","Tissues/Life stage":"Adult ovary and testis"},"storeClass":"JBrowse/Store/SeqFeature/NCList","style":{"arrowheadClass":"trellis-arrowhead","className":"container-16px","subfeatureClasses":{"CDS":"primary_gene_set-cds","UTR":"primary_gene_set-utr","exon":"transcriptome-cds","wholeCDS":null}},"trackType":null,"type":"FeatureTrack","urlTemplate":"tracks/OvaryAndTestis_Cufflinks_Cufflinks/{refseq}/trackData.json"}]}
\ No newline at end of file
+{
+   "formatVersion" : 1,
+   "names" : {
+      "type" : "Hash",
+      "url" : "names/"
+   },
+   "tracks" : [
+      {
+         "category" : "Reference sequence",
+         "faiUrlTemplate" : "seq/GCA_002778355.1_ASM277835v1_genomic_over_1000.fna.fai",
+         "key" : "Reference sequence",
+         "label" : "DNA",
+         "seqType" : "dna",
+         "storeClass" : "JBrowse/Store/Sequence/IndexedFasta",
+         "type" : "SequenceTrack",
+         "urlTemplate" : "seq/GCA_002778355.1_ASM277835v1_genomic_over_1000.fna",
+         "useAsRefSeqStore" : 1
+      },
+      {
+         "category" : "1. Clitarchus hookeri Maker annotations/1. Gene Sets/Protein Coding",
+         "compress" : 0,
+         "key" : "Clitarchus hookeri Maker annotations",
+         "label" : "clihoo_current_models",
+         "metadata" : {
+            "Data description" : "https://doi.org/10.1186/s12864-017-4245-x",
+            "Data provider" : "Chen Wu, Plant and Food New Zealand",
+            "Data source" : "https://i5k.nal.usda.gov/annotations/739260/",
+            "Method" : "https://i5k.nal.usda.gov/annotations/739260/"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "{type}",
+            "subfeatureClasses" : {
+               "CDS" : "primary_gene_set-cds",
+               "UTR" : "primary_gene_set-utr",
+               "exon" : "transcriptome-cds",
+               "wholeCDS" : null
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/OvaryAndTestis_Cufflinks_Cufflinks/{refseq}/trackData.json"
+      },
+      {
+         "category" : "RNA-Seq/Mapped Reads",
+         "key" : "Clihoo_ASM277835v1_RNA-Seq-alignments_2021-07-03",
+         "label" : "Clihoo_ASM277835v1_RNA-Seq-alignments_2021-07-03",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR6472771'>SRR6472771</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR6472772'>SRR6472772</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR6472778'>SRR6472778</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR2089867'>SRR2089867</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR5889597'>SRR5889597</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR6472774'>SRR6472774</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR6472768'>SRR6472768</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR6472766'>SRR6472766</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR6472779'>SRR6472779</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR2089868'>SRR2089868</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Dark red alignments: Mapped portion of read aligned to forward strand<br>Light red alignments: Spliced portion of read aligned to forward strand<br>Dark blue alignments: Mapped portion of read aligned to reverse strand<br>Light blue alignments: Spliced portion of read aligned to reverse strand<br>Red marking - deletion in the read relative to the reference<br>Green marking - insertion in the read relative to the reference<br>Yellow marking  - mismatch (hover over the mismatch to see what the snp is)"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
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+         "unsafePopup" : true,
+         "urlTemplate" : "analyses/Clitarchus-hookeri-RNA-Seq_2021-07-03_v1.0/Clihoo_ASM277835v1_RNA-Seq-alignments_2021-07-03.bam"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "RNA-Seq/Coverage Plots",
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+         "label" : "Clihoo_ASM277835v1_RNA-Seq-alignments_2021-07-03_coverage",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR6472771'>SRR6472771</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR6472772'>SRR6472772</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR6472778'>SRR6472778</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR2089867'>SRR2089867</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR5889597'>SRR5889597</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR6472774'>SRR6472774</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR6472768'>SRR6472768</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR6472766'>SRR6472766</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR6472779'>SRR6472779</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR2089868'>SRR2089868</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "unsafePopup" : true,
+         "urlTemplate" : "analyses/Clitarchus-hookeri-RNA-Seq_2021-07-03_v1.0/Clihoo_ASM277835v1_RNA-Seq-alignments_2021-07-03.bigwig"
+      },
+      {
+         "category" : "RNA-Seq/Splice junctions",
+         "compress" : 0,
+         "key" : "Clihoo_ASM277835v1_RNA-Seq-alignments_2021-07-03_junctions",
+         "label" : "Clihoo_ASM277835v1_RNA-Seq-alignments_2021-07-03_junctions",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR6472771'>SRR6472771</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR6472772'>SRR6472772</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR6472778'>SRR6472778</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR2089867'>SRR2089867</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR5889597'>SRR5889597</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR6472774'>SRR6472774</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR6472768'>SRR6472768</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR6472766'>SRR6472766</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR6472779'>SRR6472779</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR2089868'>SRR2089868</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Junction reads generated by Hisat2 aligner and regtools. The number of alignments supporting the junction read is listed in blue."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "className" : "feature",
+            "description" : "score"
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "unsafePopup" : true,
+         "urlTemplate" : "tracks/Clihoo_ASM277835v1_RNA-Seq-alignments_2021-07-03_junctions/{refseq}/trackData.json"
+      }
+   ]
+}
diff --git a/organisms/stage/Contarinia_nasturtii/trackList.json b/organisms/stage/Contarinia_nasturtii/trackList.json
index 237feb1..4a6542f 100644
--- a/organisms/stage/Contarinia_nasturtii/trackList.json
+++ b/organisms/stage/Contarinia_nasturtii/trackList.json
@@ -59,18 +59,18 @@
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          "label" : "NCBI_Annotation_Release_100_Pseudogene",
-"menuTemplate" : [
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-       {
-        "label": "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
-        "title": "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
-        "iconClass" : "dijitIconDatabase",
-        "action": "newWindow",
-        "url" : "function(track,feature){ return 'https://i5k.nal.usda.gov/search/site/'+feature.get('name')}",
-        },
-  ],
+         "menuTemplate" : [
+            {
+               "label" : "View details"
+            },
+            {
+               "action" : "newWindow",
+               "iconClass" : "dijitIconDatabase",
+               "label" : "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
+               "title" : "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
+               "url" : "function(track,feature){ return 'https://www.ncbi.nlm.nih.gov/nuccore/'+feature.get('name')}"
+            }
+         ],
          "metadata" : {
             "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/connas/README_CURRENT_RELEASE",
             "Data provider" : "NCBI",
@@ -80,7 +80,7 @@
          "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
             "arrowheadClass" : "trellis-arrowhead",
-            "className" : "container-16px",
+            "className" : "{type}",
             "description" : "product, note, description",
             "subfeatureClasses" : {
                "CDS" : "gnomon_CDS",
@@ -98,18 +98,18 @@
          "compress" : 0,
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-"menuTemplate" : [
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-          "label" : "View details",
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-       {
-        "label": "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
-        "title": "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
-        "iconClass" : "dijitIconDatabase",
-        "action": "newWindow",
-        "url" : "function(track,feature){ return 'https://i5k.nal.usda.gov/search/site/'+feature.get('name')}",
-        },
-  ],
+         "menuTemplate" : [
+            {
+               "label" : "View details"
+            },
+            {
+               "action" : "newWindow",
+               "iconClass" : "dijitIconDatabase",
+               "label" : "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
+               "title" : "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
+               "url" : "function(track,feature){ return 'https://i5k.nal.usda.gov/'+feature.get('name')}"
+            }
+         ],
          "metadata" : {
             "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/connas/README_CURRENT_RELEASE",
             "Data provider" : "NCBI",
@@ -119,7 +119,7 @@
          "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
             "arrowheadClass" : "trellis-arrowhead",
-            "className" : "container-16px",
+            "className" : "{type}",
             "description" : "product, note, description",
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@@ -128,9 +128,68 @@
                "wholeCDS" : null
             }
          },
-         "trackType" : "ColorByType/View/Track/ColorByTypeDraggable",
-         "type" : "ColorByType/View/Track/ColorByTypeDraggable",
+         "trackType" : "HTMLFeatures",
+         "type" : "HTMLFeatures",
          "urlTemplate" : "tracks/connas_current_models/{refseq}/trackData.json"
+      },
+      {
+         "category" : "RNA-Seq/Mapped Reads",
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+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
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+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "unsafePopup" : true,
+         "urlTemplate" : "analyses/Contarinia-nasturtii-RNA-Seq_2021-06-11_v1.0/Connas_AAFC_CNas_1.1_RNA-Seq-alignments_2021-06-11.bam"
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+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
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+         "label" : "Connas_AAFC_CNas_1.1_RNA-Seq-alignments_2021-06-11_coverage",
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+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
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+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage."
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+         "style" : {
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+         "unsafePopup" : true,
+         "urlTemplate" : "analyses/Contarinia-nasturtii-RNA-Seq_2021-06-11_v1.0/Connas_AAFC_CNas_1.1_RNA-Seq-alignments_2021-06-11.bigwig"
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+            "Track legend" : "Junction reads generated by Hisat2 aligner and regtools. The number of alignments supporting the junction read is listed in blue."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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+            "description" : "score"
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+         "unsafePopup" : true,
+         "urlTemplate" : "tracks/Connas_AAFC_CNas_1.1_RNA-Seq-alignments_2021-06-11_junctions/{refseq}/trackData.json"
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 }
diff --git a/organisms/stage/Copidosoma_floridanum/trackList.json b/organisms/stage/Copidosoma_floridanum/trackList.json
index fa15afb..172fe7d 100644
--- a/organisms/stage/Copidosoma_floridanum/trackList.json
+++ b/organisms/stage/Copidosoma_floridanum/trackList.json
@@ -1,1314 +1,1269 @@
 {
-   "css" : "./plugins/NAL_CSS/css/contrib_styles.css",
+   "alwaysOnTracks" : "DNA,Annotations",
+   "css" : "./plugins/NAL_CSS/css/main.css",
+   "favicon" : "./plugins/WebApollo/img/webapollo_favicon.ico",
+   "formatVersion" : 1,
+   "names" : {
+      "type" : "Hash",
+      "url" : "names/"
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-         "name" : "WebApollo"
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    "tracks" : [
       {
-         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
+         "category" : "Reference sequence",
          "chunkSize" : 20000,
-         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-",
+         "key" : "Reference sequence",
          "label" : "DNA",
+         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
          "type" : "SequenceTrack",
-         "category" : "Reference sequence",
-         "key" : "Reference sequence"
+         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-"
       },
       {
          "autocomplete" : "none",
+         "compress" : 0,
+         "key" : "User-created Annotations",
+         "label" : "Annotations",
+         "phase" : 0,
+         "storeClass" : "WebApollo/Store/SeqFeature/ScratchPad",
          "style" : {
-            "className" : "annot",
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             "alternateClasses" : {
-               "transposable_element" : {
-                  "renderClassName" : "blue-ibeam-render",
-                  "className" : "blue-ibeam"
+               "miRNA" : {
+                  "className" : "brightgreen-80pct",
+                  "renderClassName" : "gray-center-30pct"
                },
-               "pseudogene" : {
-                  "renderClassName" : "gray-center-30pct",
-                  "className" : "light-purple-80pct"
+               "ncRNA" : {
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+                  "renderClassName" : "gray-center-30pct"
                },
-               "snRNA" : {
-                  "renderClassName" : "gray-center-30pct",
-                  "className" : "brightgreen-80pct"
+               "pseudogene" : {
+                  "className" : "light-purple-80pct",
+                  "renderClassName" : "gray-center-30pct"
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                "rRNA" : {
-                  "renderClassName" : "gray-center-30pct",
-                  "className" : "brightgreen-80pct"
-               },
-               "snoRNA" : {
-                  "renderClassName" : "gray-center-30pct",
-                  "className" : "brightgreen-80pct"
+                  "className" : "brightgreen-80pct",
+                  "renderClassName" : "gray-center-30pct"
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                "repeat_region" : {
                   "className" : "magenta-80pct"
                },
-               "miRNA" : {
-                  "renderClassName" : "gray-center-30pct",
-                  "className" : "brightgreen-80pct"
+               "snRNA" : {
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+                  "renderClassName" : "gray-center-30pct"
+               },
+               "snoRNA" : {
+                  "className" : "brightgreen-80pct",
+                  "renderClassName" : "gray-center-30pct"
                },
                "tRNA" : {
-                  "renderClassName" : "gray-center-30pct",
-                  "className" : "brightgreen-80pct"
+                  "className" : "brightgreen-80pct",
+                  "renderClassName" : "gray-center-30pct"
                },
-               "ncRNA" : {
-                  "renderClassName" : "gray-center-30pct",
-                  "className" : "brightgreen-80pct"
+               "transposable_element" : {
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+                  "renderClassName" : "blue-ibeam-render"
                }
             },
-            "uniqueIdField" : "id",
+            "arrowheadClass" : "annot-arrowhead",
             "centerSubFeature" : {
-               "non_canonical_three_prime_splice_site" : false,
-               "non_canonical_five_prime_splice_site" : false
-            }
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+            "renderClassName" : "annot-render",
+            "subfeatureClasses" : {
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          },
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-         "storeClass" : "WebApollo/Store/SeqFeature/ScratchPad",
-         "phase" : 0,
-         "compress" : 0,
-         "label" : "Annotations",
-         "type" : "WebApollo/View/Track/AnnotTrack",
-         "subfeatures" : 1
+         "subfeatures" : 1,
+         "type" : "WebApollo/View/Track/AnnotTrack"
       },
       {
+         "category" : "BCM_v0.5.3/1. Gene Sets/Primary Gene Sets: Protein Coding",
+         "compress" : 0,
+         "key" : "CFLO_v0.5.3-Models",
+         "label" : "copflo_current_models",
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+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Consensus gene models from the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "className" : "container-16px",
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "{type}",
             "subfeatureClasses" : {
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-               "exon" : "container-100pct",
                "CDS" : "primary_gene_set-cds",
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-
-
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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-         "compress" : 0,
          "type" : "FeatureTrack",
-         "label" : "copflo_current_models"
+         "urlTemplate" : "tracks/copflo_current_models/{refseq}/trackData.json"
       },
       {
+         "category" : "BCM_v0.5.3/1. Gene Sets/Supplementary Gene Predictions",
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+            "Track legend" : "Results from the Augustus gene prediction software as part of the MAKER automated annotation pipeline."
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          "style" : {
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                "match_part" : "augustus"
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-        "Track legend" : "Results from the Augustus gene prediction software as part of the MAKER automated annotation pipeline.",
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
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-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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          "type" : "FeatureTrack",
-         "label" : "augustus_masked"
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       },
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+         "label" : "blastx_Annelida",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Blastx alignments of a set of Annelida proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "className" : "container-10px",
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-	         "metadata" : {
-        "Track legend" : "Results from Blastx alignments of a set of Annelida proteins as part of the MAKER automated annotation pipeline.", 
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
-    },
-         "key" : "blastx_Annelida",
-
-
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+            }
+         },
          "trackType" : null,
-         "urlTemplate" : "tracks/blastx_Annelida/{refseq}/trackData.json",
-         "compress" : 0,
          "type" : "FeatureTrack",
-         "label" : "blastx_Annelida"
+         "urlTemplate" : "tracks/blastx_Annelida/{refseq}/trackData.json"
       },
       {
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+         "label" : "blastx_Arthropoda",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Blastx alignments of a set of Arthropoda proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "className" : "container-10px",
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             "subfeatureClasses" : {
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-	         "metadata" : {
-        "Track legend" : "Results from Blastx alignments of a set of Arthropoda proteins as part of the MAKER automated annotation pipeline.", 
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
-    },
-         "key" : "blastx_Arthropoda",
-
-
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+            }
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          "trackType" : null,
-         "urlTemplate" : "tracks/blastx_Arthropoda/{refseq}/trackData.json",
-         "compress" : 0,
          "type" : "FeatureTrack",
-         "label" : "blastx_Arthropoda"
+         "urlTemplate" : "tracks/blastx_Arthropoda/{refseq}/trackData.json"
       },
       {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX",
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+         "key" : "blastx_Atelocerata",
+         "label" : "blastx_Atelocerata",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Blastx alignments of a set of Atelocerata proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "className" : "container-10px",
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             "subfeatureClasses" : {
                "match_part" : "blastx"
-            },
-            "arrowheadClass" : "webapollo-arrowhead"
-         },
-	 "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX",
-	         "metadata" : {
-        "Track legend" : "Results from Blastx alignments of a set of Atelocerata proteins as part of the MAKER automated annotation pipeline.", 
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
-    },
-         "key" : "blastx_Atelocerata",
-
-
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+            }
+         },
          "trackType" : null,
-         "urlTemplate" : "tracks/blastx_Atelocerata/{refseq}/trackData.json",
-         "compress" : 0,
          "type" : "FeatureTrack",
-         "label" : "blastx_Atelocerata"
+         "urlTemplate" : "tracks/blastx_Atelocerata/{refseq}/trackData.json"
       },
       {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX",
+         "compress" : 0,
+         "key" : "blastx_Cephalochordata",
+         "label" : "blastx_Cephalochordata",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Blastx alignments of a set of Cephalochordata proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "className" : "container-10px",
+            "arrowheadClass" : "webapollo-arrowhead",
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             "subfeatureClasses" : {
                "match_part" : "blastx"
-            },
-            "arrowheadClass" : "webapollo-arrowhead"
-         },
-	 "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX",
-	         "metadata" : {
-        "Track legend" : "Results from Blastx alignments of a set of Cephalochordata proteins as part of the MAKER automated annotation pipeline.", 
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
-    },
-         "key" : "blastx_Cephalochordata",
-
-
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+            }
+         },
          "trackType" : null,
-         "urlTemplate" : "tracks/blastx_Cephalochordata/{refseq}/trackData.json",
-         "compress" : 0,
          "type" : "FeatureTrack",
-         "label" : "blastx_Cephalochordata"
+         "urlTemplate" : "tracks/blastx_Cephalochordata/{refseq}/trackData.json"
       },
       {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX",
+         "compress" : 0,
+         "key" : "blastx_Chelicerata",
+         "label" : "blastx_Chelicerata",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Blastx alignments of a set of Chelicerata proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "className" : "container-10px",
+            "arrowheadClass" : "webapollo-arrowhead",
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             "subfeatureClasses" : {
                "match_part" : "blastx"
-            },
-            "arrowheadClass" : "webapollo-arrowhead"
-         },
-	 "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX",
-	         "metadata" : {
-        "Track legend" : "Results from Blastx alignments of a set of Chelicerata proteins as part of the MAKER automated annotation pipeline.", 
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
-    },
-         "key" : "blastx_Chelicerata",
-
-
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+            }
+         },
          "trackType" : null,
-         "urlTemplate" : "tracks/blastx_Chelicerata/{refseq}/trackData.json",
-         "compress" : 0,
          "type" : "FeatureTrack",
-         "label" : "blastx_Chelicerata"
+         "urlTemplate" : "tracks/blastx_Chelicerata/{refseq}/trackData.json"
       },
       {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX",
+         "compress" : 0,
+         "key" : "blastx_Cnidaria",
+         "label" : "blastx_Cnidaria",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Blastx alignments of a set of Cnidaria proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "className" : "container-10px",
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "{type}",
             "subfeatureClasses" : {
                "match_part" : "blastx"
-            },
-            "arrowheadClass" : "webapollo-arrowhead"
-         },
-	 "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX",
-	         "metadata" : {
-        "Track legend" : "Results from Blastx alignments of a set of Cnidaria proteins as part of the MAKER automated annotation pipeline.", 
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
-    },
-         "key" : "blastx_Cnidaria",
-
-
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+            }
+         },
          "trackType" : null,
-         "urlTemplate" : "tracks/blastx_Cnidaria/{refseq}/trackData.json",
-         "compress" : 0,
          "type" : "FeatureTrack",
-         "label" : "blastx_Cnidaria"
+         "urlTemplate" : "tracks/blastx_Cnidaria/{refseq}/trackData.json"
       },
       {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX",
+         "compress" : 0,
+         "key" : "blastx_Craniata",
+         "label" : "blastx_Craniata",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Blastx alignments of a set of Craniata proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "className" : "container-10px",
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "{type}",
             "subfeatureClasses" : {
                "match_part" : "blastx"
-            },
-            "arrowheadClass" : "webapollo-arrowhead"
-         },
-	 "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX",
-	         "metadata" : {
-        "Track legend" : "Results from Blastx alignments of a set of Craniata proteins as part of the MAKER automated annotation pipeline.", 
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
-    },
-         "key" : "blastx_Craniata",
-
-
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+            }
+         },
          "trackType" : null,
-         "urlTemplate" : "tracks/blastx_Craniata/{refseq}/trackData.json",
-         "compress" : 0,
          "type" : "FeatureTrack",
-         "label" : "blastx_Craniata"
+         "urlTemplate" : "tracks/blastx_Craniata/{refseq}/trackData.json"
       },
       {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX",
+         "compress" : 0,
+         "key" : "blastx_Crustacea",
+         "label" : "blastx_Crustacea",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Blastx alignments of a set of Crustacea proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "className" : "container-10px",
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "{type}",
             "subfeatureClasses" : {
                "match_part" : "blastx"
-            },
-            "arrowheadClass" : "webapollo-arrowhead"
-         },
-	 "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX",
-	         "metadata" : {
-        "Track legend" : "Results from Blastx alignments of a set of Crustacea proteins as part of the MAKER automated annotation pipeline.", 
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
-    },
-         "key" : "blastx_Crustacea",
-
-
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+            }
+         },
          "trackType" : null,
-         "urlTemplate" : "tracks/blastx_Crustacea/{refseq}/trackData.json",
-         "compress" : 0,
          "type" : "FeatureTrack",
-         "label" : "blastx_Crustacea"
+         "urlTemplate" : "tracks/blastx_Crustacea/{refseq}/trackData.json"
       },
       {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX",
+         "compress" : 0,
+         "key" : "blastx_Echinodermata",
+         "label" : "blastx_Echinodermata",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Blastx alignments of a set of Echinodermata proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "className" : "container-10px",
+            "arrowheadClass" : "webapollo-arrowhead",
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             "subfeatureClasses" : {
                "match_part" : "blastx"
-            },
-            "arrowheadClass" : "webapollo-arrowhead"
-         },
-	 "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX",
-	         "metadata" : {
-        "Track legend" : "Results from Blastx alignments of a set of Echinodermata proteins as part of the MAKER automated annotation pipeline.", 
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
-    },
-         "key" : "blastx_Echinodermata",
-
-
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+            }
+         },
          "trackType" : null,
-         "urlTemplate" : "tracks/blastx_Echinodermata/{refseq}/trackData.json",
-         "compress" : 0,
          "type" : "FeatureTrack",
-         "label" : "blastx_Echinodermata"
+         "urlTemplate" : "tracks/blastx_Echinodermata/{refseq}/trackData.json"
       },
       {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX",
+         "compress" : 0,
+         "key" : "blastx_Mollusca",
+         "label" : "blastx_Mollusca",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Blastx alignments of a set of Mollusca proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "className" : "container-10px",
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "{type}",
             "subfeatureClasses" : {
                "match_part" : "blastx"
-            },
-            "arrowheadClass" : "webapollo-arrowhead"
-         },
-	 "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX",
-	         "metadata" : {
-        "Track legend" : "Results from Blastx alignments of a set of Mollusca proteins as part of the MAKER automated annotation pipeline.", 
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
-    },
-         "key" : "blastx_Mollusca",
-
-
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+            }
+         },
          "trackType" : null,
-         "urlTemplate" : "tracks/blastx_Mollusca/{refseq}/trackData.json",
-         "compress" : 0,
          "type" : "FeatureTrack",
-         "label" : "blastx_Mollusca"
+         "urlTemplate" : "tracks/blastx_Mollusca/{refseq}/trackData.json"
       },
       {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX",
+         "compress" : 0,
+         "key" : "blastx_Nemata",
+         "label" : "blastx_Nemata",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Blastx alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "className" : "container-10px",
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "{type}",
             "subfeatureClasses" : {
                "match_part" : "blastx"
-            },
-            "arrowheadClass" : "webapollo-arrowhead"
-         },
-	 "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX",
-	         "metadata" : {
-        "Track legend" : "Results from Blastx alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline.", 
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
-    },
-         "key" : "blastx_Nemata",
-
-
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+            }
+         },
          "trackType" : null,
-         "urlTemplate" : "tracks/blastx_Nemata/{refseq}/trackData.json",
-         "compress" : 0,
          "type" : "FeatureTrack",
-         "label" : "blastx_Nemata"
+         "urlTemplate" : "tracks/blastx_Nemata/{refseq}/trackData.json"
       },
       {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX",
+         "compress" : 0,
+         "key" : "blastx_Nematomorpha",
+         "label" : "blastx_Nematomorpha",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Blastx alignments of a set of Nematomorpha proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "className" : "container-10px",
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             "subfeatureClasses" : {
                "match_part" : "blastx"
-            },
-            "arrowheadClass" : "webapollo-arrowhead"
-         },
-	 "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX",
-	         "metadata" : {
-        "Track legend" : "Results from Blastx alignments of a set of Nematomorpha proteins as part of the MAKER automated annotation pipeline.", 
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
-    },
-         "key" : "blastx_Nematomorpha",
-
-
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+            }
+         },
          "trackType" : null,
-         "urlTemplate" : "tracks/blastx_Nematomorpha/{refseq}/trackData.json",
-         "compress" : 0,
          "type" : "FeatureTrack",
-         "label" : "blastx_Nematomorpha"
+         "urlTemplate" : "tracks/blastx_Nematomorpha/{refseq}/trackData.json"
       },
       {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX",
+         "compress" : 0,
+         "key" : "blastx_Onychophora",
+         "label" : "blastx_Onychophora",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Blastx alignments of a set of Onychophora proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "className" : "container-10px",
+            "arrowheadClass" : "webapollo-arrowhead",
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             "subfeatureClasses" : {
                "match_part" : "blastx"
-            },
-            "arrowheadClass" : "webapollo-arrowhead"
-         },
-	 "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX",
-	         "metadata" : {
-        "Track legend" : "Results from Blastx alignments of a set of Onychophora proteins as part of the MAKER automated annotation pipeline.", 
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
-    },
-         "key" : "blastx_Onychophora",
-
-
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+            }
+         },
          "trackType" : null,
-         "urlTemplate" : "tracks/blastx_Onychophora/{refseq}/trackData.json",
-         "compress" : 0,
          "type" : "FeatureTrack",
-         "label" : "blastx_Onychophora"
+         "urlTemplate" : "tracks/blastx_Onychophora/{refseq}/trackData.json"
       },
       {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX",
+         "compress" : 0,
+         "key" : "blastx_Parazoa",
+         "label" : "blastx_Parazoa",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Blastx alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "className" : "container-10px",
+            "arrowheadClass" : "webapollo-arrowhead",
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             "subfeatureClasses" : {
                "match_part" : "blastx"
-            },
-            "arrowheadClass" : "webapollo-arrowhead"
-         },
-	 "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX",
-	         "metadata" : {
-        "Track legend" : "Results from Blastx alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline.", 
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
-    },
-         "key" : "blastx_Parazoa",
-
-
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+            }
+         },
          "trackType" : null,
-         "urlTemplate" : "tracks/blastx_Parazoa/{refseq}/trackData.json",
-         "compress" : 0,
          "type" : "FeatureTrack",
-         "label" : "blastx_Parazoa"
+         "urlTemplate" : "tracks/blastx_Parazoa/{refseq}/trackData.json"
       },
       {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX",
+         "compress" : 0,
+         "key" : "blastx_Placozoa",
+         "label" : "blastx_Placozoa",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Blastx alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "className" : "container-10px",
+            "arrowheadClass" : "webapollo-arrowhead",
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             "subfeatureClasses" : {
                "match_part" : "blastx"
-            },
-            "arrowheadClass" : "webapollo-arrowhead"
-         },
-	 "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX",
-	         "metadata" : {
-        "Track legend" : "Results from Blastx alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline.", 
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
-    },
-         "key" : "blastx_Placozoa",
-
-
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+            }
+         },
          "trackType" : null,
-         "urlTemplate" : "tracks/blastx_Placozoa/{refseq}/trackData.json",
-         "compress" : 0,
          "type" : "FeatureTrack",
-         "label" : "blastx_Placozoa"
+         "urlTemplate" : "tracks/blastx_Placozoa/{refseq}/trackData.json"
       },
       {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX",
+         "compress" : 0,
+         "key" : "blastx_Platyhelminthes",
+         "label" : "blastx_Platyhelminthes",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Blastx alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "className" : "container-10px",
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "{type}",
             "subfeatureClasses" : {
                "match_part" : "blastx"
-            },
-            "arrowheadClass" : "webapollo-arrowhead"
-         },
-	 "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX",
-	         "metadata" : {
-        "Track legend" : "Results from Blastx alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline.", 
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
-    },
-         "key" : "blastx_Platyhelminthes",
-
-
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+            }
+         },
          "trackType" : null,
-         "urlTemplate" : "tracks/blastx_Platyhelminthes/{refseq}/trackData.json",
-         "compress" : 0,
          "type" : "FeatureTrack",
-         "label" : "blastx_Platyhelminthes"
+         "urlTemplate" : "tracks/blastx_Platyhelminthes/{refseq}/trackData.json"
       },
       {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX",
+         "compress" : 0,
+         "key" : "blastx_Priapulida",
+         "label" : "blastx_Priapulida",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Blastx alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "className" : "container-10px",
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "{type}",
             "subfeatureClasses" : {
                "match_part" : "blastx"
-            },
-            "arrowheadClass" : "webapollo-arrowhead"
-         },
-	 "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX",
-	         "metadata" : {
-        "Track legend" : "Results from Blastx alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline.", 
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
-    },
-         "key" : "blastx_Priapulida",
-
-
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+            }
+         },
          "trackType" : null,
-         "urlTemplate" : "tracks/blastx_Priapulida/{refseq}/trackData.json",
-         "compress" : 0,
          "type" : "FeatureTrack",
-         "label" : "blastx_Priapulida"
+         "urlTemplate" : "tracks/blastx_Priapulida/{refseq}/trackData.json"
       },
       {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX",
+         "compress" : 0,
+         "key" : "blastx_Tardigrada",
+         "label" : "blastx_Tardigrada",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Blastx alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "className" : "container-10px",
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "{type}",
             "subfeatureClasses" : {
                "match_part" : "blastx"
-            },
-            "arrowheadClass" : "webapollo-arrowhead"
-         },
-	 "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX",
-	         "metadata" : {
-        "Track legend" : "Results from Blastx alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline.", 
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
-    },
-         "key" : "blastx_Tardigrada",
-
-
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+            }
+         },
          "trackType" : null,
-         "urlTemplate" : "tracks/blastx_Tardigrada/{refseq}/trackData.json",
-         "compress" : 0,
          "type" : "FeatureTrack",
-         "label" : "blastx_Tardigrada"
+         "urlTemplate" : "tracks/blastx_Tardigrada/{refseq}/trackData.json"
       },
       {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX",
+         "compress" : 0,
+         "key" : "blastx_Tunicata",
+         "label" : "blastx_Tunicata",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Blastx alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "className" : "container-10px",
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "{type}",
             "subfeatureClasses" : {
                "match_part" : "blastx"
-            },
-            "arrowheadClass" : "webapollo-arrowhead"
-         },
-	 "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX",
-	         "metadata" : {
-        "Track legend" : "Results from Blastx alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline.", 
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
-    },
-         "key" : "blastx_Tunicata",
-
-
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+            }
+         },
          "trackType" : null,
-         "urlTemplate" : "tracks/blastx_Tunicata/{refseq}/trackData.json",
-         "compress" : 0,
          "type" : "FeatureTrack",
-         "label" : "blastx_Tunicata"
+         "urlTemplate" : "tracks/blastx_Tunicata/{refseq}/trackData.json"
       },
       {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX",
+         "compress" : 0,
+         "key" : "blastx_UNCATEGORISED",
+         "label" : "blastx_UNCATEGORISED",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Blastx alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "className" : "container-10px",
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "{type}",
             "subfeatureClasses" : {
                "match_part" : "blastx"
-            },
-            "arrowheadClass" : "webapollo-arrowhead"
-         },
-	 "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX",
-	         "metadata" : {
-        "Track legend" : "Results from Blastx alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline.", 
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
-    },
-         "key" : "blastx_UNCATEGORISED",
-
-
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+            }
+         },
          "trackType" : null,
-         "urlTemplate" : "tracks/blastx_UNCATEGORISED/{refseq}/trackData.json",
-         "compress" : 0,
          "type" : "FeatureTrack",
-         "label" : "blastx_UNCATEGORISED"
+         "urlTemplate" : "tracks/blastx_UNCATEGORISED/{refseq}/trackData.json"
       },
       {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Other",
+         "compress" : 0,
+         "key" : "cegma",
+         "label" : "cegma",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from CEGMA alignments as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "className" : "container-10px",
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "{type}",
             "subfeatureClasses" : {
                "match_part" : "cegma"
-            },
-            "arrowheadClass" : "webapollo-arrowhead"
-         },
-	 "category" : "BCM_v0.5.3/3. Mapped Proteins/Other",
-	        "metadata" : {
-        "Track legend" : "Results from CEGMA alignments as part of the MAKER automated annotation pipeline.",
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
-},
-         "key" : "cegma",
-
-
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+            }
+         },
          "trackType" : null,
-         "urlTemplate" : "tracks/cegma/{refseq}/trackData.json",
-         "compress" : 0,
          "type" : "FeatureTrack",
-         "label" : "cegma"
+         "urlTemplate" : "tracks/cegma/{refseq}/trackData.json"
       },
       {
+         "category" : "BCM_v0.5.3/4. Transcriptome/Assembly",
+         "compress" : 0,
+         "key" : "est_gff:cufflinks_i5k",
+         "label" : "est_gff:cufflinks_i5k",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from EST alignments resulting from the Cufflinks software as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "className" : "container-10px",
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "{type}",
             "subfeatureClasses" : {
                "match_part" : "est"
-            },
-            "arrowheadClass" : "webapollo-arrowhead"
-         },
-	 "category" : "BCM_v0.5.3/4. Transcriptome/Assembly",
-	        "metadata" : {
-        "Track legend" : "Results from EST alignments resulting from the Cufflinks software as part of the MAKER automated annotation pipeline.",
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
-    },
-         "key" : "est_gff:cufflinks_i5k",
-
-
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+            }
+         },
          "trackType" : null,
-         "urlTemplate" : "tracks/est_gff:cufflinks_i5k/{refseq}/trackData.json",
-         "compress" : 0,
          "type" : "FeatureTrack",
-         "label" : "est_gff:cufflinks_i5k"
+         "urlTemplate" : "tracks/est_gff:cufflinks_i5k/{refseq}/trackData.json"
       },
       {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Annelida",
+         "label" : "protein2genome_Annelida",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Annelida proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "className" : "container-10px",
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "{type}",
             "subfeatureClasses" : {
                "match_part" : "protein2genome"
-            },
-            "arrowheadClass" : "webapollo-arrowhead"
-         },
-	 "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
-	         "metadata" : {
-        "Track legend" : "Results from Protein2genome alignments of a set of Annelida proteins as part of the MAKER automated annotation pipeline.",
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
-    },
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+            }
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-         "compress" : 0,
          "type" : "FeatureTrack",
-         "label" : "protein2genome_Annelida"
+         "urlTemplate" : "tracks/protein2genome_Annelida/{refseq}/trackData.json"
       },
       {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+         "key" : "protein2genome_Arthropoda",
+         "label" : "protein2genome_Arthropoda",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Arthropoda proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "className" : "container-10px",
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                "match_part" : "protein2genome"
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-	 "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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-        "Track legend" : "Results from Protein2genome alignments of a set of Arthropoda proteins as part of the MAKER automated annotation pipeline.",
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
-    },
-         "key" : "protein2genome_Arthropoda",
-
-
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+            }
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          "trackType" : null,
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-         "label" : "protein2genome_Arthropoda"
+         "urlTemplate" : "tracks/protein2genome_Arthropoda/{refseq}/trackData.json"
       },
       {
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+         "key" : "protein2genome_Atelocerata",
+         "label" : "protein2genome_Atelocerata",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Atelocerata proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "className" : "container-10px",
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                "match_part" : "protein2genome"
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-	 "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
-	         "metadata" : {
-        "Track legend" : "Results from Protein2genome alignments of a set of Atelocerata proteins as part of the MAKER automated annotation pipeline.",
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
-    },
-         "key" : "protein2genome_Atelocerata",
-
-
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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       },
       {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+         "key" : "protein2genome_Cephalochordata",
+         "label" : "protein2genome_Cephalochordata",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Cephalochordata proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "className" : "container-10px",
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                "match_part" : "protein2genome"
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-	 "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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-        "Track legend" : "Results from Protein2genome alignments of a set of Cephalochordata proteins as part of the MAKER automated annotation pipeline.",
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
-    },
-         "key" : "protein2genome_Cephalochordata",
-
-
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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          "type" : "FeatureTrack",
-         "label" : "protein2genome_Cephalochordata"
+         "urlTemplate" : "tracks/protein2genome_Cephalochordata/{refseq}/trackData.json"
       },
       {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Chelicerata",
+         "label" : "protein2genome_Chelicerata",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Chelicerata proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "className" : "container-10px",
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                "match_part" : "protein2genome"
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-	 "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
-	         "metadata" : {
-        "Track legend" : "Results from Protein2genome alignments of a set of Chelicerata proteins as part of the MAKER automated annotation pipeline.",
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
-    },
-         "key" : "protein2genome_Chelicerata",
-
-
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+            }
+         },
          "trackType" : null,
-         "urlTemplate" : "tracks/protein2genome_Chelicerata/{refseq}/trackData.json",
-         "compress" : 0,
          "type" : "FeatureTrack",
-         "label" : "protein2genome_Chelicerata"
+         "urlTemplate" : "tracks/protein2genome_Chelicerata/{refseq}/trackData.json"
       },
       {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Cnidaria",
+         "label" : "protein2genome_Cnidaria",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Cnidaria proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "className" : "container-10px",
+            "arrowheadClass" : "webapollo-arrowhead",
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             "subfeatureClasses" : {
                "match_part" : "protein2genome"
-            },
-            "arrowheadClass" : "webapollo-arrowhead"
-         },
-	 "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
-	         "metadata" : {
-        "Track legend" : "Results from Protein2genome alignments of a set of Cnidaria proteins as part of the MAKER automated annotation pipeline.",
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
-    },
-         "key" : "protein2genome_Cnidaria",
-
-
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+            }
+         },
          "trackType" : null,
-         "urlTemplate" : "tracks/protein2genome_Cnidaria/{refseq}/trackData.json",
-         "compress" : 0,
          "type" : "FeatureTrack",
-         "label" : "protein2genome_Cnidaria"
+         "urlTemplate" : "tracks/protein2genome_Cnidaria/{refseq}/trackData.json"
       },
       {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Craniata",
+         "label" : "protein2genome_Craniata",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Craniata proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "className" : "container-10px",
+            "arrowheadClass" : "webapollo-arrowhead",
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             "subfeatureClasses" : {
                "match_part" : "protein2genome"
-            },
-            "arrowheadClass" : "webapollo-arrowhead"
-         },
-	 "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
-	         "metadata" : {
-        "Track legend" : "Results from Protein2genome alignments of a set of Craniata proteins as part of the MAKER automated annotation pipeline.",
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
-    },
-         "key" : "protein2genome_Craniata",
-
-
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+            }
+         },
          "trackType" : null,
-         "urlTemplate" : "tracks/protein2genome_Craniata/{refseq}/trackData.json",
-         "compress" : 0,
          "type" : "FeatureTrack",
-         "label" : "protein2genome_Craniata"
+         "urlTemplate" : "tracks/protein2genome_Craniata/{refseq}/trackData.json"
       },
       {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Crustacea",
+         "label" : "protein2genome_Crustacea",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Crustacea proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "className" : "container-10px",
+            "arrowheadClass" : "webapollo-arrowhead",
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             "subfeatureClasses" : {
                "match_part" : "protein2genome"
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-            "arrowheadClass" : "webapollo-arrowhead"
-         },
-	 "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
-	         "metadata" : {
-        "Track legend" : "Results from Protein2genome alignments of a set of Crustacea proteins as part of the MAKER automated annotation pipeline.",
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
-    },
-         "key" : "protein2genome_Crustacea",
-
-
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+            }
+         },
          "trackType" : null,
-         "urlTemplate" : "tracks/protein2genome_Crustacea/{refseq}/trackData.json",
-         "compress" : 0,
          "type" : "FeatureTrack",
-         "label" : "protein2genome_Crustacea"
+         "urlTemplate" : "tracks/protein2genome_Crustacea/{refseq}/trackData.json"
       },
       {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Echinodermata",
+         "label" : "protein2genome_Echinodermata",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Echinodermata proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "className" : "container-10px",
+            "arrowheadClass" : "webapollo-arrowhead",
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             "subfeatureClasses" : {
                "match_part" : "protein2genome"
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-            "arrowheadClass" : "webapollo-arrowhead"
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-	 "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
-	         "metadata" : {
-        "Track legend" : "Results from Protein2genome alignments of a set of Echinodermata proteins as part of the MAKER automated annotation pipeline.",
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
-    },
-         "key" : "protein2genome_Echinodermata",
-
-
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+            }
+         },
          "trackType" : null,
-         "urlTemplate" : "tracks/protein2genome_Echinodermata/{refseq}/trackData.json",
-         "compress" : 0,
          "type" : "FeatureTrack",
-         "label" : "protein2genome_Echinodermata"
+         "urlTemplate" : "tracks/protein2genome_Echinodermata/{refseq}/trackData.json"
       },
       {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Mollusca",
+         "label" : "protein2genome_Mollusca",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Mollusca proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "className" : "container-10px",
+            "arrowheadClass" : "webapollo-arrowhead",
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             "subfeatureClasses" : {
                "match_part" : "protein2genome"
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-            "arrowheadClass" : "webapollo-arrowhead"
-         },
-	 "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
-	         "metadata" : {
-        "Track legend" : "Results from Protein2genome alignments of a set of Mollusca proteins as part of the MAKER automated annotation pipeline.",
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
-    },
-         "key" : "protein2genome_Mollusca",
-
-
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+            }
+         },
          "trackType" : null,
-         "urlTemplate" : "tracks/protein2genome_Mollusca/{refseq}/trackData.json",
-         "compress" : 0,
          "type" : "FeatureTrack",
-         "label" : "protein2genome_Mollusca"
+         "urlTemplate" : "tracks/protein2genome_Mollusca/{refseq}/trackData.json"
       },
       {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Nemata",
+         "label" : "protein2genome_Nemata",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "className" : "container-10px",
+            "arrowheadClass" : "webapollo-arrowhead",
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             "subfeatureClasses" : {
                "match_part" : "protein2genome"
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-            "arrowheadClass" : "webapollo-arrowhead"
-         },
-	 "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
-	         "metadata" : {
-        "Track legend" : "Results from Protein2genome alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline.",
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
-    },
-         "key" : "protein2genome_Nemata",
-
-
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+            }
+         },
          "trackType" : null,
-         "urlTemplate" : "tracks/protein2genome_Nemata/{refseq}/trackData.json",
-         "compress" : 0,
          "type" : "FeatureTrack",
-         "label" : "protein2genome_Nemata"
+         "urlTemplate" : "tracks/protein2genome_Nemata/{refseq}/trackData.json"
       },
       {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Nematomorpha",
+         "label" : "protein2genome_Nematomorpha",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Nematomorpha proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "className" : "container-10px",
+            "arrowheadClass" : "webapollo-arrowhead",
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             "subfeatureClasses" : {
                "match_part" : "protein2genome"
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-            "arrowheadClass" : "webapollo-arrowhead"
-         },
-	 "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
-	         "metadata" : {
-        "Track legend" : "Results from Protein2genome alignments of a set of Nematomorpha proteins as part of the MAKER automated annotation pipeline.",
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
-    },
-         "key" : "protein2genome_Nematomorpha",
-
-
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+            }
+         },
          "trackType" : null,
-         "urlTemplate" : "tracks/protein2genome_Nematomorpha/{refseq}/trackData.json",
-         "compress" : 0,
          "type" : "FeatureTrack",
-         "label" : "protein2genome_Nematomorpha"
+         "urlTemplate" : "tracks/protein2genome_Nematomorpha/{refseq}/trackData.json"
       },
       {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Onychophora",
+         "label" : "protein2genome_Onychophora",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Onychophora proteins as part of the MAKER automated annotation pipeline."
+         },
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          "style" : {
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-        "Track legend" : "Results from Protein2genome alignments of a set of Onychophora proteins as part of the MAKER automated annotation pipeline.",
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
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          "type" : "FeatureTrack",
-         "label" : "protein2genome_Onychophora"
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       },
       {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+         "key" : "protein2genome_Parazoa",
+         "label" : "protein2genome_Parazoa",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline."
+         },
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          "style" : {
-            "className" : "container-10px",
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-	 "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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-        "Track legend" : "Results from Protein2genome alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline.",
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
-    },
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-
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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          "type" : "FeatureTrack",
-         "label" : "protein2genome_Parazoa"
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       },
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+         "label" : "protein2genome_Placozoa",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "className" : "container-10px",
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-        "Track legend" : "Results from Protein2genome alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline.",
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
-    },
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-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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       },
       {
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+         "label" : "protein2genome_Platyhelminthes",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline."
+         },
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          "style" : {
-            "className" : "container-10px",
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-        "Track legend" : "Results from Protein2genome alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline.",
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
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-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
-    },
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-
-
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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          "type" : "FeatureTrack",
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+         "urlTemplate" : "tracks/protein2genome_Platyhelminthes/{refseq}/trackData.json"
       },
       {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+         "key" : "protein2genome_Priapulida",
+         "label" : "protein2genome_Priapulida",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "className" : "container-10px",
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                "match_part" : "protein2genome"
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-	         "metadata" : {
-        "Track legend" : "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline.",
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
-    },
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-
-
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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-         "compress" : 0,
          "type" : "FeatureTrack",
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+         "urlTemplate" : "tracks/protein2genome_Priapulida/{refseq}/trackData.json"
       },
       {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Tardigrada",
+         "label" : "protein2genome_Tardigrada",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "className" : "container-10px",
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-	 "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
-	         "metadata" : {
-        "Track legend" : "Results from Protein2genome alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline.",
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
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-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
-    },
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-
-
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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-         "compress" : 0,
          "type" : "FeatureTrack",
-         "label" : "protein2genome_Tardigrada"
+         "urlTemplate" : "tracks/protein2genome_Tardigrada/{refseq}/trackData.json"
       },
       {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+         "key" : "protein2genome_Tunicata",
+         "label" : "protein2genome_Tunicata",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "className" : "container-10px",
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-        "Track legend" : "Results from Protein2genome alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline.",
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-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
-    },
-         "key" : "protein2genome_Tunicata",
-
-
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+            }
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          "type" : "FeatureTrack",
-         "label" : "protein2genome_Tunicata"
+         "urlTemplate" : "tracks/protein2genome_Tunicata/{refseq}/trackData.json"
       },
       {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
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+         "label" : "protein2genome_UNCATEGORISED",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "className" : "container-10px",
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                "match_part" : "protein2genome"
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-	 "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
-	         "metadata" : {
-        "Track legend" : "Results from Protein2genome alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline.",
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
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-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
-    },
-         "key" : "protein2genome_UNCATEGORISED",
-
-
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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-         "compress" : 0,
          "type" : "FeatureTrack",
-         "label" : "protein2genome_UNCATEGORISED"
+         "urlTemplate" : "tracks/protein2genome_UNCATEGORISED/{refseq}/trackData.json"
       },
       {
+         "category" : "BCM_v0.5.3/2. Evidence/Repeats",
+         "compress" : 0,
+         "key" : "repeatmasker",
+         "label" : "repeatmasker",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from RepeatMasker as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "className" : "container-10px",
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-        "Track legend" : "Results from RepeatMasker as part of the MAKER automated annotation pipeline.",
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
-    },
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-
-
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+            }
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          "trackType" : null,
-         "urlTemplate" : "tracks/repeatmasker/{refseq}/trackData.json",
-         "compress" : 0,
          "type" : "FeatureTrack",
-         "label" : "repeatmasker"
+         "urlTemplate" : "tracks/repeatmasker/{refseq}/trackData.json"
       },
       {
+         "category" : "BCM_v0.5.3/2. Evidence/Repeats",
+         "compress" : 0,
+         "key" : "repeatrunner",
+         "label" : "repeatrunner",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Repeatrunner as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "className" : "container-10px",
+            "arrowheadClass" : "webapollo-arrowhead",
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             "subfeatureClasses" : {
                "match_part" : "repeat"
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-            "arrowheadClass" : "webapollo-arrowhead"
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-	 "category" : "BCM_v0.5.3/2. Evidence/Repeats",
-	        "metadata" : {
-        "Track legend" : "Results from Repeatrunner as part of the MAKER automated annotation pipeline.",
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
-    },
-         "key" : "repeatrunner",
-
-
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+            }
+         },
          "trackType" : null,
-         "urlTemplate" : "tracks/repeatrunner/{refseq}/trackData.json",
-         "compress" : 0,
          "type" : "FeatureTrack",
-         "label" : "repeatrunner"
+         "urlTemplate" : "tracks/repeatrunner/{refseq}/trackData.json"
       },
       {
+         "category" : "BCM_v0.5.3/1. Gene Sets/Supplementary Gene Predictions",
+         "compress" : 0,
+         "key" : "snap_masked",
+         "label" : "snap_masked",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "className" : "container-10px",
+            "arrowheadClass" : "webapollo-arrowhead",
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             "subfeatureClasses" : {
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-	 "category" : "BCM_v0.5.3/1. Gene Sets/Supplementary Gene Predictions",
-	        "metadata" : {
-        "Track legend" : "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline.",
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
-    },
-         "key" : "snap_masked",
-
-
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+            }
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          "trackType" : null,
-         "urlTemplate" : "tracks/snap_masked/{refseq}/trackData.json",
-         "compress" : 0,
          "type" : "FeatureTrack",
-         "label" : "snap_masked"
+         "urlTemplate" : "tracks/snap_masked/{refseq}/trackData.json"
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       {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Reference Assembly",
+         "key" : "Gaps in assembly",
+         "label" : "Gaps in assembly",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
          "style" : {
             "neg_color" : "white",
             "pos_color" : "black"
          },
-         "bicolor_pivot" : "zero",
-	 "category" : "Reference Assembly",
-	        "metadata" : {
-        "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank",
-        "Track contact" : "The i5k workspace@NAL",
-        "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
-},
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-         "autoscale" : "local",
-         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
-         "urlTemplate" : "bigwig/Cflo.scaffolds.fa.gaps.bigwig",
-         "label" : "Gaps in assembly",
-         "type" : "JBrowse/View/Track/Wiggle/Density"
+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/Cflo.scaffolds.fa.gaps.bigwig"
       },
       {
+         "autoscale" : "local",
+         "bicolor_pivot" : "0.5",
+         "category" : "Reference Assembly",
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diff --git a/organisms/stage/Culex_quinquefasciatus/trackList.json b/organisms/stage/Culex_quinquefasciatus/trackList.json
new file mode 100644
index 0000000..b9308b5
--- /dev/null
+++ b/organisms/stage/Culex_quinquefasciatus/trackList.json
@@ -0,0 +1,149 @@
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index a9be2aa..16e4899 100644
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+      "label": "Diavir_Dvir_v2.0_RNA-Seq-alignments_2021-06-11_coverage",
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+        "Analysis method": "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
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+        "Track legend": "This track represents an X-Y plot of RNA-Seq coverage."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
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+      "metadata": {
+        "Analysis method": "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+        "Analysis provider": "i5k Workspace@NAL",
+        "Data source": "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR7818014'>SRR7818014</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR7818015'>SRR7818015</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR7818012'>SRR7818012</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR6506228'>SRR6506228</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR6506226'>SRR6506226</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR6506229'>SRR6506229</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR6506227'>SRR6506227</a>",
+        "Publication status": "Analysis: NA; Source data: see individual SRA accessions",
+        "Track legend": "Junction reads generated by Hisat2 aligner and regtools. The number of alignments supporting the junction read is listed in blue."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "className": "feature",
+        "description": "score"
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/Diavir_Dvir_v2.0_RNA-Seq-alignments_2021-06-11_junctions/{refseq}/trackData.json"
+    }
+  ]
 }
diff --git a/organisms/stage/Diachasma_alloeum/trackList.json b/organisms/stage/Diachasma_alloeum/trackList.json
index 88202e2..9334d5d 100644
--- a/organisms/stage/Diachasma_alloeum/trackList.json
+++ b/organisms/stage/Diachasma_alloeum/trackList.json
@@ -1,123 +1,124 @@
 {
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-         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-"
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       },
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-        "url" : "function(track,feature){ return 'https://i5k.nal.usda.gov/search/site/'+feature.get('id')}"
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+              "label": "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
+              "title": "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
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+              "url" : "function(track,feature){ return 'https://www.ncbi.nlm.nih.gov/nuccore/'+feature.get('name')}"
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-         "type" : "HTMLFeatures",
-         "urlTemplate" : "tracks/NCBI_Annotation_Release_101_Pseudogene/{refseq}/trackData.json"
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+      "trackType": "HTMLFeatures",
+      "type": "HTMLFeatures",
+      "urlTemplate": "tracks/NCBI_Annotation_Release_101_Pseudogene/{refseq}/trackData.json"
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 }
diff --git a/organisms/stage/Diaphorina_citri/trackList.json b/organisms/stage/Diaphorina_citri/trackList.json
index c9115fc..ae490ea 100644
--- a/organisms/stage/Diaphorina_citri/trackList.json
+++ b/organisms/stage/Diaphorina_citri/trackList.json
@@ -1,957 +1,1015 @@
 {
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+   "names" : {
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          "metadata" : {
             "Analysis method" : "Mascot, Scaffold, Proteogenomic Mapping Tool",
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             "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
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-            "Data Provider" : "John Ramsey, Surya Saha and Michelle Cilia, Boyce Thompson Institute"
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                "CDS" : "ogs-cds",
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-            },
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-         "key" : "OGSv1.0 ncRNA",
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "trackType" : null,
-         "urlTemplate" : "tracks/OGSv1.0_ncRNA/{refseq}/trackData.json",
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/OGSv1.0_pseudogenes/{refseq}/trackData.json"
+      },
+      {
+         "category" : "Official Gene Set v1.0//1. Gene Sets/Noncoding",
          "compress" : 0,
+         "key" : "OGSv1.0 ncRNA",
          "label" : "OGSv1.0_ncRNA",
          "metadata" : {
+            "Data description" : "Official Gene Set v1.0 of Diaphorina citri",
+            "Data provider" : "Surya Saha, Cornell University",
             "Data source" : "https://i5k.nal.usda.gov/data/Arthropoda/diacit-(Diaphorina_citri)/Current%20Genome%20Assembly/2.Official%20or%20Primary%20Gene%20Set/OGSv1.0/",
             "Method" : "https://i5k.nal.usda.gov/data/Arthropoda/diacit-(Diaphorina_citri)/Current%20Genome%20Assembly/2.Official%20or%20Primary%20Gene%20Set/OGSv1.0/Dcitr_OGSv1.0_readme",
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-            "Data provider" : "Surya Saha, Cornell University",
-            "Data description" : "Official Gene Set v1.0 of Diaphorina citri"
+            "Track Legend" : "Official Gene Set OGS_v1.2"
          },
-         "category" : "Official Gene Set v1.0//1. Gene Sets/Noncoding",
-         "type" : "FeatureTrack"
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+            "arrowheadClass" : "trellis-arrowhead",
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+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/OGSv1.0_ncRNA/{refseq}/trackData.json"
       },
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-         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
-         "urlTemplate" : "user_contributed_data/ssaha/12-15-2015/rnaseq_nymph.bam",
          "category" : "Transcriptome/Mapped Reads",
+         "key" : "RNAseq reads from nymph tissue",
+         "label" : "RNAseq reads from nymph tissue",
          "metadata" : {
-            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
             "Analysis method (program and version)" : "Tophat2 v2.1.0",
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-            "Sequencing platform and version (Illumina Hi-Seq 200 bp)" : "Illumina Hiseq paired end",
-            "Other notes" : "Parameters used for alignment: –min-intron-length 4 --max-intron-length 136000",
-            "NCBI SRA accession #" : "SRX199348",
+            "Data source URL" : "http://www.ncbi.nlm.nih.gov/sra/SRX199348[accn]",
+            "Date completed" : "12/16/15",
+            "Description" : "RNAseq from nymph tissue reads were mapped to maker predicted genes on NCBI-diaci1.1",
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-            "Description" : "RNAseq from nymph tissue reads were mapped to maker predicted genes on NCBI-diaci1.1"
+            "Legend" : "Mapped reads are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)",
+            "NCBI SRA accession #" : "SRX199348",
+            "Other notes" : "Parameters used for alignment: –min-intron-length 4 --max-intron-length 136000",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version (Illumina Hi-Seq 200 bp)" : "Illumina Hiseq paired end",
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          },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
          "type" : "WebApollo/View/Track/DraggableAlignments",
-         "label" : "RNAseq reads from nymph tissue",
-         "key" : "RNAseq reads from nymph tissue"
+         "urlTemplate" : "user_contributed_data/ssaha/12-15-2015/rnaseq_nymph.bam"
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-         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
-         "urlTemplate" : "user_contributed_data/ssaha/12-15-2015/AdultNymph_Clas_infected.bam",
          "category" : "Transcriptome/Mapped Reads",
+         "key" : "Infected adult and nymph psyllids (Vyas 2015)",
+         "label" : "Infected adult and nymph psyllids (Vyas 2015)",
          "metadata" : {
-            "Publication status" : "Published: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0130328",
             "Analysis method (program and version)" : "Tophat2 v2.1.0",
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-            "Sequencing platform and version (Illumina Hi-Seq 200 bp)" : "Illumina GA II paired end",
-            "Other notes" : "Parameters used for alignment: –min-intron-length 4 --max-intron-length 136000",
-            "NCBI SRA accession #" : "SRR1259432, SRR1259434",
+            "Data source URL" : "http://www.ncbi.nlm.nih.gov/sra/SRR1259432",
+            "Date completed" : "12/08/15",
+            "Description" : "2x54bp paired-end RNAseq reads were mapped to NCBI-diaci1.1 genome from the Clas positive adult and nymph psyllids. See Vyas 2015",
             "File provider (name and affiliation)" : "Prashant Hosmani and Surya Saha, Boyce Thompson Institute",
             "Geographical location of specimen collection (Country, Site, Latitude, Longitude)" : "US, Florida",
-            "TaxID" : "121845",
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-            "Data source URL" : "http://www.ncbi.nlm.nih.gov/sra/SRR1259432",
-            "Description" : "2x54bp paired-end RNAseq reads were mapped to NCBI-diaci1.1 genome from the Clas positive adult and nymph psyllids. See Vyas 2015"
+            "Legend" : "Mapped reads are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)",
+            "NCBI SRA accession #" : "SRR1259432, SRR1259434",
+            "Other notes" : "Parameters used for alignment: –min-intron-length 4 --max-intron-length 136000",
+            "Publication status" : "Published: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0130328",
+            "Sequencing platform and version (Illumina Hi-Seq 200 bp)" : "Illumina GA II paired end",
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          },
-         "label" : "Infected adult and nymph psyllids (Vyas 2015)",
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
          "type" : "WebApollo/View/Track/DraggableAlignments",
-         "key" : "Infected adult and nymph psyllids (Vyas 2015)"
+         "urlTemplate" : "user_contributed_data/ssaha/12-15-2015/AdultNymph_Clas_infected.bam"
       },
       {
-         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
-         "urlTemplate" : "user_contributed_data/ssaha/12-15-2015/rnaseq_adult.bam",
          "category" : "Transcriptome/Mapped Reads",
+         "key" : "RNAseq reads from adult tissue",
+         "label" : "RNAseq reads from adult tissue",
          "metadata" : {
-            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
             "Analysis method (program and version)" : "Tophat2 v2.1.0",
-            "Legend" : "Mapped reads are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)",
-            "Sequencing platform and version (Illumina Hi-Seq 200 bp)" : "Illumina Hiseq paired end",
-            "Other notes" : "Parameters used for alignment: –min-intron-length 4 --max-intron-length 136000",
-            "NCBI SRA accession #" : "SRX199348",
+            "Data source URL" : "http://www.ncbi.nlm.nih.gov/sra/SRX199348[accn]",
+            "Date completed" : "12/16/15",
+            "Description" : "RNAseq reads from adult tissue were mapped to maker predicted genes on NCBI-diaci1.1",
             "File provider (name and affiliation)" : "Surya Saha, Boyce Thompson Institute",
             "Geographical location of specimen collection (Country, Site, Latitude, Longitude)" : "US, Florida",
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-            "Date completed" : "12/16/15",
-            "Data source URL" : "http://www.ncbi.nlm.nih.gov/sra/SRX199348[accn]",
-            "Description" : "RNAseq reads from adult tissue were mapped to maker predicted genes on NCBI-diaci1.1"
+            "Legend" : "Mapped reads are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)",
+            "NCBI SRA accession #" : "SRX199348",
+            "Other notes" : "Parameters used for alignment: –min-intron-length 4 --max-intron-length 136000",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version (Illumina Hi-Seq 200 bp)" : "Illumina Hiseq paired end",
+            "TaxID" : "121845"
          },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
          "type" : "WebApollo/View/Track/DraggableAlignments",
-         "label" : "RNAseq reads from adult tissue",
-         "key" : "RNAseq reads from adult tissue"
+         "urlTemplate" : "user_contributed_data/ssaha/12-15-2015/rnaseq_adult.bam"
       },
       {
-         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
-         "urlTemplate" : "user_contributed_data/ssaha/12-15-2015/AdultNymph_uninfected.bam",
          "category" : "Transcriptome/Mapped Reads",
+         "key" : "Control adult and nymph psyllids (Vyas 2015)",
+         "label" : "Control adult and nymph psyllids (Vyas 2015)",
          "metadata" : {
-            "Publication status" : "Published: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0130328",
             "Analysis method (program and version)" : "Tophat2 v2.1.0",
-            "Legend" : "Mapped reads are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)",
-            "Sequencing platform and version (Illumina Hi-Seq 200 bp)" : "Illumina GA II paired end",
-            "Other notes" : "Parameters used for alignment: –min-intron-length 4 --max-intron-length 136000",
-            "NCBI SRA accession #" : "SRR1259429, SRR1259461",
+            "Data source URL" : "http://www.ncbi.nlm.nih.gov/sra/SRR1259429",
+            "Date completed" : "12/08/15",
+            "Description" : "2x54bp paired-end RNAseq reads were mapped to NCBI-diaci1.1 genome from the control adult and nymph psyllids. See Vyas 2015",
             "File provider (name and affiliation)" : "Prashant Hosmani and Surya Saha, Boyce Thompson Institute",
             "Geographical location of specimen collection (Country, Site, Latitude, Longitude)" : "US, Florida",
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-            "Description" : "2x54bp paired-end RNAseq reads were mapped to NCBI-diaci1.1 genome from the control adult and nymph psyllids. See Vyas 2015"
+            "Legend" : "Mapped reads are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)",
+            "NCBI SRA accession #" : "SRR1259429, SRR1259461",
+            "Other notes" : "Parameters used for alignment: –min-intron-length 4 --max-intron-length 136000",
+            "Publication status" : "Published: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0130328",
+            "Sequencing platform and version (Illumina Hi-Seq 200 bp)" : "Illumina GA II paired end",
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-         "label" : "Control adult and nymph psyllids (Vyas 2015)",
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
          "type" : "WebApollo/View/Track/DraggableAlignments",
-         "key" : "Control adult and nymph psyllids (Vyas 2015)"
+         "urlTemplate" : "user_contributed_data/ssaha/12-15-2015/AdultNymph_uninfected.bam"
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       {
-         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
-         "urlTemplate" : "user_contributed_data/ssaha/12-15-2015/rnaseq_egg.bam",
          "category" : "Transcriptome/Mapped Reads",
+         "key" : "RNAseq reads from egg tissue",
+         "label" : "RNAseq reads from egg tissue",
          "metadata" : {
-            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
             "Analysis method (program and version)" : "Tophat2 v2.1.0",
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-            "Sequencing platform and version (Illumina Hi-Seq 200 bp)" : "Illumina Hiseq paired end",
-            "Other notes" : "Parameters used for alignment: –min-intron-length 4 --max-intron-length 136000",
-            "NCBI SRA accession #" : "SRX199348",
+            "Data source URL" : "http://www.ncbi.nlm.nih.gov/sra/SRX199348[accn]",
+            "Date completed" : "12/16/15",
+            "Description" : "RNAseq reads from egg tissue were mapped to maker predicted genes on NCBI-diaci1.1",
             "File provider (name and affiliation)" : "Surya Saha, Boyce Thompson Institute",
             "Geographical location of specimen collection (Country, Site, Latitude, Longitude)" : "US, Florida",
-            "TaxID" : "121845",
-            "Date completed" : "12/16/15",
-            "Data source URL" : "http://www.ncbi.nlm.nih.gov/sra/SRX199348[accn]",
-            "Description" : "RNAseq reads from egg tissue were mapped to maker predicted genes on NCBI-diaci1.1"
+            "Legend" : "Mapped reads are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)",
+            "NCBI SRA accession #" : "SRX199348",
+            "Other notes" : "Parameters used for alignment: –min-intron-length 4 --max-intron-length 136000",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version (Illumina Hi-Seq 200 bp)" : "Illumina Hiseq paired end",
+            "TaxID" : "121845"
          },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
          "type" : "WebApollo/View/Track/DraggableAlignments",
-         "label" : "RNAseq reads from egg tissue",
-         "key" : "RNAseq reads from egg tissue"
+         "urlTemplate" : "user_contributed_data/ssaha/12-15-2015/rnaseq_egg.bam"
       },
       {
-         "style" : {
-            "pos_color" : "#00BFFF"
-         },
+         "autoscale" : "local",
          "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
          "key" : "RNAseq reads from nymph tissue (Coverage Plot)",
-         "autoscale" : "local",
-         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
-         "urlTemplate" : "user_contributed_data/ssaha/12-15-2015/rnaseq_nymph.bw",
+         "label" : "RNAseq reads from nymph tissue (Coverage Plot)",
          "metadata" : {
-            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
             "Analysis method (program and version)" : "Tophat2 v2.1.0 and bedtools v2.16.1",
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-            "NCBI SRA accession #" : "SRX199348",
+            "Data source URL" : "http://www.ncbi.nlm.nih.gov/sra/SRX199348[accn]",
+            "Date completed" : "12/17/15",
+            "Description" : "Summary plot for RNAseq reads from nymph tissue mapped to NCBI-diaci1.1",
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-            "Data source URL" : "http://www.ncbi.nlm.nih.gov/sra/SRX199348[accn]",
-            "Description" : "Summary plot for RNAseq reads from nymph tissue mapped to NCBI-diaci1.1"
+            "Legend" : "This track represents an X-Y plot of RNA-Seq coverage.",
+            "NCBI SRA accession #" : "SRX199348",
+            "Other notes" : "Parameters used for tophat alignment: –min-intron-length 4 --max-intron-length 136000. bedtools used to create bigwig file from tophat BAM file. bedtools genomecov -split -ibam accepted_hits.bam -bga > accepted_hits.coverage.bedgraph. bedGraphToBigWig accepted_hits.sorted.coverage.bedgraph diaci1.chrom.sizes accepted_hits.bw",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version (Illumina Hi-Seq 200 bp)" : "Illumina Hiseq paired end",
+            "TaxID" : "121845"
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-         "category" : "Transcriptome/Coverage Plots (BigWig)",
-         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
-         "label" : "RNAseq reads from nymph tissue (Coverage Plot)"
-      },
-      {
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
          "style" : {
             "pos_color" : "#00BFFF"
          },
-         "bicolor_pivot" : "zero",
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ssaha/12-15-2015/rnaseq_nymph.bw"
+      },
+      {
          "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
          "key" : "RNAseq reads from egg tissue (Coverage Plot)",
-         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
-         "urlTemplate" : "user_contributed_data/ssaha/12-15-2015/rnaseq_egg.bw",
+         "label" : "RNAseq reads from egg tissue (Coverage Plot)",
          "metadata" : {
-            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
             "Analysis method (program and version)" : "Tophat2 v2.1.0 and bedtools v2.16.1",
-            "Legend" : "This track represents an X-Y plot of RNA-Seq coverage.",
-            "Sequencing platform and version (Illumina Hi-Seq 200 bp)" : "Illumina Hiseq paired end",
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-            "NCBI SRA accession #" : "SRX199348",
+            "Data source URL" : "http://www.ncbi.nlm.nih.gov/sra/SRX199348[accn]",
+            "Date completed" : "12/17/15",
+            "Description" : "Summary plot for RNAseq reads from egg tissue mapped to NCBI-diaci1.1",
             "File provider (name and affiliation)" : "Prashant Hosmani and Surya Saha, Boyce Thompson Institute",
             "Geographical location of specimen collection (Country, Site, Latitude, Longitude)" : "US, Florida",
-            "TaxID" : "121845",
-            "Date completed" : "12/17/15",
-            "Data source URL" : "http://www.ncbi.nlm.nih.gov/sra/SRX199348[accn]",
-            "Description" : "Summary plot for RNAseq reads from egg tissue mapped to NCBI-diaci1.1"
+            "Legend" : "This track represents an X-Y plot of RNA-Seq coverage.",
+            "NCBI SRA accession #" : "SRX199348",
+            "Other notes" : "Parameters used for tophat alignment: –min-intron-length 4 --max-intron-length 136000. bedtools used to create bigwig file from tophat BAM file. bedtools genomecov -split -ibam accepted_hits.bam -bga > accepted_hits.coverage.bedgraph. bedGraphToBigWig accepted_hits.sorted.coverage.bedgraph diaci1.chrom.sizes accepted_hits.bw",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version (Illumina Hi-Seq 200 bp)" : "Illumina Hiseq paired end",
+            "TaxID" : "121845"
          },
-         "category" : "Transcriptome/Coverage Plots (BigWig)",
-         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
-         "label" : "RNAseq reads from egg tissue (Coverage Plot)"
-      },
-      {
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
          "style" : {
             "pos_color" : "#00BFFF"
          },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ssaha/12-15-2015/rnaseq_egg.bw"
+      },
+      {
+         "autoscale" : "local",
          "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
          "key" : "Control adult and nymph psyllids (Vyas 2015; Coverage Plot)",
-         "autoscale" : "local",
-         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
-         "urlTemplate" : "user_contributed_data/ssaha/12-15-2015/AdultNymph_uninfected.bw",
+         "label" : "Control adult and nymph psyllids (Vyas 2015; Coverage Plot)",
          "metadata" : {
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             "Analysis method (program and version)" : "Tophat2 v2.1.0 and bedtools v2.16.1",
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-            "NCBI SRA accession #" : "SRR1259429, SRR1259461",
+            "Data source URL" : "http://www.ncbi.nlm.nih.gov/sra/SRR1259429",
+            "Date completed" : "12/17/15",
+            "Description" : "Summary plot for 2x54bp paired-end RNAseq reads mapped to NCBI-diaci1.1 genome from the control adult and nymph psyllid samples. See Vyas 2015 for more details.",
             "File provider (name and affiliation)" : "Prashant Hosmani and Surya Saha, Boyce Thompson Institute",
             "Geographical location of specimen collection (Country, Site, Latitude, Longitude)" : "US, Florida",
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-            "Data source URL" : "http://www.ncbi.nlm.nih.gov/sra/SRR1259429",
-            "Description" : "Summary plot for 2x54bp paired-end RNAseq reads mapped to NCBI-diaci1.1 genome from the control adult and nymph psyllid samples. See Vyas 2015 for more details."
+            "Legend" : "This track represents an X-Y plot of RNA-Seq coverage.",
+            "NCBI SRA accession #" : "SRR1259429, SRR1259461",
+            "Other notes" : "Parameters used for tophat alignment: –min-intron-length 4 --max-intron-length 136000. bedtools used to create bigwig file from tophat BAM file. bedtools genomecov -split -ibam accepted_hits.bam -bga > accepted_hits.coverage.bedgraph. bedGraphToBigWig accepted_hits.sorted.coverage.bedgraph diaci1.chrom.sizes accepted_hits.bw",
+            "Publication status" : "Published: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0130328",
+            "Sequencing platform and version (Illumina Hi-Seq 200 bp)" : "Illumina GA II paired end",
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-         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
-         "label" : "Control adult and nymph psyllids (Vyas 2015; Coverage Plot)"
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          "style" : {
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+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ssaha/12-15-2015/AdultNymph_uninfected.bw"
+      },
+      {
          "autoscale" : "local",
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+         "category" : "Transcriptome/Coverage Plots (BigWig)",
          "key" : "RNAseq reads from adult tissue (Coverage Plot)",
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-         "urlTemplate" : "user_contributed_data/ssaha/12-15-2015/rnaseq_adult.bw",
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          "metadata" : {
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             "Analysis method (program and version)" : "Tophat2 v2.1.0 and bedtools v2.16.1",
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-            "NCBI SRA accession #" : "SRX199348",
+            "Data source URL" : "http://www.ncbi.nlm.nih.gov/sra/SRX199348[accn]",
+            "Date completed" : "12/17/15",
+            "Description" : "Summary plot for RNAseq reads from adult tissue mapped to NCBI-diaci1.1",
             "File provider (name and affiliation)" : "Prashant Hosmani and Surya Saha, Boyce Thompson Institute",
             "Geographical location of specimen collection (Country, Site, Latitude, Longitude)" : "US, Florida",
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-            "Data source URL" : "http://www.ncbi.nlm.nih.gov/sra/SRX199348[accn]",
-            "Description" : "Summary plot for RNAseq reads from adult tissue mapped to NCBI-diaci1.1"
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+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
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-         "label" : "RNAseq reads from adult tissue (Coverage Plot)"
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          "key" : "Infected adult and nymph psyllids (Vyas 2015; Coverage Plot)",
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          "metadata" : {
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-            "NCBI SRA accession #" : "SRR1259432, SRR1259434",
+            "Data source URL" : "http://www.ncbi.nlm.nih.gov/sra/SRR1259432",
+            "Date completed" : "12/17/15",
+            "Description" : "Summary plot for 2x54bp paired-end RNAseq reads mapped to NCBI-diaci1.1 genome from the experimental adult and nymph psyllid samples. See Vyas 2015 for more details.",
             "File provider (name and affiliation)" : "Prashant Hosmani and Surya Saha, Boyce Thompson Institute",
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-            "Description" : "Summary plot for 2x54bp paired-end RNAseq reads mapped to NCBI-diaci1.1 genome from the experimental adult and nymph psyllid samples. See Vyas 2015 for more details."
-         }
+            "Legend" : "This track represents an X-Y plot of RNA-Seq coverage.",
+            "NCBI SRA accession #" : "SRR1259432, SRR1259434",
+            "Other notes" : "Parameters used for tophat alignment: –min-intron-length 4 --max-intron-length 136000. bedtools used to create bigwig file from tophat BAM file. bedtools genomecov -split -ibam accepted_hits.bam -bga > accepted_hits.coverage.bedgraph. bedGraphToBigWig accepted_hits.sorted.coverage.bedgraph diaci1.chrom.sizes accepted_hits.bw",
+            "Publication status" : "Published: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0130328",
+            "Sequencing platform and version (Illumina Hi-Seq 200 bp)" : "Illumina GA II paired end",
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+         "category" : "DNAseq/Mapped Reads",
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+         "label" : "Alignment plot for DNAseq paired-end reads",
+         "metadata" : {
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-            "File type (e.g. bam, bigwig, gff3)" : "BAM",
-            "NCBI SRA accession #" : "SRX057205",
-            "Date completed" : "03/30/16",
             "Assembly name" : "NCBI-diaci",
+            "Assembly version" : "1.1",
             "Data source URL" : "http://www.ncbi.nlm.nih.gov/sra/SRX057205[accn]",
-            "Organism common name" : "Asian citrus psyllid",
-            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Date completed" : "03/30/16",
+            "Descriptive track name" : "Alignment plot for DNAseq paired-end reads mapped to NCBI-diaci1.1",
+            "File provider (name and affiliation)" : "Surya Saha, Boyce Thompson Institute",
+            "File type (e.g. bam, bigwig, gff3)" : "BAM",
+            "Geographical location of specimen collection" : "US, Florida",
             "Legend" : "Mapped reads are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)",
+            "NCBI SRA accession #" : "SRX057205",
+            "Organism common name" : "Asian citrus psyllid",
             "Organism scientific name" : "Diaphorina citri",
-            "File provider (name and affiliation)" : "Surya Saha, Boyce Thompson Institute",
             "Other notes" : "Parameters used for bowtie alignment: --very-fast-local --threads 30 --mm -x ncbi-diaci1.1 --rf --maxins 11000",
-            "Geographical location of specimen collection" : "US, Florida",
-            "TaxID" : "121845",
-            "Assembly version" : "1.1",
-            "Sequencing platform and version" : "Illumina Hiseq paired end"
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version" : "Illumina Hiseq paired end",
+            "TaxID" : "121845"
          },
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+         "autoscale" : "local",
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+         "key" : "Summary plot for DNAseq paired-end reads",
+         "label" : "Summary plot for DNAseq paired-end reads",
+         "metadata" : {
             "Analysis method (program and version)" : "Bowtie v2-2.2.6 and bedtools v2.16.1",
-            "Legend" : "This track represents an X-Y plot of RNA-Seq coverage.",
-            "Sequencing platform and version (Illumina Hi-Seq 200 bp)" : "Illumina Hiseq paired end",
-            "Organism scientific name" : "Diaphorina citri",
+            "Assembly name" : "NCBI-diacil",
+            "Assembly version" : "1.1",
+            "Data source URL" : "http://www.ncbi.nlm.nih.gov/sra/SRX057205[accn]",
+            "Date completed" : "03/30/16",
+            "Descriptive track name" : "Summary plot for DNAseq paired-end reads mapped to NCBI-diaci1.1",
             "File provider (name and affiliation)" : "Prashant Hosmani and Surya Saha, Boyce Thompson Institute",
+            "Geographical location of specimen collection (Country, Site, Latitude, Longitude)" : "US, Florida",
+            "Legend" : "This track represents an X-Y plot of RNA-Seq coverage.",
             "NCBI SRA accession #" : "SRX057205",
+            "Organism common name" : "Asian citrus psyllid",
+            "Organism scientific name" : "Diaphorina citri",
             "Other notes" : "Parameters used for bowtie alignment: --very-fast-local --threads 30 --mm -x ncbi-diaci1.1 --rf --maxins 11000. bedtools used to create bigwig file from bowtie BAM file. bedtools genomecov -split -ibam all_PE.bam -bga > all_PE.coverage.bedgraph. bedGraphToBigWig all_PE.sorted.coverage.bedgraph diaci1.chrom.sizes all_PE.bw",
-            "TaxID" : "121845",
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-            "Data source URL" : "http://www.ncbi.nlm.nih.gov/sra/SRX057205[accn]",
-            "Assembly name" : "NCBI-diacil",
-            "Assembly version" : "1.1",
-            "Organism common name" : "Asian citrus psyllid"
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version (Illumina Hi-Seq 200 bp)" : "Illumina Hiseq paired end",
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+         "label" : "Diacit_Diaci_psyllid_genome_assembly_version_1.1_RNA-Seq-alignments_2021-07-03",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR7079312'>SRR7079312</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR10915940'>SRR10915940</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR5514650'>SRR5514650</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR10915942'>SRR10915942</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR6965168'>SRR6965168</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11822617'>SRR11822617</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR5514647'>SRR5514647</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR10352887'>SRR10352887</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR5514643'>SRR5514643</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11822614'>SRR11822614</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
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+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
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+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
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+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR7079312'>SRR7079312</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR10915940'>SRR10915940</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR5514650'>SRR5514650</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR10915942'>SRR10915942</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR6965168'>SRR6965168</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11822617'>SRR11822617</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR5514647'>SRR5514647</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR10352887'>SRR10352887</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR5514643'>SRR5514643</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11822614'>SRR11822614</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
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diff --git a/organisms/stage/Diaphorina_citri_legacy/trackList.json b/organisms/stage/Diaphorina_citri_legacy/trackList.json
index ca82ad1..39aaf53 100644
--- a/organisms/stage/Diaphorina_citri_legacy/trackList.json
+++ b/organisms/stage/Diaphorina_citri_legacy/trackList.json
@@ -1,294 +1,280 @@
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 }
diff --git a/organisms/stage/Diprion_similis/trackList.json b/organisms/stage/Diprion_similis/trackList.json
new file mode 100644
index 0000000..79a60bb
--- /dev/null
+++ b/organisms/stage/Diprion_similis/trackList.json
@@ -0,0 +1,183 @@
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+               "label" : "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
+               "title" : "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
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+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "container-16px",
+            "description" : "product, note, description",
+            "subfeatureClasses" : {
+               "CDS" : "gnomon_CDS",
+               "UTR" : "gnomon_UTR",
+               "exon" : "container-100pct",
+               "wholeCDS" : null
+            }
+         },
+         "trackType" : "HTMLFeatures",
+         "type" : "HTMLFeatures",
+         "urlTemplate" : "tracks/NCBI_Annotation_Release_100_Pseudogene/{refseq}/trackData.json"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Reference Assembly",
+         "key" : "Gaps in assembly",
+         "label" : "Gaps in assembly",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "white",
+            "pos_color" : "black"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/GCF_021155765.1_iyDipSimi1.1_genomic.fna.gaps.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "0.5",
+         "category" : "Reference Assembly",
+         "key" : "GC Content",
+         "label" : "GC Content",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+         },
+         "scoreType" : "avgScore",
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "rgba(255,255,0,50)",
+            "pos_color" : "rgba(0,0,255,50)"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/GCF_021155765.1_iyDipSimi1.1_genomic.fna.gc.bigwig"
+      },
+      {
+         "category" : "RNA-Seq/Mapped Reads",
+         "key" : "Neodiprion lecontei RNA-Seq alignments against Diprion similis iyDipSimi1.1",
+         "label" : "Neolec_iyDipSimi1.1_RNA-Seq-alignments_2022-03-29",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR12814084'>SRR12814084</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR12814056'>SRR12814056</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR12814082'>SRR12814082</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR2970131'>SRR2970131</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR12814122'>SRR12814122</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR12814101'>SRR12814101</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR12814112'>SRR12814112</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR12814120'>SRR12814120</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR2970129'>SRR2970129</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR12814118'>SRR12814118</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Dark red alignments: Mapped portion of read aligned to forward strand<br>Light red alignments: Spliced portion of read aligned to forward strand<br>Dark blue alignments: Mapped portion of read aligned to reverse strand<br>Light blue alignments: Spliced portion of read aligned to reverse strand<br>Red marking - deletion in the read relative to the reference<br>Green marking - insertion in the read relative to the reference<br>Yellow marking  - mismatch (hover over the mismatch to see what the snp is)"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "unsafePopup" : true,
+         "urlTemplate" : "analyses/Diprion-similis-RNA-Seq_2022-03-29_v1.0/Neolec_iyDipSimi1.1_RNA-Seq-alignments_2022-03-29.bam"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "RNA-Seq/Coverage Plots",
+         "key" : "Neodiprion lecontei RNA-Seq alignments against Diprion similis iyDipSimi1.1, coverage",
+         "label" : "Neolec_iyDipSimi1.1_RNA-Seq-alignments_2022-03-29_coverage",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR12814084'>SRR12814084</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR12814056'>SRR12814056</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR12814082'>SRR12814082</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR2970131'>SRR2970131</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR12814122'>SRR12814122</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR12814101'>SRR12814101</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR12814112'>SRR12814112</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR12814120'>SRR12814120</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR2970129'>SRR2970129</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR12814118'>SRR12814118</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "unsafePopup" : true,
+         "urlTemplate" : "analyses/Diprion-similis-RNA-Seq_2022-03-29_v1.0/Neolec_iyDipSimi1.1_RNA-Seq-alignments_2022-03-29.bigwig"
+      },
+      {
+         "category" : "RNA-Seq/Splice junctions",
+         "compress" : 0,
+         "key" : "Neodiprion lecontei RNA-Seq alignments against Diprion similis iyDipSimi1.1, splice junctions",
+         "label" : "Neolec_iyDipSimi1.1_RNA-Seq-alignments_2022-03-29_junctions",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR12814084'>SRR12814084</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR12814056'>SRR12814056</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR12814082'>SRR12814082</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR2970131'>SRR2970131</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR12814122'>SRR12814122</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR12814101'>SRR12814101</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR12814112'>SRR12814112</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR12814120'>SRR12814120</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR2970129'>SRR2970129</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR12814118'>SRR12814118</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Junction reads generated by Hisat2 aligner and regtools. The number of alignments supporting the junction read is listed in blue."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "className" : "feature",
+            "description" : "score"
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "unsafePopup" : true,
+         "urlTemplate" : "tracks/Neolec_iyDipSimi1.1_RNA-Seq-alignments_2022-03-29_junctions/{refseq}/trackData.json"
+      }
+   ]
+}
diff --git a/organisms/stage/Drosophila_biarmipes/trackList.json b/organisms/stage/Drosophila_biarmipes/trackList.json
index 6e9181e..65f08ab 100644
--- a/organisms/stage/Drosophila_biarmipes/trackList.json
+++ b/organisms/stage/Drosophila_biarmipes/trackList.json
@@ -30,9 +30,9 @@
          },
          "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "description": "product, note, description",
-		"arrowheadClass" : "trellis-arrowhead",
-            "className" : "container-16px",
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "{type}",
+            "description" : "product, note, description",
             "subfeatureClasses" : {
                "CDS" : "primary_gene_set-cds",
                "UTR" : "primary_gene_set-utr",
@@ -68,14 +68,13 @@
          "bicolor_pivot" : "0.5",
          "category" : "Reference Assembly",
          "key" : "GC Content",
-         "scoreType": "avgScore",
-         "scoreType": "avgScore",
          "label" : "GC Content",
          "metadata" : {
             "Track contact" : "The i5k workspace@NAL",
             "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
             "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
          },
+         "scoreType" : "avgScore",
          "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
          "style" : {
             "neg_color" : "rgba(255,255,0,50)",
@@ -98,7 +97,7 @@
          "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
             "arrowheadClass" : "webapollo-arrowhead",
-            "className" : "container-10px"
+            "className" : "{type}"
          },
          "trackType" : null,
          "type" : "FeatureTrack",
@@ -117,9 +116,9 @@
          },
          "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "description": "product, note, description",
-		"arrowheadClass" : "trellis-arrowhead",
-            "className" : "container-16px",
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "{type}",
+            "description" : "product, note, description",
             "subfeatureClasses" : {
                "CDS" : "gnomon_CDS",
                "UTR" : "gnomon_UTR",
@@ -144,9 +143,9 @@
          },
          "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "description": "product, note, description",
-		"arrowheadClass" : "trellis-arrowhead",
-            "className" : "container-16px",
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "{type}",
+            "description" : "product, note, description",
             "subfeatureClasses" : {
                "CDS" : "gnomon_CDS",
                "UTR" : "gnomon_UTR",
@@ -171,9 +170,9 @@
          },
          "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "description": "product, note, description",
-		"arrowheadClass" : "trellis-arrowhead",
-            "className" : "container-16px",
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "{type}",
+            "description" : "product, note, description",
             "subfeatureClasses" : {
                "CDS" : "gnomon_CDS",
                "UTR" : "gnomon_UTR",
@@ -184,6 +183,65 @@
          "trackType" : null,
          "type" : "FeatureTrack",
          "urlTemplate" : "tracks/NCBI_Annotation_Release_101_tRNA/{refseq}/trackData.json"
+      },
+      {
+         "category" : "RNA-Seq/Mapped Reads",
+         "key" : "Drobia_Dbia_2.0_RNA-Seq-alignments_2021-06-19",
+         "label" : "Drobia_Dbia_2.0_RNA-Seq-alignments_2021-06-19",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346720'>SRR346720</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346718'>SRR346718</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346719'>SRR346719</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR13628020'>SRR13628020</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR13628019'>SRR13628019</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR13628018'>SRR13628018</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR8705030'>SRR8705030</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR6161783'>SRR6161783</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Dark red alignments: Mapped portion of read aligned to forward strand<br>Light red alignments: Spliced portion of read aligned to forward strand<br>Dark blue alignments: Mapped portion of read aligned to reverse strand<br>Light blue alignments: Spliced portion of read aligned to reverse strand<br>Red marking - deletion in the read relative to the reference<br>Green marking - insertion in the read relative to the reference<br>Yellow marking  - mismatch (hover over the mismatch to see what the snp is)"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "unsafePopup" : true,
+         "urlTemplate" : "analyses/Drosophila-biarmipes-RNA-Seq_2021-06-19_v1.0/Drobia_Dbia_2.0_RNA-Seq-alignments_2021-06-19.bam"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "RNA-Seq/Coverage Plots",
+         "key" : "Drobia_Dbia_2.0_RNA-Seq-alignments_2021-06-19_coverage",
+         "label" : "Drobia_Dbia_2.0_RNA-Seq-alignments_2021-06-19_coverage",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346720'>SRR346720</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346718'>SRR346718</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346719'>SRR346719</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR13628020'>SRR13628020</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR13628019'>SRR13628019</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR13628018'>SRR13628018</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR8705030'>SRR8705030</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR6161783'>SRR6161783</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "unsafePopup" : true,
+         "urlTemplate" : "analyses/Drosophila-biarmipes-RNA-Seq_2021-06-19_v1.0/Drobia_Dbia_2.0_RNA-Seq-alignments_2021-06-19.bigwig"
+      },
+      {
+         "category" : "RNA-Seq/Splice junctions",
+         "compress" : 0,
+         "key" : "Drobia_Dbia_2.0_RNA-Seq-alignments_2021-06-19_junctions",
+         "label" : "Drobia_Dbia_2.0_RNA-Seq-alignments_2021-06-19_junctions",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346720'>SRR346720</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346718'>SRR346718</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346719'>SRR346719</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR13628020'>SRR13628020</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR13628019'>SRR13628019</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR13628018'>SRR13628018</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR8705030'>SRR8705030</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR6161783'>SRR6161783</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Junction reads generated by Hisat2 aligner and regtools. The number of alignments supporting the junction read is listed in blue."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "className" : "feature",
+            "description" : "score"
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "unsafePopup" : true,
+         "urlTemplate" : "tracks/Drobia_Dbia_2.0_RNA-Seq-alignments_2021-06-19_junctions/{refseq}/trackData.json"
       }
    ]
 }
diff --git a/organisms/stage/Drosophila_bipectinata/trackList.json b/organisms/stage/Drosophila_bipectinata/trackList.json
index de3a8a1..bf33697 100644
--- a/organisms/stage/Drosophila_bipectinata/trackList.json
+++ b/organisms/stage/Drosophila_bipectinata/trackList.json
@@ -7,183 +7,158 @@
    "tracks" : [
       {
          "category" : "Reference sequence",
-         "faiUrlTemplate" : "seq/GCF_000236285.1_Dbip_2.0_genomic.fna.fai",
+         "chunkSize" : 20000,
          "key" : "Reference sequence",
          "label" : "DNA",
          "seqType" : "dna",
-         "storeClass" : "JBrowse/Store/Sequence/IndexedFasta",
+         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
          "type" : "SequenceTrack",
-         "urlTemplate" : "seq/GCF_000236285.1_Dbip_2.0_genomic.fna",
-         "useAsRefSeqStore" : 1
+         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-"
       },
       {
-         "category" : "NCBI Annotation Release 101/1. Gene Sets/Protein Coding",
+         "category" : "NCBI Annotation Release 102",
          "compress" : 0,
-         "key" : "NCBI Predicted protein coding genes, Annotation Release 101",
+         "key" : "NCBI_Annotation_Release_102_Gene",
          "label" : "drobip_current_models",
+         "menuTemplate" : [
+            {
+               "label" : "View details"
+            },
+            {
+               "action" : "newWindow",
+               "iconClass" : "dijitIconDatabase",
+               "label" : "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
+               "title" : "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
+               "url" : "function(track,feature){ return 'https://i5k.nal.usda.gov/'+feature.get('name')}"
+            }
+         ],
          "metadata" : {
             "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Drosophila_bipectinata/README_CURRENT_RELEASE",
             "Data provider" : "NCBI",
-            "Data source" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/236/285/GCF_000236285.1_Dbip_2.0/GCF_000236285.1_Dbip_2.0_genomic.gff.gz",
-            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/",
-            "Note" : "Some genes may have non-coding transcripts"
+            "Data source" : "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/018/153/845/GCF_018153845.1_ASM1815384v1/GCF_018153845.1_ASM1815384v1_genomic.gff.gz",
+            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
          },
          "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "description": "product, note, description",
-		"arrowheadClass" : "trellis-arrowhead",
+            "arrowheadClass" : "trellis-arrowhead",
             "className" : "container-16px",
+            "description" : "product, note, description",
             "subfeatureClasses" : {
-               "CDS" : "primary_gene_set-cds",
-               "UTR" : "primary_gene_set-utr",
+               "CDS" : "gnomon_CDS",
+               "UTR" : "gnomon_UTR",
                "exon" : "container-100pct",
                "wholeCDS" : null
             }
          },
-         "trackType" : null,
-         "type" : "FeatureTrack",
+         "trackType" : "HTMLFeatures",
+         "type" : "HTMLFeatures",
          "urlTemplate" : "tracks/drobip_current_models/{refseq}/trackData.json"
       },
       {
-         "autoscale" : "local",
-         "bicolor_pivot" : "zero",
-         "category" : "Reference Assembly",
-         "key" : "Gaps in assembly",
-         "label" : "Gaps in assembly",
+         "category" : "NCBI Annotation Release 102",
+         "compress" : 0,
+         "key" : "NCBI_Annotation_Release_102_Pseudogene",
+         "label" : "NCBI_Annotation_Release_102_Pseudogene",
          "metadata" : {
-            "Track contact" : "The i5k workspace@NAL",
-            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
-            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Drosophila_bipectinata/README_CURRENT_RELEASE",
+            "Data provider" : "NCBI",
+            "Data source" : "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/018/153/845/GCF_018153845.1_ASM1815384v1/GCF_018153845.1_ASM1815384v1_genomic.gff.gz",
+            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
          },
-         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "neg_color" : "white",
-            "pos_color" : "black"
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "container-16px",
+            "description" : "product, note, description",
+            "subfeatureClasses" : {
+               "CDS" : "gnomon_CDS",
+               "UTR" : "gnomon_UTR",
+               "exon" : "container-100pct",
+               "wholeCDS" : null
+            }
          },
-         "type" : "JBrowse/View/Track/Wiggle/Density",
-         "urlTemplate" : "bigwig/GCF_000236285.1_Dbip_2.0_genomic.fna.gaps.bigwig"
+         "trackType" : "HTMLFeatures",
+         "type" : "HTMLFeatures",
+         "urlTemplate" : "tracks/NCBI_Annotation_Release_102_Pseudogene/{refseq}/trackData.json"
       },
       {
          "autoscale" : "local",
          "bicolor_pivot" : "0.5",
          "category" : "Reference Assembly",
          "key" : "GC Content",
-         "scoreType": "avgScore",
-         "scoreType": "avgScore",
          "label" : "GC Content",
          "metadata" : {
             "Track contact" : "The i5k workspace@NAL",
             "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
             "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
          },
+         "scoreType" : "avgScore",
          "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
          "style" : {
             "neg_color" : "rgba(255,255,0,50)",
             "pos_color" : "rgba(0,0,255,50)"
          },
          "type" : "JBrowse/View/Track/Wiggle/Density",
-         "urlTemplate" : "bigwig/GCF_000236285.1_Dbip_2.0_genomic.fna.gc.bigwig"
+         "urlTemplate" : "bigwig/GCF_018153845.1_ASM1815384v1_genomic.fna.gc.bigwig"
       },
       {
-         "category" : "NCBI Annotation Release 101/2. Evidence",
-         "compress" : 0,
-         "key" : "cDNA match evidence from NCBI Annotation Release 101",
-         "label" : "NCBI_Annotation_Release_101_cDNA_match",
+         "category" : "RNA-Seq/Mapped Reads",
+         "key" : "Drobip_ASM1815384v1_RNA-Seq-alignments_2021-10-12",
+         "label" : "Drobip_ASM1815384v1_RNA-Seq-alignments_2021-10-12",
          "metadata" : {
-            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Drosophila_bipectinata/README_CURRENT_RELEASE",
-            "Data provider" : "NCBI",
-            "Data source" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/236/285/GCF_000236285.1_Dbip_2.0/GCF_000236285.1_Dbip_2.0_genomic.gff.gz",
-            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
-         },
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
-         "style" : {
-            "arrowheadClass" : "webapollo-arrowhead",
-            "className" : "container-10px"
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346722'>SRR346722</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346721'>SRR346721</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346723'>SRR346723</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR15048520'>SRR15048520</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR6161778'>SRR6161778</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Dark red alignments: Mapped portion of read aligned to forward strand<br>Light red alignments: Spliced portion of read aligned to forward strand<br>Dark blue alignments: Mapped portion of read aligned to reverse strand<br>Light blue alignments: Spliced portion of read aligned to reverse strand<br>Red marking - deletion in the read relative to the reference<br>Green marking - insertion in the read relative to the reference<br>Yellow marking  - mismatch (hover over the mismatch to see what the snp is)"
          },
-         "trackType" : null,
-         "type" : "FeatureTrack",
-         "urlTemplate" : "tracks/NCBI_Annotation_Release_101_cDNA_match/{refseq}/trackData.json"
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+	"unsafePopup":true,
+         "urlTemplate" : "analyses/Drosophila-bipectinata-RNA-Seq_2021-10-12_v1.0/Drobip_ASM1815384v1_RNA-Seq-alignments_2021-10-12.bam"
       },
       {
-         "category" : "NCBI Annotation Release 101/1. Gene Sets/Noncoding",
-         "compress" : 0,
-         "key" : "NCBI Predicted lncRNA, Annotation Release 101",
-         "label" : "NCBI_Annotation_Release_101_lncRNA",
-         "metadata" : {
-            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Drosophila_bipectinata/README_CURRENT_RELEASE",
-            "Data provider" : "NCBI",
-            "Data source" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/236/285/GCF_000236285.1_Dbip_2.0/GCF_000236285.1_Dbip_2.0_genomic.gff.gz",
-            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
-         },
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
-         "style" : {
-            "description": "product, note, description",
-		"arrowheadClass" : "trellis-arrowhead",
-            "className" : "container-16px",
-            "subfeatureClasses" : {
-               "CDS" : "gnomon_CDS",
-               "UTR" : "gnomon_UTR",
-               "exon" : "container-100pct",
-               "wholeCDS" : null
-            }
-         },
-         "trackType" : null,
-         "type" : "FeatureTrack",
-         "urlTemplate" : "tracks/NCBI_Annotation_Release_101_lncRNA/{refseq}/trackData.json"
-      },
-      {
-         "category" : "NCBI Annotation Release 101/1. Gene Sets/Pseudogenes",
-         "compress" : 0,
-         "key" : "NCBI Predicted pseudogenes, Annotation Release 101",
-         "label" : "NCBI_Annotation_Release_101_Pseudogene",
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "RNA-Seq/Coverage Plots",
+         "key" : "Drobip_ASM1815384v1_RNA-Seq-alignments_2021-10-12_coverage",
+         "label" : "Drobip_ASM1815384v1_RNA-Seq-alignments_2021-10-12_coverage",
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
          "metadata" : {
-            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Drosophila_bipectinata/README_CURRENT_RELEASE",
-            "Data provider" : "NCBI",
-            "Data source" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/236/285/GCF_000236285.1_Dbip_2.0/GCF_000236285.1_Dbip_2.0_genomic.gff.gz",
-            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346722'>SRR346722</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346721'>SRR346721</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346723'>SRR346723</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR15048520'>SRR15048520</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR6161778'>SRR6161778</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage."
          },
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "description": "product, note, description",
-		"arrowheadClass" : "trellis-arrowhead",
-            "className" : "container-16px",
-            "subfeatureClasses" : {
-               "CDS" : "gnomon_CDS",
-               "UTR" : "gnomon_UTR",
-               "exon" : "container-100pct",
-               "wholeCDS" : null
-            }
+            "pos_color" : "#00BFFF"
          },
-         "trackType" : null,
-         "type" : "FeatureTrack",
-         "urlTemplate" : "tracks/NCBI_Annotation_Release_101_Pseudogene/{refseq}/trackData.json"
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+	"unsafePopup":true,
+         "urlTemplate" : "analyses/Drosophila-bipectinata-RNA-Seq_2021-10-12_v1.0/Drobip_ASM1815384v1_RNA-Seq-alignments_2021-10-12.bigwig"
       },
       {
-         "category" : "NCBI Annotation Release 101/1. Gene Sets/Noncoding",
+         "category" : "RNA-Seq/Splice junctions",
          "compress" : 0,
-         "key" : "NCBI Predicted tRNAs, Annotation Release 101",
-         "label" : "NCBI_Annotation_Release_101_tRNA",
+         "key" : "Drobip_ASM1815384v1_RNA-Seq-alignments_2021-10-12_junctions",
+         "label" : "Drobip_ASM1815384v1_RNA-Seq-alignments_2021-10-12_junctions",
          "metadata" : {
-            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Drosophila_bipectinata/README_CURRENT_RELEASE",
-            "Data provider" : "NCBI",
-            "Data source" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/236/285/GCF_000236285.1_Dbip_2.0/GCF_000236285.1_Dbip_2.0_genomic.gff.gz",
-            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346722'>SRR346722</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346721'>SRR346721</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346723'>SRR346723</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR15048520'>SRR15048520</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR6161778'>SRR6161778</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Junction reads generated by Hisat2 aligner and regtools. The number of alignments supporting the junction read is listed in blue."
          },
          "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "description": "product, note, description",
-		"arrowheadClass" : "trellis-arrowhead",
-            "className" : "container-16px",
-            "subfeatureClasses" : {
-               "CDS" : "gnomon_CDS",
-               "UTR" : "gnomon_UTR",
-               "exon" : "container-100pct",
-               "wholeCDS" : null
-            }
+	     "description":"score",
+            "className" : "feature"
          },
          "trackType" : null,
          "type" : "FeatureTrack",
-         "urlTemplate" : "tracks/NCBI_Annotation_Release_101_tRNA/{refseq}/trackData.json"
+	"unsafePopup":true,
+         "urlTemplate" : "tracks/Drobip_ASM1815384v1_RNA-Seq-alignments_2021-10-12_junctions/{refseq}/trackData.json"
       }
    ]
 }
diff --git a/organisms/stage/Drosophila_elegans/trackList.json b/organisms/stage/Drosophila_elegans/trackList.json
index 62a843e..75c3686 100644
--- a/organisms/stage/Drosophila_elegans/trackList.json
+++ b/organisms/stage/Drosophila_elegans/trackList.json
@@ -7,182 +7,168 @@
    "tracks" : [
       {
          "category" : "Reference sequence",
-         "faiUrlTemplate" : "seq/GCF_000224195.1_Dele_2.0_genomic.fna.fai",
+         "chunkSize" : 20000,
          "key" : "Reference sequence",
          "label" : "DNA",
          "seqType" : "dna",
-         "storeClass" : "JBrowse/Store/Sequence/IndexedFasta",
+         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
          "type" : "SequenceTrack",
-         "urlTemplate" : "seq/GCF_000224195.1_Dele_2.0_genomic.fna",
-         "useAsRefSeqStore" : 1
+         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-"
       },
       {
-         "category" : "NCBI Annotation Release 101/1. Gene Sets/Protein Coding",
+         "category" : "NCBI Annotation Release 102",
          "compress" : 0,
-         "key" : "NCBI Predicted protein coding genes, Annotation Release 101",
+         "key" : "NCBI_Annotation_Release_102_Gene",
          "label" : "droele_current_models",
+         "menuTemplate" : [
+             {
+                "label" : "View details"
+             },
+             {
+              "label": "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
+              "title": "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
+              "iconClass" : "dijitIconDatabase",
+              "action": "newWindow",
+              "url" : "function(track,feature){ return 'https://www.ncbi.nlm.nih.gov/nuccore/'+feature.get('name')}"
+              }
+        ],
          "metadata" : {
             "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Drosophila_elegans/README_CURRENT_RELEASE",
             "Data provider" : "NCBI",
-            "Data source" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/224/195/GCF_000224195.1_Dele_2.0/GCF_000224195.1_Dele_2.0_genomic.gff.gz",
-            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/",
-            "Note" : "Some genes may have non-coding transcripts"
+            "Data source" : "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/018/152/505/GCF_018152505.1_ASM1815250v1/GCF_018152505.1_ASM1815250v1_genomic.gff.gz",
+            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
          },
          "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "description": "product, note, description",
-		"arrowheadClass" : "trellis-arrowhead",
+            "arrowheadClass" : "trellis-arrowhead",
             "className" : "container-16px",
+            "description" : "product, note, description",
             "subfeatureClasses" : {
-               "CDS" : "primary_gene_set-cds",
-               "UTR" : "primary_gene_set-utr",
+               "CDS" : "gnomon_CDS",
+               "UTR" : "gnomon_UTR",
                "exon" : "container-100pct",
                "wholeCDS" : null
             }
          },
-         "trackType" : null,
-         "type" : "FeatureTrack",
+         "trackType" : "HTMLFeatures",
+         "type" : "HTMLFeatures",
          "urlTemplate" : "tracks/droele_current_models/{refseq}/trackData.json"
       },
       {
-         "autoscale" : "local",
-         "bicolor_pivot" : "zero",
-         "category" : "Reference Assembly",
-         "key" : "Gaps in assembly",
-         "label" : "Gaps in assembly",
+         "category" : "NCBI Annotation Release 102",
+         "compress" : 0,
+         "key" : "NCBI_Annotation_Release_102_Pseudogene",
+         "label" : "NCBI_Annotation_Release_102_Pseudogene",
          "metadata" : {
-            "Track contact" : "The i5k workspace@NAL",
-            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
-            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Drosophila_elegans/README_CURRENT_RELEASE",
+            "Data provider" : "NCBI",
+            "Data source" : "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/018/152/505/GCF_018152505.1_ASM1815250v1/GCF_018152505.1_ASM1815250v1_genomic.gff.gz",
+            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
          },
-         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "neg_color" : "white",
-            "pos_color" : "black"
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "container-16px",
+            "description" : "product, note, description",
+            "subfeatureClasses" : {
+               "CDS" : "gnomon_CDS",
+               "UTR" : "gnomon_UTR",
+               "exon" : "container-100pct",
+               "wholeCDS" : null
+            }
          },
-         "type" : "JBrowse/View/Track/Wiggle/Density",
-         "urlTemplate" : "bigwig/GCF_000224195.1_Dele_2.0_genomic.fna.gaps.bigwig"
+         "trackType" : "HTMLFeatures",
+         "type" : "HTMLFeatures",
+         "urlTemplate" : "tracks/NCBI_Annotation_Release_102_Pseudogene/{refseq}/trackData.json"
       },
       {
          "autoscale" : "local",
          "bicolor_pivot" : "0.5",
          "category" : "Reference Assembly",
          "key" : "GC Content",
-         "scoreType": "avgScore",
          "label" : "GC Content",
          "metadata" : {
             "Track contact" : "The i5k workspace@NAL",
             "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
             "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
          },
+         "scoreType" : "avgScore",
          "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
          "style" : {
             "neg_color" : "rgba(255,255,0,50)",
             "pos_color" : "rgba(0,0,255,50)"
          },
          "type" : "JBrowse/View/Track/Wiggle/Density",
-         "urlTemplate" : "bigwig/GCF_000224195.1_Dele_2.0_genomic.fna.gc.bigwig"
-      },
-      {
-         "category" : "NCBI Annotation Release 101/2. Evidence",
-         "compress" : 0,
-         "key" : "cDNA match evidence from NCBI Annotation Release 101",
-         "label" : "NCBI_Annotation_Release_101_cDNA_match",
-         "metadata" : {
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-            "Data source" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/224/195/GCF_000224195.1_Dele_2.0/GCF_000224195.1_Dele_2.0_genomic.gff.gz",
-            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
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-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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-            "arrowheadClass" : "webapollo-arrowhead",
-            "className" : "container-10px"
-         },
-         "trackType" : null,
-         "type" : "FeatureTrack",
-         "urlTemplate" : "tracks/NCBI_Annotation_Release_101_cDNA_match/{refseq}/trackData.json"
+         "urlTemplate" : "bigwig/GCF_018152505.1_ASM1815250v1_genomic.fna.gc.bigwig"
       },
       {
-         "category" : "NCBI Annotation Release 101/1. Gene Sets/Noncoding",
-         "compress" : 0,
-         "key" : "NCBI Predicted lncRNA, Annotation Release 101",
-         "label" : "NCBI_Annotation_Release_101_lncRNA",
+         "category" : "RNA-Seq/Mapped Reads",
+         "key" : "Droele_ASM1815250v1_RNA-Seq-alignments_2021-09-28",
+         "label" : "Droele_ASM1815250v1_RNA-Seq-alignments_2021-09-28",
          "metadata" : {
-            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Drosophila_elegans/README_CURRENT_RELEASE",
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-         },
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
-         "style" : {
-            "description": "product, note, description",
-		"arrowheadClass" : "trellis-arrowhead",
-            "className" : "container-16px",
-            "subfeatureClasses" : {
-               "CDS" : "gnomon_CDS",
-               "UTR" : "gnomon_UTR",
-               "exon" : "container-100pct",
-               "wholeCDS" : null
-            }
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346725'>SRR346725</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346724'>SRR346724</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346726'>SRR346726</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Dark red alignments: Mapped portion of read aligned to forward strand<br>Light red alignments: Spliced portion of read aligned to forward strand<br>Dark blue alignments: Mapped portion of read aligned to reverse strand<br>Light blue alignments: Spliced portion of read aligned to reverse strand<br>Red marking - deletion in the read relative to the reference<br>Green marking - insertion in the read relative to the reference<br>Yellow marking  - mismatch (hover over the mismatch to see what the snp is)"
          },
-         "trackType" : null,
-         "type" : "FeatureTrack",
-         "urlTemplate" : "tracks/NCBI_Annotation_Release_101_lncRNA/{refseq}/trackData.json"
+         "unsafePopup": true,
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "analyses/Drosophila-elegans-RNA-Seq_2021-09-28_v1.0/Droele_ASM1815250v1_RNA-Seq-alignments_2021-09-28.bam"
       },
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-         "category" : "NCBI Annotation Release 101/1. Gene Sets/Pseudogenes",
-         "compress" : 0,
-         "key" : "NCBI Predicted pseudogenes, Annotation Release 101",
-         "label" : "NCBI_Annotation_Release_101_Pseudogene",
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "RNA-Seq/Coverage Plots",
+         "key" : "Droele_ASM1815250v1_RNA-Seq-alignments_2021-09-28_coverage",
+         "label" : "Droele_ASM1815250v1_RNA-Seq-alignments_2021-09-28_coverage",
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "unsafePopup": true,
          "metadata" : {
-            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Drosophila_elegans/README_CURRENT_RELEASE",
-            "Data provider" : "NCBI",
-            "Data source" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/224/195/GCF_000224195.1_Dele_2.0/GCF_000224195.1_Dele_2.0_genomic.gff.gz",
-            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346725'>SRR346725</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346724'>SRR346724</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346726'>SRR346726</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage."
          },
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "description": "product, note, description",
-		"arrowheadClass" : "trellis-arrowhead",
-            "className" : "container-16px",
-            "subfeatureClasses" : {
-               "CDS" : "gnomon_CDS",
-               "UTR" : "gnomon_UTR",
-               "exon" : "container-100pct",
-               "wholeCDS" : null
-            }
+            "pos_color" : "#00BFFF"
          },
-         "trackType" : null,
-         "type" : "FeatureTrack",
-         "urlTemplate" : "tracks/NCBI_Annotation_Release_101_Pseudogene/{refseq}/trackData.json"
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "analyses/Drosophila-elegans-RNA-Seq_2021-09-28_v1.0/Droele_ASM1815250v1_RNA-Seq-alignments_2021-09-28.bigwig"
       },
       {
-         "category" : "NCBI Annotation Release 101/1. Gene Sets/Noncoding",
+         "category" : "RNA-Seq/Splice junctions",
          "compress" : 0,
-         "key" : "NCBI Predicted tRNAs, Annotation Release 101",
-         "label" : "NCBI_Annotation_Release_101_tRNA",
+         "key" : "Droele_ASM1815250v1_RNA-Seq-alignments_2021-09-28_junctions",
+         "label" : "Droele_ASM1815250v1_RNA-Seq-alignments_2021-09-28_junctions",
+         "unsafePopup": true,
          "metadata" : {
-            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Drosophila_elegans/README_CURRENT_RELEASE",
-            "Data provider" : "NCBI",
-            "Data source" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/224/195/GCF_000224195.1_Dele_2.0/GCF_000224195.1_Dele_2.0_genomic.gff.gz",
-            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346725'>SRR346725</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346724'>SRR346724</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346726'>SRR346726</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Junction reads generated by Hisat2 aligner and regtools. The number of alignments supporting the junction read is listed in blue."
          },
          "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "description": "product, note, description",
-		"arrowheadClass" : "trellis-arrowhead",
-            "className" : "container-16px",
-            "subfeatureClasses" : {
-               "CDS" : "gnomon_CDS",
-               "UTR" : "gnomon_UTR",
-               "exon" : "container-100pct",
-               "wholeCDS" : null
-            }
+	     "description" : "score",
+            "className" : "feature",
+    "subfeatureClasses": {
+      "UTR": "webapollo-UTR",
+      "CDS": "junction-cds",
+      "exon": "container-100pct",
+      "intron": null,
+      "wholeCDS": null,
+      "start_codon": null,
+      "stop_codon": null,
+      "match_part": "darkblue-80pct"
+    }
          },
          "trackType" : null,
          "type" : "FeatureTrack",
-         "urlTemplate" : "tracks/NCBI_Annotation_Release_101_tRNA/{refseq}/trackData.json"
+         "urlTemplate" : "tracks/Droele_ASM1815250v1_RNA-Seq-alignments_2021-09-28_junctions/{refseq}/trackData.json"
       }
    ]
 }
diff --git a/organisms/stage/Drosophila_eugracilis/trackList.json b/organisms/stage/Drosophila_eugracilis/trackList.json
index ad170b3..d83a689 100644
--- a/organisms/stage/Drosophila_eugracilis/trackList.json
+++ b/organisms/stage/Drosophila_eugracilis/trackList.json
@@ -7,183 +7,168 @@
    "tracks" : [
       {
          "category" : "Reference sequence",
-         "faiUrlTemplate" : "seq/GCF_000236325.1_Deug_2.0_genomic.fna.fai",
+         "chunkSize" : 20000,
          "key" : "Reference sequence",
          "label" : "DNA",
          "seqType" : "dna",
-         "storeClass" : "JBrowse/Store/Sequence/IndexedFasta",
+         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
          "type" : "SequenceTrack",
-         "urlTemplate" : "seq/GCF_000236325.1_Deug_2.0_genomic.fna",
-         "useAsRefSeqStore" : 1
+         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-"
       },
       {
-         "category" : "NCBI Annotation Release 101/1. Gene Sets/Protein Coding",
+         "category" : "NCBI Annotation Release 102",
          "compress" : 0,
-         "key" : "NCBI Predicted protein coding genes, Annotation Release 101",
+         "key" : "NCBI_Annotation_Release_102_Gene",
          "label" : "droeug_current_models",
+         "menuTemplate" : [
+             {
+                "label" : "View details"
+             },
+             {
+              "label": "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
+              "title": "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
+              "iconClass" : "dijitIconDatabase",
+              "action": "newWindow",
+              "url" : "function(track,feature){ return 'https://www.ncbi.nlm.nih.gov/nuccore/'+feature.get('name')}"
+              }
+        ],
          "metadata" : {
             "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Drosophila_eugracilis/README_CURRENT_RELEASE",
             "Data provider" : "NCBI",
-            "Data source" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/236/325/GCF_000236325.1_Deug_2.0/GCF_000236325.1_Deug_2.0_genomic.gff.gz",
-            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/",
-            "Note" : "Some genes may have non-coding transcripts"
+            "Data source" : "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/018/153/835/GCF_018153835.1_ASM1815383v1/GCF_018153835.1_ASM1815383v1_genomic.gff.gz",
+            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
          },
          "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "description": "product, note, description",
-		"arrowheadClass" : "trellis-arrowhead",
+            "arrowheadClass" : "trellis-arrowhead",
             "className" : "container-16px",
+            "description" : "product, note, description",
             "subfeatureClasses" : {
-               "CDS" : "primary_gene_set-cds",
-               "UTR" : "primary_gene_set-utr",
+               "CDS" : "gnomon_CDS",
+               "UTR" : "gnomon_UTR",
                "exon" : "container-100pct",
                "wholeCDS" : null
             }
          },
-         "trackType" : null,
-         "type" : "FeatureTrack",
+         "trackType" : "HTMLFeatures",
+         "type" : "HTMLFeatures",
          "urlTemplate" : "tracks/droeug_current_models/{refseq}/trackData.json"
       },
       {
-         "autoscale" : "local",
-         "bicolor_pivot" : "zero",
-         "category" : "Reference Assembly",
-         "key" : "Gaps in assembly",
-         "label" : "Gaps in assembly",
+         "category" : "NCBI Annotation Release 102",
+         "compress" : 0,
+         "key" : "NCBI_Annotation_Release_102_Pseudogene",
+         "label" : "NCBI_Annotation_Release_102_Pseudogene",
          "metadata" : {
-            "Track contact" : "The i5k workspace@NAL",
-            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
-            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Drosophila_eugracilis/README_CURRENT_RELEASE",
+            "Data provider" : "NCBI",
+            "Data source" : "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/018/153/835/GCF_018153835.1_ASM1815383v1/GCF_018153835.1_ASM1815383v1_genomic.gff.gz",
+            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
          },
-         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "neg_color" : "white",
-            "pos_color" : "black"
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "container-16px",
+            "description" : "product, note, description",
+            "subfeatureClasses" : {
+               "CDS" : "gnomon_CDS",
+               "UTR" : "gnomon_UTR",
+               "exon" : "container-100pct",
+               "wholeCDS" : null
+            }
          },
-         "type" : "JBrowse/View/Track/Wiggle/Density",
-         "urlTemplate" : "bigwig/GCF_000236325.1_Deug_2.0_genomic.fna.gaps.bigwig"
+         "trackType" : "HTMLFeatures",
+         "type" : "HTMLFeatures",
+         "urlTemplate" : "tracks/NCBI_Annotation_Release_102_Pseudogene/{refseq}/trackData.json"
       },
       {
          "autoscale" : "local",
          "bicolor_pivot" : "0.5",
          "category" : "Reference Assembly",
          "key" : "GC Content",
-         "scoreType": "avgScore",
-         "scoreType": "avgScore",
          "label" : "GC Content",
          "metadata" : {
             "Track contact" : "The i5k workspace@NAL",
             "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
             "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
          },
+         "scoreType" : "avgScore",
          "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
          "style" : {
             "neg_color" : "rgba(255,255,0,50)",
             "pos_color" : "rgba(0,0,255,50)"
          },
          "type" : "JBrowse/View/Track/Wiggle/Density",
-         "urlTemplate" : "bigwig/GCF_000236325.1_Deug_2.0_genomic.fna.gc.bigwig"
-      },
-      {
-         "category" : "NCBI Annotation Release 101/2. Evidence",
-         "compress" : 0,
-         "key" : "cDNA match evidence from NCBI Annotation Release 101",
-         "label" : "NCBI_Annotation_Release_101_cDNA_match",
-         "metadata" : {
-            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Drosophila_eugracilis/README_CURRENT_RELEASE",
-            "Data provider" : "NCBI",
-            "Data source" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/236/325/GCF_000236325.1_Deug_2.0/GCF_000236325.1_Deug_2.0_genomic.gff.gz",
-            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
-         },
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
-         "style" : {
-            "arrowheadClass" : "webapollo-arrowhead",
-            "className" : "container-10px"
-         },
-         "trackType" : null,
-         "type" : "FeatureTrack",
-         "urlTemplate" : "tracks/NCBI_Annotation_Release_101_cDNA_match/{refseq}/trackData.json"
+         "urlTemplate" : "bigwig/GCF_018153835.1_ASM1815383v1_genomic.fna.gc.bigwig"
       },
       {
-         "category" : "NCBI Annotation Release 101/1. Gene Sets/Noncoding",
-         "compress" : 0,
-         "key" : "NCBI Predicted lncRNA, Annotation Release 101",
-         "label" : "NCBI_Annotation_Release_101_lncRNA",
+         "category" : "RNA-Seq/Mapped Reads",
+         "key" : "Droeug_ASM1815383v1_RNA-Seq-alignments_2021-08-20",
+         "label" : "Droeug_ASM1815383v1_RNA-Seq-alignments_2021-08-20",
          "metadata" : {
-            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Drosophila_eugracilis/README_CURRENT_RELEASE",
-            "Data provider" : "NCBI",
-            "Data source" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/236/325/GCF_000236325.1_Deug_2.0/GCF_000236325.1_Deug_2.0_genomic.gff.gz",
-            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
-         },
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
-         "style" : {
-            "description": "product, note, description",
-		"arrowheadClass" : "trellis-arrowhead",
-            "className" : "container-16px",
-            "subfeatureClasses" : {
-               "CDS" : "gnomon_CDS",
-               "UTR" : "gnomon_UTR",
-               "exon" : "container-100pct",
-               "wholeCDS" : null
-            }
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346729'>SRR346729</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346727'>SRR346727</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346728'>SRR346728</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Dark red alignments: Mapped portion of read aligned to forward strand<br>Light red alignments: Spliced portion of read aligned to forward strand<br>Dark blue alignments: Mapped portion of read aligned to reverse strand<br>Light blue alignments: Spliced portion of read aligned to reverse strand<br>Red marking - deletion in the read relative to the reference<br>Green marking - insertion in the read relative to the reference<br>Yellow marking  - mismatch (hover over the mismatch to see what the snp is)"
          },
-         "trackType" : null,
-         "type" : "FeatureTrack",
-         "urlTemplate" : "tracks/NCBI_Annotation_Release_101_lncRNA/{refseq}/trackData.json"
+         "unsafePopup": true,
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "analyses/Drosophila-eugracilis-RNA-Seq_2021-08-20_v1.0/Droeug_ASM1815383v1_RNA-Seq-alignments_2021-08-20.bam"
       },
       {
-         "category" : "NCBI Annotation Release 101/1. Gene Sets/Pseudogenes",
-         "compress" : 0,
-         "key" : "NCBI Predicted pseudogenes, Annotation Release 101",
-         "label" : "NCBI_Annotation_Release_101_Pseudogene",
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "RNA-Seq/Coverage Plots",
+         "key" : "Droeug_ASM1815383v1_RNA-Seq-alignments_2021-08-20_coverage",
+         "label" : "Droeug_ASM1815383v1_RNA-Seq-alignments_2021-08-20_coverage",
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "unsafePopup": true,
          "metadata" : {
-            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Drosophila_eugracilis/README_CURRENT_RELEASE",
-            "Data provider" : "NCBI",
-            "Data source" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/236/325/GCF_000236325.1_Deug_2.0/GCF_000236325.1_Deug_2.0_genomic.gff.gz",
-            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346729'>SRR346729</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346727'>SRR346727</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346728'>SRR346728</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage."
          },
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "description": "product, note, description",
-		"arrowheadClass" : "trellis-arrowhead",
-            "className" : "container-16px",
-            "subfeatureClasses" : {
-               "CDS" : "gnomon_CDS",
-               "UTR" : "gnomon_UTR",
-               "exon" : "container-100pct",
-               "wholeCDS" : null
-            }
+            "pos_color" : "#00BFFF"
          },
-         "trackType" : null,
-         "type" : "FeatureTrack",
-         "urlTemplate" : "tracks/NCBI_Annotation_Release_101_Pseudogene/{refseq}/trackData.json"
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "analyses/Drosophila-eugracilis-RNA-Seq_2021-08-20_v1.0/Droeug_ASM1815383v1_RNA-Seq-alignments_2021-08-20.bigwig"
       },
       {
-         "category" : "NCBI Annotation Release 101/1. Gene Sets/Noncoding",
+         "category" : "RNA-Seq/Splice junctions",
          "compress" : 0,
-         "key" : "NCBI Predicted tRNAs, Annotation Release 101",
-         "label" : "NCBI_Annotation_Release_101_tRNA",
+         "key" : "Droeug_ASM1815383v1_RNA-Seq-alignments_2021-08-20_junctions",
+         "label" : "Droeug_ASM1815383v1_RNA-Seq-alignments_2021-08-20_junctions",
+         "unsafePopup": true,
          "metadata" : {
-            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Drosophila_eugracilis/README_CURRENT_RELEASE",
-            "Data provider" : "NCBI",
-            "Data source" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/236/325/GCF_000236325.1_Deug_2.0/GCF_000236325.1_Deug_2.0_genomic.gff.gz",
-            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346729'>SRR346729</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346727'>SRR346727</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346728'>SRR346728</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Junction reads generated by Hisat2 aligner and regtools. The number of alignments supporting the junction read is listed in blue."
          },
          "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "description": "product, note, description",
-		"arrowheadClass" : "trellis-arrowhead",
-            "className" : "container-16px",
-            "subfeatureClasses" : {
-               "CDS" : "gnomon_CDS",
-               "UTR" : "gnomon_UTR",
-               "exon" : "container-100pct",
-               "wholeCDS" : null
-            }
+    "subfeatureClasses": {
+      "UTR": "webapollo-UTR",
+      "CDS": "junction-cds",
+      "exon": "container-100pct",
+      "intron": null,
+      "wholeCDS": null,
+      "start_codon": null,
+      "stop_codon": null,
+      "match_part": "darkblue-80pct"
+    },
+	     "description" : "score",
+            "className" : "feature"
          },
          "trackType" : null,
          "type" : "FeatureTrack",
-         "urlTemplate" : "tracks/NCBI_Annotation_Release_101_tRNA/{refseq}/trackData.json"
+         "urlTemplate" : "tracks/Droeug_ASM1815383v1_RNA-Seq-alignments_2021-08-20_junctions/{refseq}/trackData.json"
       }
    ]
 }
diff --git a/organisms/stage/Drosophila_ficusphila/trackList.json b/organisms/stage/Drosophila_ficusphila/trackList.json
index 7525b72..660cdc9 100644
--- a/organisms/stage/Drosophila_ficusphila/trackList.json
+++ b/organisms/stage/Drosophila_ficusphila/trackList.json
@@ -7,183 +7,158 @@
    "tracks" : [
       {
          "category" : "Reference sequence",
-         "faiUrlTemplate" : "seq/GCF_000220665.1_Dfic_2.0_genomic.fna.fai",
+         "chunkSize" : 20000,
          "key" : "Reference sequence",
          "label" : "DNA",
          "seqType" : "dna",
-         "storeClass" : "JBrowse/Store/Sequence/IndexedFasta",
+         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
          "type" : "SequenceTrack",
-         "urlTemplate" : "seq/GCF_000220665.1_Dfic_2.0_genomic.fna",
-         "useAsRefSeqStore" : 1
+         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-"
       },
       {
-         "category" : "NCBI Annotation Release 101/1. Gene Sets/Protein Coding",
+         "category" : "NCBI Annotation Release 102",
          "compress" : 0,
-         "key" : "NCBI Predicted protein coding genes, Annotation Release 101",
+         "key" : "NCBI_Annotation_Release_102_Gene",
          "label" : "drofic_current_models",
+         "menuTemplate" : [
+            {
+               "label" : "View details"
+            },
+            {
+               "action" : "newWindow",
+               "iconClass" : "dijitIconDatabase",
+               "label" : "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
+               "title" : "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
+               "url" : "function(track,feature){ return 'https://i5k.nal.usda.gov/'+feature.get('name')}"
+            }
+         ],
          "metadata" : {
             "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Drosophila_ficusphila/README_CURRENT_RELEASE",
             "Data provider" : "NCBI",
-            "Data source" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/220/665/GCF_000220665.1_Dfic_2.0/GCF_000220665.1_Dfic_2.0_genomic.gff.gz",
-            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/",
-            "Note" : "Some genes may have non-coding transcripts"
+            "Data source" : "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/018/152/265/GCF_018152265.1_ASM1815226v1/GCF_018152265.1_ASM1815226v1_genomic.gff.gz",
+            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
          },
          "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "description": "product, note, description",
-		"arrowheadClass" : "trellis-arrowhead",
+            "arrowheadClass" : "trellis-arrowhead",
             "className" : "container-16px",
+            "description" : "product, note, description",
             "subfeatureClasses" : {
-               "CDS" : "primary_gene_set-cds",
-               "UTR" : "primary_gene_set-utr",
+               "CDS" : "gnomon_CDS",
+               "UTR" : "gnomon_UTR",
                "exon" : "container-100pct",
                "wholeCDS" : null
             }
          },
-         "trackType" : null,
-         "type" : "FeatureTrack",
+         "trackType" : "HTMLFeatures",
+         "type" : "HTMLFeatures",
          "urlTemplate" : "tracks/drofic_current_models/{refseq}/trackData.json"
       },
       {
-         "autoscale" : "local",
-         "bicolor_pivot" : "zero",
-         "category" : "Reference Assembly",
-         "key" : "Gaps in assembly",
-         "label" : "Gaps in assembly",
+         "category" : "NCBI Annotation Release 102",
+         "compress" : 0,
+         "key" : "NCBI_Annotation_Release_102_Pseudogene",
+         "label" : "NCBI_Annotation_Release_102_Pseudogene",
          "metadata" : {
-            "Track contact" : "The i5k workspace@NAL",
-            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
-            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Drosophila_ficusphila/README_CURRENT_RELEASE",
+            "Data provider" : "NCBI",
+            "Data source" : "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/018/152/265/GCF_018152265.1_ASM1815226v1/GCF_018152265.1_ASM1815226v1_genomic.gff.gz",
+            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
          },
-         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "neg_color" : "white",
-            "pos_color" : "black"
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "container-16px",
+            "description" : "product, note, description",
+            "subfeatureClasses" : {
+               "CDS" : "gnomon_CDS",
+               "UTR" : "gnomon_UTR",
+               "exon" : "container-100pct",
+               "wholeCDS" : null
+            }
          },
-         "type" : "JBrowse/View/Track/Wiggle/Density",
-         "urlTemplate" : "bigwig/GCF_000220665.1_Dfic_2.0_genomic.fna.gaps.bigwig"
+         "trackType" : "HTMLFeatures",
+         "type" : "HTMLFeatures",
+         "urlTemplate" : "tracks/NCBI_Annotation_Release_102_Pseudogene/{refseq}/trackData.json"
       },
       {
          "autoscale" : "local",
          "bicolor_pivot" : "0.5",
          "category" : "Reference Assembly",
          "key" : "GC Content",
-         "scoreType": "avgScore",
-         "scoreType": "avgScore",
          "label" : "GC Content",
          "metadata" : {
             "Track contact" : "The i5k workspace@NAL",
             "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
             "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
          },
+         "scoreType" : "avgScore",
          "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
          "style" : {
             "neg_color" : "rgba(255,255,0,50)",
             "pos_color" : "rgba(0,0,255,50)"
          },
          "type" : "JBrowse/View/Track/Wiggle/Density",
-         "urlTemplate" : "bigwig/GCF_000220665.1_Dfic_2.0_genomic.fna.gc.bigwig"
+         "urlTemplate" : "bigwig/GCF_018152265.1_ASM1815226v1_genomic.fna.gc.bigwig"
       },
       {
-         "category" : "NCBI Annotation Release 101/2. Evidence",
-         "compress" : 0,
-         "key" : "cDNA match evidence from NCBI Annotation Release 101",
-         "label" : "NCBI_Annotation_Release_101_cDNA_match",
+         "category" : "RNA-Seq/Mapped Reads",
+         "key" : "Drofic_ASM1815226v1_RNA-Seq-alignments_2021-10-08",
+         "label" : "Drofic_ASM1815226v1_RNA-Seq-alignments_2021-10-08",
          "metadata" : {
-            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Drosophila_ficusphila/README_CURRENT_RELEASE",
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-            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
-         },
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
-         "style" : {
-            "arrowheadClass" : "webapollo-arrowhead",
-            "className" : "container-10px"
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346750'>SRR346750</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346751'>SRR346751</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346748'>SRR346748</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346749'>SRR346749</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346752'>SRR346752</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Dark red alignments: Mapped portion of read aligned to forward strand<br>Light red alignments: Spliced portion of read aligned to forward strand<br>Dark blue alignments: Mapped portion of read aligned to reverse strand<br>Light blue alignments: Spliced portion of read aligned to reverse strand<br>Red marking - deletion in the read relative to the reference<br>Green marking - insertion in the read relative to the reference<br>Yellow marking  - mismatch (hover over the mismatch to see what the snp is)"
          },
-         "trackType" : null,
-         "type" : "FeatureTrack",
-         "urlTemplate" : "tracks/NCBI_Annotation_Release_101_cDNA_match/{refseq}/trackData.json"
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+	"unsafePopup":true,
+         "urlTemplate" : "analyses/Drosophila-ficusphila-RNA-Seq_2021-10-08_v1.0/Drofic_ASM1815226v1_RNA-Seq-alignments_2021-10-08.bam"
       },
       {
-         "category" : "NCBI Annotation Release 101/1. Gene Sets/Noncoding",
-         "compress" : 0,
-         "key" : "NCBI Predicted lncRNA, Annotation Release 101",
-         "label" : "NCBI_Annotation_Release_101_lncRNA",
-         "metadata" : {
-            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Drosophila_ficusphila/README_CURRENT_RELEASE",
-            "Data provider" : "NCBI",
-            "Data source" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/220/665/GCF_000220665.1_Dfic_2.0/GCF_000220665.1_Dfic_2.0_genomic.gff.gz",
-            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
-         },
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
-         "style" : {
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-         "type" : "FeatureTrack",
-         "urlTemplate" : "tracks/NCBI_Annotation_Release_101_lncRNA/{refseq}/trackData.json"
-      },
-      {
-         "category" : "NCBI Annotation Release 101/1. Gene Sets/Pseudogenes",
-         "compress" : 0,
-         "key" : "NCBI Predicted pseudogenes, Annotation Release 101",
-         "label" : "NCBI_Annotation_Release_101_Pseudogene",
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "RNA-Seq/Coverage Plots",
+         "key" : "Drofic_ASM1815226v1_RNA-Seq-alignments_2021-10-08_coverage",
+         "label" : "Drofic_ASM1815226v1_RNA-Seq-alignments_2021-10-08_coverage",
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
          "metadata" : {
-            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Drosophila_ficusphila/README_CURRENT_RELEASE",
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-            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346750'>SRR346750</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346751'>SRR346751</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346748'>SRR346748</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346749'>SRR346749</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346752'>SRR346752</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage."
          },
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "description": "product, note, description",
-		"arrowheadClass" : "trellis-arrowhead",
-            "className" : "container-16px",
-            "subfeatureClasses" : {
-               "CDS" : "gnomon_CDS",
-               "UTR" : "gnomon_UTR",
-               "exon" : "container-100pct",
-               "wholeCDS" : null
-            }
+            "pos_color" : "#00BFFF"
          },
-         "trackType" : null,
-         "type" : "FeatureTrack",
-         "urlTemplate" : "tracks/NCBI_Annotation_Release_101_Pseudogene/{refseq}/trackData.json"
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+	"unsafePopup":true,
+         "urlTemplate" : "analyses/Drosophila-ficusphila-RNA-Seq_2021-10-08_v1.0/Drofic_ASM1815226v1_RNA-Seq-alignments_2021-10-08.bigwig"
       },
       {
-         "category" : "NCBI Annotation Release 101/1. Gene Sets/Noncoding",
+         "category" : "RNA-Seq/Splice junctions",
          "compress" : 0,
-         "key" : "NCBI Predicted tRNAs, Annotation Release 101",
-         "label" : "NCBI_Annotation_Release_101_tRNA",
+         "key" : "Drofic_ASM1815226v1_RNA-Seq-alignments_2021-10-08_junctions",
+         "label" : "Drofic_ASM1815226v1_RNA-Seq-alignments_2021-10-08_junctions",
          "metadata" : {
-            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Drosophila_ficusphila/README_CURRENT_RELEASE",
-            "Data provider" : "NCBI",
-            "Data source" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/220/665/GCF_000220665.1_Dfic_2.0/GCF_000220665.1_Dfic_2.0_genomic.gff.gz",
-            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346750'>SRR346750</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346751'>SRR346751</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346748'>SRR346748</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346749'>SRR346749</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346752'>SRR346752</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Junction reads generated by Hisat2 aligner and regtools. The number of alignments supporting the junction read is listed in blue."
          },
          "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "description": "product, note, description",
-		"arrowheadClass" : "trellis-arrowhead",
-            "className" : "container-16px",
-            "subfeatureClasses" : {
-               "CDS" : "gnomon_CDS",
-               "UTR" : "gnomon_UTR",
-               "exon" : "container-100pct",
-               "wholeCDS" : null
-            }
+	     "description":"score",
+            "className" : "feature"
          },
          "trackType" : null,
          "type" : "FeatureTrack",
-         "urlTemplate" : "tracks/NCBI_Annotation_Release_101_tRNA/{refseq}/trackData.json"
+	"unsafePopup":true,
+         "urlTemplate" : "tracks/Drofic_ASM1815226v1_RNA-Seq-alignments_2021-10-08_junctions/{refseq}/trackData.json"
       }
    ]
 }
diff --git a/organisms/stage/Drosophila_kikkawai/trackList.json b/organisms/stage/Drosophila_kikkawai/trackList.json
index ea1281c..a92921c 100644
--- a/organisms/stage/Drosophila_kikkawai/trackList.json
+++ b/organisms/stage/Drosophila_kikkawai/trackList.json
@@ -7,183 +7,169 @@
    "tracks" : [
       {
          "category" : "Reference sequence",
-         "faiUrlTemplate" : "seq/GCF_000224215.1_Dkik_2.0_genomic.fna.fai",
+         "chunkSize" : 20000,
          "key" : "Reference sequence",
          "label" : "DNA",
          "seqType" : "dna",
-         "storeClass" : "JBrowse/Store/Sequence/IndexedFasta",
+         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
          "type" : "SequenceTrack",
-         "urlTemplate" : "seq/GCF_000224215.1_Dkik_2.0_genomic.fna",
-         "useAsRefSeqStore" : 1
+         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-"
       },
       {
-         "category" : "NCBI Annotation Release 101/1. Gene Sets/Protein Coding",
+         "category" : "NCBI Annotation Release 102",
          "compress" : 0,
-         "key" : "NCBI Predicted protein coding genes, Annotation Release 101",
+         "key" : "NCBI_Annotation_Release_102_Gene",
          "label" : "drokik_current_models",
+         "menuTemplate" : [
+             {
+                "label" : "View details"
+             },
+             {
+              "label": "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
+              "title": "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
+              "iconClass" : "dijitIconDatabase",
+              "action": "newWindow",
+              "url" : "function(track,feature){ return 'https://www.ncbi.nlm.nih.gov/nuccore/'+feature.get('name')}"
+              }
+        ],
          "metadata" : {
             "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Drosophila_kikkawai/README_CURRENT_RELEASE",
             "Data provider" : "NCBI",
-            "Data source" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/224/215/GCF_000224215.1_Dkik_2.0/GCF_000224215.1_Dkik_2.0_genomic.gff.gz",
-            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/",
-            "Note" : "Some genes may have non-coding transcripts"
+            "Data source" : "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/018/152/535/GCF_018152535.1_ASM1815253v1/GCF_018152535.1_ASM1815253v1_genomic.gff.gz",
+            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
          },
          "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "description": "product, note, description",
-		"arrowheadClass" : "trellis-arrowhead",
+            "arrowheadClass" : "trellis-arrowhead",
             "className" : "container-16px",
+            "description" : "product, note, description",
             "subfeatureClasses" : {
-               "CDS" : "primary_gene_set-cds",
-               "UTR" : "primary_gene_set-utr",
+               "CDS" : "gnomon_CDS",
+               "UTR" : "gnomon_UTR",
                "exon" : "container-100pct",
                "wholeCDS" : null
             }
          },
-         "trackType" : null,
-         "type" : "FeatureTrack",
+         "trackType" : "HTMLFeatures",
+         "type" : "HTMLFeatures",
          "urlTemplate" : "tracks/drokik_current_models/{refseq}/trackData.json"
       },
       {
-         "autoscale" : "local",
-         "bicolor_pivot" : "zero",
-         "category" : "Reference Assembly",
-         "key" : "Gaps in assembly",
-         "label" : "Gaps in assembly",
+         "category" : "NCBI Annotation Release 102",
+         "compress" : 0,
+         "key" : "NCBI_Annotation_Release_102_Pseudogene",
+         "label" : "NCBI_Annotation_Release_102_Pseudogene",
          "metadata" : {
-            "Track contact" : "The i5k workspace@NAL",
-            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
-            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Drosophila_kikkawai/README_CURRENT_RELEASE",
+            "Data provider" : "NCBI",
+            "Data source" : "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/018/152/535/GCF_018152535.1_ASM1815253v1/GCF_018152535.1_ASM1815253v1_genomic.gff.gz",
+            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
          },
-         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "neg_color" : "white",
-            "pos_color" : "black"
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "container-16px",
+            "description" : "product, note, description",
+            "subfeatureClasses" : {
+               "CDS" : "gnomon_CDS",
+               "UTR" : "gnomon_UTR",
+               "exon" : "container-100pct",
+               "wholeCDS" : null
+            }
          },
-         "type" : "JBrowse/View/Track/Wiggle/Density",
-         "urlTemplate" : "bigwig/GCF_000224215.1_Dkik_2.0_genomic.fna.gaps.bigwig"
+         "trackType" : "HTMLFeatures",
+         "type" : "HTMLFeatures",
+         "urlTemplate" : "tracks/NCBI_Annotation_Release_102_Pseudogene/{refseq}/trackData.json"
       },
       {
          "autoscale" : "local",
          "bicolor_pivot" : "0.5",
          "category" : "Reference Assembly",
          "key" : "GC Content",
-         "scoreType": "avgScore",
-         "scoreType": "avgScore",
          "label" : "GC Content",
          "metadata" : {
             "Track contact" : "The i5k workspace@NAL",
             "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
             "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
          },
+         "scoreType" : "avgScore",
          "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
          "style" : {
             "neg_color" : "rgba(255,255,0,50)",
             "pos_color" : "rgba(0,0,255,50)"
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          "type" : "JBrowse/View/Track/Wiggle/Density",
-         "urlTemplate" : "bigwig/GCF_000224215.1_Dkik_2.0_genomic.fna.gc.bigwig"
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-         "key" : "cDNA match evidence from NCBI Annotation Release 101",
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-            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
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-         },
-         "trackType" : null,
-         "type" : "FeatureTrack",
-         "urlTemplate" : "tracks/NCBI_Annotation_Release_101_cDNA_match/{refseq}/trackData.json"
+         "urlTemplate" : "bigwig/GCF_018152535.1_ASM1815253v1_genomic.fna.gc.bigwig"
       },
       {
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-         "compress" : 0,
-         "key" : "NCBI Predicted lncRNA, Annotation Release 101",
-         "label" : "NCBI_Annotation_Release_101_lncRNA",
+         "category" : "RNA-Seq/Mapped Reads",
+         "key" : "Drokik_ASM1815253v1_RNA-Seq-alignments_2021-08-20",
+         "label" : "Drokik_ASM1815253v1_RNA-Seq-alignments_2021-08-20",
          "metadata" : {
-            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Drosophila_kikkawai/README_CURRENT_RELEASE",
-            "Data provider" : "NCBI",
-            "Data source" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/224/215/GCF_000224215.1_Dkik_2.0/GCF_000224215.1_Dkik_2.0_genomic.gff.gz",
-            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
-         },
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
-         "style" : {
-            "description": "product, note, description",
-		"arrowheadClass" : "trellis-arrowhead",
-            "className" : "container-16px",
-            "subfeatureClasses" : {
-               "CDS" : "gnomon_CDS",
-               "UTR" : "gnomon_UTR",
-               "exon" : "container-100pct",
-               "wholeCDS" : null
-            }
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346731'>SRR346731</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346730'>SRR346730</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346732'>SRR346732</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR15048565'>SRR15048565</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR6161786'>SRR6161786</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Dark red alignments: Mapped portion of read aligned to forward strand<br>Light red alignments: Spliced portion of read aligned to forward strand<br>Dark blue alignments: Mapped portion of read aligned to reverse strand<br>Light blue alignments: Spliced portion of read aligned to reverse strand<br>Red marking - deletion in the read relative to the reference<br>Green marking - insertion in the read relative to the reference<br>Yellow marking  - mismatch (hover over the mismatch to see what the snp is)"
          },
-         "trackType" : null,
-         "type" : "FeatureTrack",
-         "urlTemplate" : "tracks/NCBI_Annotation_Release_101_lncRNA/{refseq}/trackData.json"
+         "unsafePopup": true,
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "analyses/Drosophila-kikkawai-RNA-Seq_2021-08-20_v1.0/Drokik_ASM1815253v1_RNA-Seq-alignments_2021-08-20.bam"
       },
       {
-         "category" : "NCBI Annotation Release 101/1. Gene Sets/Pseudogenes",
-         "compress" : 0,
-         "key" : "NCBI Predicted pseudogenes, Annotation Release 101",
-         "label" : "NCBI_Annotation_Release_101_Pseudogene",
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "RNA-Seq/Coverage Plots",
+         "key" : "Drokik_ASM1815253v1_RNA-Seq-alignments_2021-08-20_coverage",
+         "label" : "Drokik_ASM1815253v1_RNA-Seq-alignments_2021-08-20_coverage",
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "unsafePopup": true,
          "metadata" : {
-            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Drosophila_kikkawai/README_CURRENT_RELEASE",
-            "Data provider" : "NCBI",
-            "Data source" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/224/215/GCF_000224215.1_Dkik_2.0/GCF_000224215.1_Dkik_2.0_genomic.gff.gz",
-            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346731'>SRR346731</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346730'>SRR346730</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346732'>SRR346732</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR15048565'>SRR15048565</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR6161786'>SRR6161786</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage."
          },
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+
          "style" : {
-            "description": "product, note, description",
-		"arrowheadClass" : "trellis-arrowhead",
-            "className" : "container-16px",
-            "subfeatureClasses" : {
-               "CDS" : "gnomon_CDS",
-               "UTR" : "gnomon_UTR",
-               "exon" : "container-100pct",
-               "wholeCDS" : null
-            }
+            "pos_color" : "#00BFFF"
          },
-         "trackType" : null,
-         "type" : "FeatureTrack",
-         "urlTemplate" : "tracks/NCBI_Annotation_Release_101_Pseudogene/{refseq}/trackData.json"
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "analyses/Drosophila-kikkawai-RNA-Seq_2021-08-20_v1.0/Drokik_ASM1815253v1_RNA-Seq-alignments_2021-08-20.bigwig"
       },
       {
-         "category" : "NCBI Annotation Release 101/1. Gene Sets/Noncoding",
+         "category" : "RNA-Seq/Splice junctions",
          "compress" : 0,
-         "key" : "NCBI Predicted tRNAs, Annotation Release 101",
-         "label" : "NCBI_Annotation_Release_101_tRNA",
+         "key" : "Drokik_ASM1815253v1_RNA-Seq-alignments_2021-08-20_junctions",
+         "label" : "Drokik_ASM1815253v1_RNA-Seq-alignments_2021-08-20_junctions",
+         "unsafePopup": true,
          "metadata" : {
-            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Drosophila_kikkawai/README_CURRENT_RELEASE",
-            "Data provider" : "NCBI",
-            "Data source" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/224/215/GCF_000224215.1_Dkik_2.0/GCF_000224215.1_Dkik_2.0_genomic.gff.gz",
-            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346731'>SRR346731</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346730'>SRR346730</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346732'>SRR346732</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR15048565'>SRR15048565</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR6161786'>SRR6161786</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Junction reads generated by Hisat2 aligner and regtools. The number of alignments supporting the junction read is listed in blue."
          },
          "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "description": "product, note, description",
-		"arrowheadClass" : "trellis-arrowhead",
-            "className" : "container-16px",
-            "subfeatureClasses" : {
-               "CDS" : "gnomon_CDS",
-               "UTR" : "gnomon_UTR",
-               "exon" : "container-100pct",
-               "wholeCDS" : null
-            }
+    "subfeatureClasses": {
+      "UTR": "webapollo-UTR",
+      "CDS": "junction-cds",
+      "exon": "container-100pct",
+      "intron": null,
+      "wholeCDS": null,
+      "start_codon": null,
+      "stop_codon": null,
+      "match_part": "darkblue-80pct"
+    },
+	     "description" : "score",
+            "className" : "feature"
          },
          "trackType" : null,
          "type" : "FeatureTrack",
-         "urlTemplate" : "tracks/NCBI_Annotation_Release_101_tRNA/{refseq}/trackData.json"
+         "urlTemplate" : "tracks/Drokik_ASM1815253v1_RNA-Seq-alignments_2021-08-20_junctions/{refseq}/trackData.json"
       }
    ]
 }
diff --git a/organisms/stage/Drosophila_rhopaloa/trackList.json b/organisms/stage/Drosophila_rhopaloa/trackList.json
index 4a5ca3a..ffcaa0e 100644
--- a/organisms/stage/Drosophila_rhopaloa/trackList.json
+++ b/organisms/stage/Drosophila_rhopaloa/trackList.json
@@ -7,183 +7,158 @@
    "tracks" : [
       {
          "category" : "Reference sequence",
-         "faiUrlTemplate" : "seq/GCF_000236305.1_Drho_2.0_genomic.fna.fai",
+         "chunkSize" : 20000,
          "key" : "Reference sequence",
          "label" : "DNA",
          "seqType" : "dna",
-         "storeClass" : "JBrowse/Store/Sequence/IndexedFasta",
+         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
          "type" : "SequenceTrack",
-         "urlTemplate" : "seq/GCF_000236305.1_Drho_2.0_genomic.fna",
-         "useAsRefSeqStore" : 1
+         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-"
       },
       {
-         "category" : "NCBI Annotation Release 101/1. Gene Sets/Protein Coding",
+         "category" : "NCBI Annotation Release 102",
          "compress" : 0,
-         "key" : "NCBI Predicted protein coding genes, Annotation Release 101",
+         "key" : "NCBI_Annotation_Release_102_Gene",
          "label" : "drorho_current_models",
+         "menuTemplate" : [
+             {
+                "label" : "View details"
+             },
+             {
+              "label": "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
+              "title": "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
+              "iconClass" : "dijitIconDatabase",
+              "action": "newWindow",
+              "url" : "function(track,feature){ return 'https://www.ncbi.nlm.nih.gov/nuccore/'+feature.get('name')}"
+              }
+        ],
          "metadata" : {
             "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Drosophila_rhopaloa/README_CURRENT_RELEASE",
             "Data provider" : "NCBI",
-            "Data source" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/236/305/GCF_000236305.1_Drho_2.0/GCF_000236305.1_Drho_2.0_genomic.gff.gz",
-            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/",
-            "Note" : "Some genes may have non-coding transcripts"
+            "Data source" : "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/018/152/115/GCF_018152115.1_ASM1815211v1/GCF_018152115.1_ASM1815211v1_genomic.gff.gz",
+            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
          },
          "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "description": "product, note, description",
-		"arrowheadClass" : "trellis-arrowhead",
+            "arrowheadClass" : "trellis-arrowhead",
             "className" : "container-16px",
+            "description" : "product, note, description",
             "subfeatureClasses" : {
-               "CDS" : "primary_gene_set-cds",
-               "UTR" : "primary_gene_set-utr",
+               "CDS" : "gnomon_CDS",
+               "UTR" : "gnomon_UTR",
                "exon" : "container-100pct",
                "wholeCDS" : null
             }
          },
-         "trackType" : null,
-         "type" : "FeatureTrack",
+         "trackType" : "HTMLFeatures",
+         "type" : "HTMLFeatures",
          "urlTemplate" : "tracks/drorho_current_models/{refseq}/trackData.json"
       },
       {
-         "autoscale" : "local",
-         "bicolor_pivot" : "zero",
-         "category" : "Reference Assembly",
-         "key" : "Gaps in assembly",
-         "label" : "Gaps in assembly",
+         "category" : "NCBI Annotation Release 102",
+         "compress" : 0,
+         "key" : "NCBI_Annotation_Release_102_Pseudogene",
+         "label" : "NCBI_Annotation_Release_102_Pseudogene",
          "metadata" : {
-            "Track contact" : "The i5k workspace@NAL",
-            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
-            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Drosophila_rhopaloa/README_CURRENT_RELEASE",
+            "Data provider" : "NCBI",
+            "Data source" : "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/018/152/115/GCF_018152115.1_ASM1815211v1/GCF_018152115.1_ASM1815211v1_genomic.gff.gz",
+            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
          },
-         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "neg_color" : "white",
-            "pos_color" : "black"
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "container-16px",
+            "description" : "product, note, description",
+            "subfeatureClasses" : {
+               "CDS" : "gnomon_CDS",
+               "UTR" : "gnomon_UTR",
+               "exon" : "container-100pct",
+               "wholeCDS" : null
+            }
          },
-         "type" : "JBrowse/View/Track/Wiggle/Density",
-         "urlTemplate" : "bigwig/GCF_000236305.1_Drho_2.0_genomic.fna.gaps.bigwig"
+         "trackType" : "HTMLFeatures",
+         "type" : "HTMLFeatures",
+         "urlTemplate" : "tracks/NCBI_Annotation_Release_102_Pseudogene/{refseq}/trackData.json"
       },
       {
          "autoscale" : "local",
          "bicolor_pivot" : "0.5",
          "category" : "Reference Assembly",
          "key" : "GC Content",
-         "scoreType": "avgScore",
-         "scoreType": "avgScore",
          "label" : "GC Content",
          "metadata" : {
             "Track contact" : "The i5k workspace@NAL",
             "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
             "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
          },
+         "scoreType" : "avgScore",
          "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
          "style" : {
             "neg_color" : "rgba(255,255,0,50)",
             "pos_color" : "rgba(0,0,255,50)"
          },
          "type" : "JBrowse/View/Track/Wiggle/Density",
-         "urlTemplate" : "bigwig/GCF_000236305.1_Drho_2.0_genomic.fna.gc.bigwig"
+         "urlTemplate" : "bigwig/GCF_018152115.1_ASM1815211v1_genomic.fna.gc.bigwig"
       },
       {
-         "category" : "NCBI Annotation Release 101/2. Evidence",
-         "compress" : 0,
-         "key" : "cDNA match evidence from NCBI Annotation Release 101",
-         "label" : "NCBI_Annotation_Release_101_cDNA_match",
+         "category" : "RNA-Seq/Mapped Reads",
+         "key" : "Drorho_ASM1815211v1_RNA-Seq-alignments_2021-12-20",
+         "label" : "Drorho_ASM1815211v1_RNA-Seq-alignments_2021-12-20",
          "metadata" : {
-            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Drosophila_rhopaloa/README_CURRENT_RELEASE",
-            "Data provider" : "NCBI",
-            "Data source" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/236/305/GCF_000236305.1_Drho_2.0/GCF_000236305.1_Drho_2.0_genomic.gff.gz",
-            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
-         },
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
-         "style" : {
-            "arrowheadClass" : "webapollo-arrowhead",
-            "className" : "container-10px"
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346755'>SRR346755</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346753'>SRR346753</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346754'>SRR346754</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Dark red alignments: Mapped portion of read aligned to forward strand<br>Light red alignments: Spliced portion of read aligned to forward strand<br>Dark blue alignments: Mapped portion of read aligned to reverse strand<br>Light blue alignments: Spliced portion of read aligned to reverse strand<br>Red marking - deletion in the read relative to the reference<br>Green marking - insertion in the read relative to the reference<br>Yellow marking  - mismatch (hover over the mismatch to see what the snp is)"
          },
-         "trackType" : null,
-         "type" : "FeatureTrack",
-         "urlTemplate" : "tracks/NCBI_Annotation_Release_101_cDNA_match/{refseq}/trackData.json"
+	 "unsafePopup": true,
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "analyses/Drosophila-rhopaloa-RNA-Seq_2021-12-20_v1.0/Drorho_ASM1815211v1_RNA-Seq-alignments_2021-12-20.bam"
       },
       {
-         "category" : "NCBI Annotation Release 101/1. Gene Sets/Noncoding",
-         "compress" : 0,
-         "key" : "NCBI Predicted lncRNA, Annotation Release 101",
-         "label" : "NCBI_Annotation_Release_101_lncRNA",
-         "metadata" : {
-            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Drosophila_rhopaloa/README_CURRENT_RELEASE",
-            "Data provider" : "NCBI",
-            "Data source" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/236/305/GCF_000236305.1_Drho_2.0/GCF_000236305.1_Drho_2.0_genomic.gff.gz",
-            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
-         },
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "RNA-Seq/Coverage Plots",
+         "key" : "Drorho_ASM1815211v1_RNA-Seq-alignments_2021-12-20_coverage",
+         "label" : "Drorho_ASM1815211v1_RNA-Seq-alignments_2021-12-20_coverage",
+         "unsafePopup": true,
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
          "style" : {
-            "description": "product, note, description",
-		"arrowheadClass" : "trellis-arrowhead",
-            "className" : "container-16px",
-            "subfeatureClasses" : {
-               "CDS" : "gnomon_CDS",
-               "UTR" : "gnomon_UTR",
-               "exon" : "container-100pct",
-               "wholeCDS" : null
-            }
+            "pos_color" : "#00BFFF"
          },
-         "trackType" : null,
-         "type" : "FeatureTrack",
-         "urlTemplate" : "tracks/NCBI_Annotation_Release_101_lncRNA/{refseq}/trackData.json"
-      },
-      {
-         "category" : "NCBI Annotation Release 101/1. Gene Sets/Pseudogenes",
-         "compress" : 0,
-         "key" : "NCBI Predicted pseudogenes, Annotation Release 101",
-         "label" : "NCBI_Annotation_Release_101_Pseudogene",
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "analyses/Drosophila-rhopaloa-RNA-Seq_2021-12-20_v1.0/Drorho_ASM1815211v1_RNA-Seq-alignments_2021-12-20.bigwig",
          "metadata" : {
-            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Drosophila_rhopaloa/README_CURRENT_RELEASE",
-            "Data provider" : "NCBI",
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-            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
-         },
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
-         "style" : {
-            "description": "product, note, description",
-		"arrowheadClass" : "trellis-arrowhead",
-            "className" : "container-16px",
-            "subfeatureClasses" : {
-               "CDS" : "gnomon_CDS",
-               "UTR" : "gnomon_UTR",
-               "exon" : "container-100pct",
-               "wholeCDS" : null
-            }
-         },
-         "trackType" : null,
-         "type" : "FeatureTrack",
-         "urlTemplate" : "tracks/NCBI_Annotation_Release_101_Pseudogene/{refseq}/trackData.json"
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346755'>SRR346755</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346753'>SRR346753</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346754'>SRR346754</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage."
+         }
       },
       {
-         "category" : "NCBI Annotation Release 101/1. Gene Sets/Noncoding",
+         "category" : "RNA-Seq/Splice junctions",
          "compress" : 0,
-         "key" : "NCBI Predicted tRNAs, Annotation Release 101",
-         "label" : "NCBI_Annotation_Release_101_tRNA",
+         "key" : "Drorho_ASM1815211v1_RNA-Seq-alignments_2021-12-20_junctions",
+         "label" : "Drorho_ASM1815211v1_RNA-Seq-alignments_2021-12-20_junctions",
          "metadata" : {
-            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Drosophila_rhopaloa/README_CURRENT_RELEASE",
-            "Data provider" : "NCBI",
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-            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346755'>SRR346755</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346753'>SRR346753</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346754'>SRR346754</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Junction reads generated by Hisat2 aligner and regtools. The number of alignments supporting the junction read is listed in blue."
          },
+         "unsafePopup": true,
          "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "description": "product, note, description",
-		"arrowheadClass" : "trellis-arrowhead",
-            "className" : "container-16px",
-            "subfeatureClasses" : {
-               "CDS" : "gnomon_CDS",
-               "UTR" : "gnomon_UTR",
-               "exon" : "container-100pct",
-               "wholeCDS" : null
-            }
+            "className" : "feature",
+            "description": "score"
          },
          "trackType" : null,
          "type" : "FeatureTrack",
-         "urlTemplate" : "tracks/NCBI_Annotation_Release_101_tRNA/{refseq}/trackData.json"
+         "urlTemplate" : "tracks/Drorho_ASM1815211v1_RNA-Seq-alignments_2021-12-20_junctions/{refseq}/trackData.json"
       }
    ]
 }
diff --git a/organisms/stage/Drosophila_takahashii/trackList.json b/organisms/stage/Drosophila_takahashii/trackList.json
index 4d8e1c7..92e5a51 100644
--- a/organisms/stage/Drosophila_takahashii/trackList.json
+++ b/organisms/stage/Drosophila_takahashii/trackList.json
@@ -7,183 +7,158 @@
    "tracks" : [
       {
          "category" : "Reference sequence",
-         "faiUrlTemplate" : "seq/GCF_000224235.1_Dtak_2.0_genomic.fna.fai",
+         "chunkSize" : 20000,
          "key" : "Reference sequence",
          "label" : "DNA",
          "seqType" : "dna",
-         "storeClass" : "JBrowse/Store/Sequence/IndexedFasta",
+         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
          "type" : "SequenceTrack",
-         "urlTemplate" : "seq/GCF_000224235.1_Dtak_2.0_genomic.fna",
-         "useAsRefSeqStore" : 1
+         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-"
       },
       {
-         "category" : "NCBI Annotation Release 101/1. Gene Sets/Protein Coding",
+         "category" : "NCBI Annotation Release 102",
          "compress" : 0,
-         "key" : "NCBI Predicted protein coding genes, Annotation Release 101",
+         "key" : "NCBI_Annotation_Release_102_Gene",
          "label" : "drotak_current_models",
+         "menuTemplate" : [
+             {
+                "label" : "View details"
+             },
+             {
+              "label": "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
+              "title": "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
+              "iconClass" : "dijitIconDatabase",
+              "action": "newWindow",
+              "url" : "function(track,feature){ return 'https://www.ncbi.nlm.nih.gov/nuccore/'+feature.get('name')}"
+              }
+        ],
          "metadata" : {
             "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Drosophila_takahashii/README_CURRENT_RELEASE",
             "Data provider" : "NCBI",
-            "Data source" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/224/235/GCF_000224235.1_Dtak_2.0/GCF_000224235.1_Dtak_2.0_genomic.gff.gz",
-            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/",
-            "Note" : "Some genes may have non-coding transcripts"
+            "Data source" : "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/018/152/695/GCF_018152695.1_ASM1815269v1/GCF_018152695.1_ASM1815269v1_genomic.gff.gz",
+            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
          },
          "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "description": "product, note, description",
-		"arrowheadClass" : "trellis-arrowhead",
+            "arrowheadClass" : "trellis-arrowhead",
             "className" : "container-16px",
+            "description" : "product, note, description",
             "subfeatureClasses" : {
-               "CDS" : "primary_gene_set-cds",
-               "UTR" : "primary_gene_set-utr",
+               "CDS" : "gnomon_CDS",
+               "UTR" : "gnomon_UTR",
                "exon" : "container-100pct",
                "wholeCDS" : null
             }
          },
-         "trackType" : null,
-         "type" : "FeatureTrack",
+         "trackType" : "HTMLFeatures",
+         "type" : "HTMLFeatures",
          "urlTemplate" : "tracks/drotak_current_models/{refseq}/trackData.json"
       },
       {
-         "autoscale" : "local",
-         "bicolor_pivot" : "zero",
-         "category" : "Reference Assembly",
-         "key" : "Gaps in assembly",
-         "label" : "Gaps in assembly",
+         "category" : "NCBI Annotation Release 102",
+         "compress" : 0,
+         "key" : "NCBI_Annotation_Release_102_Pseudogene",
+         "label" : "NCBI_Annotation_Release_102_Pseudogene",
          "metadata" : {
-            "Track contact" : "The i5k workspace@NAL",
-            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
-            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Drosophila_takahashii/README_CURRENT_RELEASE",
+            "Data provider" : "NCBI",
+            "Data source" : "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/018/152/695/GCF_018152695.1_ASM1815269v1/GCF_018152695.1_ASM1815269v1_genomic.gff.gz",
+            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
          },
-         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "neg_color" : "white",
-            "pos_color" : "black"
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "container-16px",
+            "description" : "product, note, description",
+            "subfeatureClasses" : {
+               "CDS" : "gnomon_CDS",
+               "UTR" : "gnomon_UTR",
+               "exon" : "container-100pct",
+               "wholeCDS" : null
+            }
          },
-         "type" : "JBrowse/View/Track/Wiggle/Density",
-         "urlTemplate" : "bigwig/GCF_000224235.1_Dtak_2.0_genomic.fna.gaps.bigwig"
+         "trackType" : "HTMLFeatures",
+         "type" : "HTMLFeatures",
+         "urlTemplate" : "tracks/NCBI_Annotation_Release_102_Pseudogene/{refseq}/trackData.json"
       },
       {
          "autoscale" : "local",
          "bicolor_pivot" : "0.5",
          "category" : "Reference Assembly",
          "key" : "GC Content",
-         "scoreType": "avgScore",
-         "scoreType": "avgScore",
          "label" : "GC Content",
          "metadata" : {
             "Track contact" : "The i5k workspace@NAL",
             "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
             "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
          },
+         "scoreType" : "avgScore",
          "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
          "style" : {
             "neg_color" : "rgba(255,255,0,50)",
             "pos_color" : "rgba(0,0,255,50)"
          },
          "type" : "JBrowse/View/Track/Wiggle/Density",
-         "urlTemplate" : "bigwig/GCF_000224235.1_Dtak_2.0_genomic.fna.gc.bigwig"
+         "urlTemplate" : "bigwig/GCF_018152695.1_ASM1815269v1_genomic.fna.gc.bigwig"
       },
       {
-         "category" : "NCBI Annotation Release 101/2. Evidence",
-         "compress" : 0,
-         "key" : "cDNA match evidence from NCBI Annotation Release 101",
-         "label" : "NCBI_Annotation_Release_101_cDNA_match",
+         "category" : "RNA-Seq/Mapped Reads",
+         "key" : "Drotak_ASM1815269v1_RNA-Seq-alignments_2021-12-20",
+         "label" : "Drotak_ASM1815269v1_RNA-Seq-alignments_2021-12-20",
          "metadata" : {
-            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Drosophila_takahashii/README_CURRENT_RELEASE",
-            "Data provider" : "NCBI",
-            "Data source" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/224/235/GCF_000224235.1_Dtak_2.0/GCF_000224235.1_Dtak_2.0_genomic.gff.gz",
-            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
-         },
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
-         "style" : {
-            "arrowheadClass" : "webapollo-arrowhead",
-            "className" : "container-10px"
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346758'>SRR346758</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346756'>SRR346756</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346757'>SRR346757</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Dark red alignments: Mapped portion of read aligned to forward strand<br>Light red alignments: Spliced portion of read aligned to forward strand<br>Dark blue alignments: Mapped portion of read aligned to reverse strand<br>Light blue alignments: Spliced portion of read aligned to reverse strand<br>Red marking - deletion in the read relative to the reference<br>Green marking - insertion in the read relative to the reference<br>Yellow marking  - mismatch (hover over the mismatch to see what the snp is)"
          },
-         "trackType" : null,
-         "type" : "FeatureTrack",
-         "urlTemplate" : "tracks/NCBI_Annotation_Release_101_cDNA_match/{refseq}/trackData.json"
+	  "unsafePopup": true,
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "analyses/Drosophila-takahashii-RNA-Seq_2021-12-20_v1.0/Drotak_ASM1815269v1_RNA-Seq-alignments_2021-12-20.bam"
       },
       {
-         "category" : "NCBI Annotation Release 101/1. Gene Sets/Noncoding",
-         "compress" : 0,
-         "key" : "NCBI Predicted lncRNA, Annotation Release 101",
-         "label" : "NCBI_Annotation_Release_101_lncRNA",
-         "metadata" : {
-            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Drosophila_takahashii/README_CURRENT_RELEASE",
-            "Data provider" : "NCBI",
-            "Data source" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/224/235/GCF_000224235.1_Dtak_2.0/GCF_000224235.1_Dtak_2.0_genomic.gff.gz",
-            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
-         },
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "RNA-Seq/Coverage Plots",
+         "key" : "Drotak_ASM1815269v1_RNA-Seq-alignments_2021-12-20_coverage",
+         "label" : "Drotak_ASM1815269v1_RNA-Seq-alignments_2021-12-20_coverage",
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+	  "unsafePopup": true,
          "style" : {
-            "description": "product, note, description",
-		"arrowheadClass" : "trellis-arrowhead",
-            "className" : "container-16px",
-            "subfeatureClasses" : {
-               "CDS" : "gnomon_CDS",
-               "UTR" : "gnomon_UTR",
-               "exon" : "container-100pct",
-               "wholeCDS" : null
-            }
+            "pos_color" : "#00BFFF"
          },
-         "trackType" : null,
-         "type" : "FeatureTrack",
-         "urlTemplate" : "tracks/NCBI_Annotation_Release_101_lncRNA/{refseq}/trackData.json"
-      },
-      {
-         "category" : "NCBI Annotation Release 101/1. Gene Sets/Pseudogenes",
-         "compress" : 0,
-         "key" : "NCBI Predicted pseudogenes, Annotation Release 101",
-         "label" : "NCBI_Annotation_Release_101_Pseudogene",
          "metadata" : {
-            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Drosophila_takahashii/README_CURRENT_RELEASE",
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-            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
-         },
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
-         "style" : {
-            "description": "product, note, description",
-		"arrowheadClass" : "trellis-arrowhead",
-            "className" : "container-16px",
-            "subfeatureClasses" : {
-               "CDS" : "gnomon_CDS",
-               "UTR" : "gnomon_UTR",
-               "exon" : "container-100pct",
-               "wholeCDS" : null
-            }
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346758'>SRR346758</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346756'>SRR346756</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346757'>SRR346757</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage"
          },
-         "trackType" : null,
-         "type" : "FeatureTrack",
-         "urlTemplate" : "tracks/NCBI_Annotation_Release_101_Pseudogene/{refseq}/trackData.json"
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "analyses/Drosophila-takahashii-RNA-Seq_2021-12-20_v1.0/Drotak_ASM1815269v1_RNA-Seq-alignments_2021-12-20.bigwig"
       },
       {
-         "category" : "NCBI Annotation Release 101/1. Gene Sets/Noncoding",
+         "category" : "RNA-Seq/Splice junctions",
          "compress" : 0,
-         "key" : "NCBI Predicted tRNAs, Annotation Release 101",
-         "label" : "NCBI_Annotation_Release_101_tRNA",
+         "key" : "Drotak_ASM1815269v1_RNA-Seq-alignments_2021-12-20_junctions",
+         "label" : "Drotak_ASM1815269v1_RNA-Seq-alignments_2021-12-20_junctions",
          "metadata" : {
-            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Drosophila_takahashii/README_CURRENT_RELEASE",
-            "Data provider" : "NCBI",
-            "Data source" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/224/235/GCF_000224235.1_Dtak_2.0/GCF_000224235.1_Dtak_2.0_genomic.gff.gz",
-            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346758'>SRR346758</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346756'>SRR346756</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346757'>SRR346757</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Junction reads generated by Hisat2 aligner and regtools. The number of alignments supporting the junction read is listed in blue."
          },
+	  "unsafePopup": true,
          "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "description": "product, note, description",
-		"arrowheadClass" : "trellis-arrowhead",
-            "className" : "container-16px",
-            "subfeatureClasses" : {
-               "CDS" : "gnomon_CDS",
-               "UTR" : "gnomon_UTR",
-               "exon" : "container-100pct",
-               "wholeCDS" : null
-            }
+            "className" : "feature",
+	     "description": "score"
          },
          "trackType" : null,
          "type" : "FeatureTrack",
-         "urlTemplate" : "tracks/NCBI_Annotation_Release_101_tRNA/{refseq}/trackData.json"
+         "urlTemplate" : "tracks/Drotak_ASM1815269v1_RNA-Seq-alignments_2021-12-20_junctions/{refseq}/trackData.json"
       }
    ]
 }
diff --git a/organisms/stage/Dufourea_novaeangliae/trackList.json b/organisms/stage/Dufourea_novaeangliae/trackList.json
index a2d31e0..6f70532 100644
--- a/organisms/stage/Dufourea_novaeangliae/trackList.json
+++ b/organisms/stage/Dufourea_novaeangliae/trackList.json
@@ -1,393 +1,447 @@
 {
+   "alwaysOnTracks" : "DNA,Annotations",
+   "css" : "./plugins/NAL_CSS/css/main.css",
+   "favicon" : "./plugins/WebApollo/img/webapollo_favicon.ico",
+   "formatVersion" : 1,
+   "names" : {
+      "type" : "Hash",
+      "url" : "names/"
+   },
    "share_link" : 0,
-   "css" : "data/contrib_styles.css",
    "tracks" : [
       {
+         "category" : "Reference sequence",
          "chunkSize" : 20000,
+         "key" : "Reference sequence",
+         "label" : "DNA",
          "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
-         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-",
-         "category" : "Reference sequence",
          "type" : "SequenceTrack",
-         "label" : "DNA",
-         "key" : "Reference sequence"
+         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-"
       },
       {
          "autocomplete" : "none",
+         "compress" : 0,
+         "key" : "User-created Annotations",
+         "label" : "Annotations",
+         "phase" : 0,
+         "storeClass" : "WebApollo/Store/SeqFeature/ScratchPad",
          "style" : {
-            "renderClassName" : "annot-render",
-            "className" : "annot",
-            "subfeatureClasses" : {
-               "wholeCDS" : null,
-               "non_canonical_three_prime_splice_site" : "noncanonical-splice-site",
-               "exon" : "container-100pct",
-               "CDS" : "annot-CDS",
-               "UTR" : "annot-UTR",
-               "non_canonical_five_prime_splice_site" : "noncanonical-splice-site"
-            },
             "alternateClasses" : {
-               "transposable_element" : {
-                  "className" : "blue-ibeam",
-                  "renderClassName" : "blue-ibeam-render"
-               },
-               "pseudogene" : {
-                  "className" : "light-purple-80pct",
+               "miRNA" : {
+                  "className" : "brightgreen-80pct",
                   "renderClassName" : "gray-center-30pct"
                },
-               "snRNA" : {
+               "ncRNA" : {
                   "className" : "brightgreen-80pct",
                   "renderClassName" : "gray-center-30pct"
                },
-               "rRNA" : {
-                  "className" : "brightgreen-80pct",
+               "pseudogene" : {
+                  "className" : "light-purple-80pct",
                   "renderClassName" : "gray-center-30pct"
                },
-               "snoRNA" : {
+               "rRNA" : {
                   "className" : "brightgreen-80pct",
                   "renderClassName" : "gray-center-30pct"
                },
                "repeat_region" : {
                   "className" : "magenta-80pct"
                },
-               "miRNA" : {
+               "snRNA" : {
                   "className" : "brightgreen-80pct",
                   "renderClassName" : "gray-center-30pct"
                },
-               "tRNA" : {
+               "snoRNA" : {
                   "className" : "brightgreen-80pct",
                   "renderClassName" : "gray-center-30pct"
                },
-               "ncRNA" : {
+               "tRNA" : {
                   "className" : "brightgreen-80pct",
                   "renderClassName" : "gray-center-30pct"
+               },
+               "transposable_element" : {
+                  "className" : "blue-ibeam",
+                  "renderClassName" : "blue-ibeam-render"
                }
             },
             "arrowheadClass" : "annot-arrowhead",
-            "uniqueIdField" : "id",
             "centerSubFeature" : {
-               "non_canonical_three_prime_splice_site" : false,
-               "non_canonical_five_prime_splice_site" : false
-            }
-         },
-         "key" : "User-created Annotations",
-         "storeClass" : "WebApollo/Store/SeqFeature/ScratchPad",
-         "phase" : 0,
-         "compress" : 0,
-         "label" : "Annotations",
-         "type" : "WebApollo/View/Track/AnnotTrack",
-         "subfeatures" : 1
-      },
-      {
-         "style" : {
-            "className" : "container-16px",
+               "non_canonical_five_prime_splice_site" : false,
+               "non_canonical_three_prime_splice_site" : false
+            },
+            "className" : "annot",
+            "renderClassName" : "annot-render",
             "subfeatureClasses" : {
-               "wholeCDS" : null,
+               "CDS" : "annot-CDS",
+               "UTR" : "annot-UTR",
                "exon" : "container-100pct",
-               "CDS" : "primary_gene_set-cds",
-               "UTR" : "primary_gene_set-utr"
+               "non_canonical_five_prime_splice_site" : "noncanonical-splice-site",
+               "non_canonical_three_prime_splice_site" : "noncanonical-splice-site",
+               "wholeCDS" : null
             },
-            "arrowheadClass" : "trellis-arrowhead"
+            "uniqueIdField" : "id"
          },
-         "key" : "NCBI Dufourea novaeangliae Annotation Release 100",
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
-         "trackType" : null,
-         "urlTemplate" : "tracks/dufnov_current_models/{refseq}/trackData.json",
+         "subfeatures" : 1,
+         "type" : "WebApollo/View/Track/AnnotTrack"
+      },
+      {
+         "category" : "NCBI Annotation Release 100/1. Gene Sets/Protein Coding",
          "compress" : 0,
+         "key" : "NCBI Dufourea novaeangliae Annotation Release 100",
          "label" : "dufnov_current_models",
          "menuTemplate" : [
-             {
-                "label" : "View details",
-             },
-             {
-              "label": "function(track,feature){ return 'Search HymenopteraMine for '+feature.get('name')}",
-              "title": "function(track,feature){ return 'Search HymenopteraMine for '+feature.get('name')}",
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-        ],
+            {
+               "label" : "View details"
+            },
+            {
+               "action" : "newWindow",
+               "iconClass" : "dijitIconDatabase",
+               "label" : "function(track,feature){ return 'Search HymenopteraMine for '+feature.get('id')}",
+               "title" : "function(track,feature){ return 'Search HymenopteraMine for '+feature.get('id')}",
+               "url" : "function(track,feature){ return 'http://128.206.116.3:8080/hymenopteramine/keywordSearchResults.do?searchTerm='+feature.get('id')+'&searchSubmit=Search'}"
+            }
+         ],
          "metadata" : {
-            "Other notes" : "Gff3 file transformed to RefSeq coordinates by NAL",
             "Analysis method" : "Genomic signatures of evolutionary transitions from solitary to group living. Science. 2015 Jun 5;348(6239):1139-43. doi: 10.1126/science.aaa4788. Epub 2015 May 14.",
+            "Data provider" : "Hailin Pan, BGI",
             "Data source" : "http://hymenopteragenome.org/beebase/sites/hymenopteragenome.org.beebase/files/data/consortium_data/Dufourea_novaeangliae_v1.1.gff.gz",
-            "Data provider" : "Hailin Pan, BGI"
+            "Other notes" : "Gff3 file transformed to RefSeq coordinates by NAL"
          },
-         "label" : "Dufourea_novaeangliae_v1.1",
-         "category" : "Dufourea novaeangliae v1.1/1. Gene Sets/Protein Coding"
-      }
-   ],
-   "plugins" : [
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "{type}",
+            "subfeatureClasses" : {
+               "CDS" : "gnomon_CDS",
+               "UTR" : "gnomon_UTR",
+               "exon" : "container-100pct",
+               "wholeCDS" : null
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/Dufourea_novaeangliae_v1.1/{refseq}/trackData.json"
+      },
+      {
+         "category" : "RNA-Seq/Mapped Reads",
+         "key" : "Dufnov_ASM127255v1_RNA-Seq-alignments_2021-06-11",
+         "label" : "Dufnov_ASM127255v1_RNA-Seq-alignments_2021-06-11",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR2001766'>SRR2001766</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR13061845'>SRR13061845</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR13061838'>SRR13061838</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR13061843'>SRR13061843</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR13061836'>SRR13061836</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR13061844'>SRR13061844</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR13061837'>SRR13061837</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR13061840'>SRR13061840</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR13061842'>SRR13061842</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR13061841'>SRR13061841</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Dark red alignments: Mapped portion of read aligned to forward strand<br>Light red alignments: Spliced portion of read aligned to forward strand<br>Dark blue alignments: Mapped portion of read aligned to reverse strand<br>Light blue alignments: Spliced portion of read aligned to reverse strand<br>Red marking - deletion in the read relative to the reference<br>Green marking - insertion in the read relative to the reference<br>Yellow marking  - mismatch (hover over the mismatch to see what the snp is)"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "unsafePopup" : true,
+         "urlTemplate" : "analyses/Dufourea-novaeangliae-RNA-Seq_2021-06-11_v1.0/Dufnov_ASM127255v1_RNA-Seq-alignments_2021-06-11.bam"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "RNA-Seq/Coverage Plots",
+         "key" : "Dufnov_ASM127255v1_RNA-Seq-alignments_2021-06-11_coverage",
+         "label" : "Dufnov_ASM127255v1_RNA-Seq-alignments_2021-06-11_coverage",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR2001766'>SRR2001766</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR13061845'>SRR13061845</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR13061838'>SRR13061838</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR13061843'>SRR13061843</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR13061836'>SRR13061836</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR13061844'>SRR13061844</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR13061837'>SRR13061837</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR13061840'>SRR13061840</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR13061842'>SRR13061842</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR13061841'>SRR13061841</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "unsafePopup" : true,
+         "urlTemplate" : "analyses/Dufourea-novaeangliae-RNA-Seq_2021-06-11_v1.0/Dufnov_ASM127255v1_RNA-Seq-alignments_2021-06-11.bigwig"
+      },
       {
-         "location" : "./plugins/WebApollo",
-         "name" : "WebApollo"
+         "category" : "RNA-Seq/Splice junctions",
+         "compress" : 0,
+         "key" : "Dufnov_ASM127255v1_RNA-Seq-alignments_2021-06-11_junctions",
+         "label" : "Dufnov_ASM127255v1_RNA-Seq-alignments_2021-06-11_junctions",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR2001766'>SRR2001766</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR13061845'>SRR13061845</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR13061838'>SRR13061838</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR13061843'>SRR13061843</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR13061836'>SRR13061836</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR13061844'>SRR13061844</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR13061837'>SRR13061837</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR13061840'>SRR13061840</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR13061842'>SRR13061842</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR13061841'>SRR13061841</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Junction reads generated by Hisat2 aligner and regtools. The number of alignments supporting the junction read is listed in blue."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "className" : "feature",
+            "description" : "score"
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "unsafePopup" : true,
+         "urlTemplate" : "tracks/Dufnov_ASM127255v1_RNA-Seq-alignments_2021-06-11_junctions/{refseq}/trackData.json"
       }
-   ],
-   "names" : {
-      "url" : "names/",
-      "type" : "Hash"
-   },
-   "favicon" : "./plugins/WebApollo/img/webapollo_favicon.ico",
-   "formatVersion" : 1,
-   "alwaysOnTracks" : "DNA,Annotations"
+   ]
 }
diff --git a/organisms/stage/Ephemera_danica/trackList.json b/organisms/stage/Ephemera_danica/trackList.json
index 57037b1..fcbf4ed 100644
--- a/organisms/stage/Ephemera_danica/trackList.json
+++ b/organisms/stage/Ephemera_danica/trackList.json
@@ -46,6 +46,7 @@
             "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
             "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
          },
+         "scoreType" : "avgScore",
          "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
          "style" : {
             "neg_color" : "rgba(255,255,0,50)",
@@ -57,8 +58,21 @@
       {
          "category" : "Official Gene Set",
          "compress" : 0,
+         "fmtDetailValue_Id" : "function (id, feature) {  var name2 = id.replace(/-R./, '');  if(feature.get('type')=='mRNA') {    return '<a target=_blank href=https://i5k.nal.usda.gov/'+name2+'>'+id+'</a>';} else { return id;}}",
          "key" : "OGSv1.0 Gene",
          "label" : "ephdan_current_models",
+         "menuTemplate" : [
+            {
+               "label" : "View details"
+            },
+            {
+               "action" : "newWindow",
+               "iconClass" : "dijitIconDatabase",
+               "label" : "function(track,feature){ return 'Find NCBI record for '+feature.get('id')}",
+               "title" : "function(track,feature){ return 'Find NCBI record for '+feature.get('id')}",
+               "url" : "function(track,feature){ return 'https://www.ncbi.nlm.nih.gov/protein/'+feature.get('id')}"
+            }
+         ],
          "metadata" : {
             "Data description" : "This dataset presents the Ephemera danica Official Gene Set (OGS) v1.0. The OGS is an integration of automatic gene predictions from Ephemera danica genome annotations v0.5.3 (https://10.15482/USDA.ADC/1503792), with manual annotations by the research community (https://data.nal.usda.gov/dataset/ephemera-danica-manual-annotations-genome-assembly-edan10, performed via the Apollo manual curation software, http://genomearchitect.org/).",
             "Data provider" : "i5k Workspace@NAL",
@@ -66,22 +80,9 @@
             "Method" : "Manual and automated annotations were lifted over from genome assembly Ephemera danica genome assembly v1.0 (https://10.15482/USDA.ADC/1503791) to genome assembly Edan_2.0 (https://www.ncbi.nlm.nih.gov/assembly/GCA_000507165.2) using the coordinates_conversion and remap-gff3 programs (https://github.com/NAL-i5K/coordinates_conversion/; https://github.com/NAL-i5K/remap-gff3)"
          },
          "storeClass" : "JBrowse/Store/SeqFeature/NCList",
-   "fmtDetailValue_Id": "function (id, feature) {  var name2 = id.replace(/\-R./, '');  if(feature.get('type')=='mRNA') {    return '<a target=_blank href=https://i5k.nal.usda.gov/'+name2+'>'+id+'</a>';} else { return id;}}",
-   "menuTemplate" : [
-       {
-          "label" : "View details",
-       },
-       {
-        "label": "function(track,feature){ return 'Open gene page for '+feature.get('id').replace(/\-R./, '')}",
-        "title": "function(track,feature){ return 'Open gene page for '+feature.get('id').replace(/\-R./, '')}",
-        "iconClass" : "dijitIconDatabase",
-        "action": "newWindow",
-        "url" : "function(track,feature){ return 'https://i5k.nal.usda.gov/'+feature.get('id').replace(/\-R./, '')}",
-        },
-  ],
          "style" : {
             "arrowheadClass" : "trellis-arrowhead",
-            "className" : "container-16px",
+            "className" : "{type}",
             "description" : "product, note, description",
             "subfeatureClasses" : {
                "CDS" : "gnomon_CDS",
@@ -90,9 +91,68 @@
                "wholeCDS" : null
             }
          },
-         "trackType" : "ColorByType/View/Track/ColorByTypeDraggable",
-         "type" : "ColorByType/View/Track/ColorByTypeDraggable",
+         "trackType" : "HTMLFeatures",
+         "type" : "HTMLFeatures",
          "urlTemplate" : "tracks/ephdan_current_models/{refseq}/trackData.json"
+      },
+      {
+         "category" : "RNA-Seq/Mapped Reads",
+         "key" : "Ephdan_Edan_2.0_RNA-Seq-alignments_2021-06-11",
+         "label" : "Ephdan_Edan_2.0_RNA-Seq-alignments_2021-06-11",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR1793079'>SRR1793079</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR1793080'>SRR1793080</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Dark red alignments: Mapped portion of read aligned to forward strand<br>Light red alignments: Spliced portion of read aligned to forward strand<br>Dark blue alignments: Mapped portion of read aligned to reverse strand<br>Light blue alignments: Spliced portion of read aligned to reverse strand<br>Red marking - deletion in the read relative to the reference<br>Green marking - insertion in the read relative to the reference<br>Yellow marking  - mismatch (hover over the mismatch to see what the snp is)"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "unsafePopup" : true,
+         "urlTemplate" : "analyses/Ephemera-danica-RNA-Seq_2021-06-11_v1.0/Ephdan_Edan_2.0_RNA-Seq-alignments_2021-06-11.bam"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "RNA-Seq/Coverage Plots",
+         "key" : "Ephdan_Edan_2.0_RNA-Seq-alignments_2021-06-11_coverage",
+         "label" : "Ephdan_Edan_2.0_RNA-Seq-alignments_2021-06-11_coverage",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR1793079'>SRR1793079</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR1793080'>SRR1793080</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "unsafePopup" : true,
+         "urlTemplate" : "analyses/Ephemera-danica-RNA-Seq_2021-06-11_v1.0/Ephdan_Edan_2.0_RNA-Seq-alignments_2021-06-11.bigwig"
+      },
+      {
+         "category" : "RNA-Seq/Splice junctions",
+         "compress" : 0,
+         "key" : "Ephdan_Edan_2.0_RNA-Seq-alignments_2021-06-11_junctions",
+         "label" : "Ephdan_Edan_2.0_RNA-Seq-alignments_2021-06-11_junctions",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR1793079'>SRR1793079</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR1793080'>SRR1793080</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Junction reads generated by Hisat2 aligner and regtools. The number of alignments supporting the junction read is listed in blue."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "className" : "feature",
+            "description" : "score"
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "unsafePopup" : true,
+         "urlTemplate" : "tracks/Ephdan_Edan_2.0_RNA-Seq-alignments_2021-06-11_junctions/{refseq}/trackData.json"
       }
    ]
 }
diff --git a/organisms/stage/Eufriesea_mexicana/trackList.json b/organisms/stage/Eufriesea_mexicana/trackList.json
index 89e0854..7c10db4 100644
--- a/organisms/stage/Eufriesea_mexicana/trackList.json
+++ b/organisms/stage/Eufriesea_mexicana/trackList.json
@@ -19,7 +19,7 @@
          "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
             "arrowheadClass" : "trellis-arrowhead",
-            "className" : "container-16px",
+            "className" : "{type}",
             "description" : "product, note, description",
             "subfeatureClasses" : {
                "CDS" : "gnomon_CDS",
@@ -38,17 +38,17 @@
          "key" : "NCBI_Annotation_Release_100_Gene",
          "label" : "NCBI_Annotation_Release_100_Gene",
          "menuTemplate" : [
-             {
-                "label" : "View details",
-             },
-             {
-              "label": "function(track,feature){ return 'Search HymenopteraMine for '+feature.get('name')}",
-              "title": "function(track,feature){ return 'Search HymenopteraMine for '+feature.get('name')}",
-              "iconClass" : "dijitIconDatabase",
-              "action": "newWindow",
-              "url" : "function(track,feature){ return 'http://128.206.116.3:8080/hymenopteramine/keywordSearchResults.do?searchTerm='+feature.get('name')+'&searchSubmit=Search'}",
-              },
-        ],
+            {
+               "label" : "View details"
+            },
+            {
+               "action" : "newWindow",
+               "iconClass" : "dijitIconDatabase",
+               "label" : "function(track,feature){ return 'Search HymenopteraMine for '+feature.get('name')}",
+               "title" : "function(track,feature){ return 'Search HymenopteraMine for '+feature.get('name')}",
+               "url" : "function(track,feature){ return 'http://128.206.116.3:8080/hymenopteramine/keywordSearchResults.do?searchTerm='+feature.get('name')+'&searchSubmit=Search'}"
+            }
+         ],
          "metadata" : {
             "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Eufriesea_mexicana/README_CURRENT_RELEASE",
             "Data provider" : "NCBI",
@@ -58,7 +58,7 @@
          "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
             "arrowheadClass" : "trellis-arrowhead",
-            "className" : "container-16px",
+            "className" : "{type}",
             "description" : "product, note, description",
             "subfeatureClasses" : {
                "CDS" : "gnomon_CDS",
@@ -67,8 +67,8 @@
                "wholeCDS" : null
             }
          },
-         "trackType" : "ColorByType/View/Track/ColorByTypeDraggable",
-         "type" : "ColorByType/View/Track/ColorByTypeDraggable",
+         "trackType" : "HTMLFeatures",
+         "type" : "HTMLFeatures",
          "urlTemplate" : "tracks/NCBI_Annotation_Release_100_Gene/{refseq}/trackData.json"
       },
       {
@@ -83,9 +83,9 @@
          "useAsRefSeqStore" : 1
       },
       {
-         "category" : "Reference sequence",
          "autoscale" : "local",
          "bicolor_pivot" : "zero",
+         "category" : "Reference sequence",
          "key" : "Gaps in assembly",
          "label" : "Gaps in assembly",
          "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
@@ -97,9 +97,9 @@
          "urlTemplate" : "bigwig/GCF_001483705.1_ASM148370v1_genomic.fna.gaps.bigwig"
       },
       {
-         "category" : "Reference sequence",
          "autoscale" : "local",
          "bicolor_pivot" : "0.5",
+         "category" : "Reference sequence",
          "key" : "GC Content",
          "label" : "GC Content",
          "scoreType" : "avgScore",
@@ -117,17 +117,17 @@
          "key" : "Eufriesea_mexicana_v1.2",
          "label" : "Eufriesea_mexicana_v1.2",
          "menuTemplate" : [
-             {
-                "label" : "View details",
-             },
-             {
-              "label": "function(track,feature){ return 'Search HymenopteraMine for '+feature.get('id')}",
-              "title": "function(track,feature){ return 'Search HymenopteraMine for '+feature.get('id')}",
-              "iconClass" : "dijitIconDatabase",
-              "action": "newWindow",
-              "url" : "function(track,feature){ return 'http://128.206.116.3:8080/hymenopteramine/keywordSearchResults.do?searchTerm='+feature.get('id')+'&searchSubmit=Search'}",
-              },
-        ],
+            {
+               "label" : "View details"
+            },
+            {
+               "action" : "newWindow",
+               "iconClass" : "dijitIconDatabase",
+               "label" : "function(track,feature){ return 'Search HymenopteraMine for '+feature.get('id')}",
+               "title" : "function(track,feature){ return 'Search HymenopteraMine for '+feature.get('id')}",
+               "url" : "function(track,feature){ return 'http://128.206.116.3:8080/hymenopteramine/keywordSearchResults.do?searchTerm='+feature.get('id')+'&searchSubmit=Search'}"
+            }
+         ],
          "metadata" : {
             "Data description" : "https://www.ncbi.nlm.nih.gov/pubmed/25977371",
             "Data provider" : "BeeBase",
@@ -137,7 +137,7 @@
          "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
             "arrowheadClass" : "trellis-arrowhead",
-            "className" : "container-16px",
+            "className" : "{type}",
             "subfeatureClasses" : {
                "CDS" : "ogs-cds",
                "UTR" : "ogs-utr",
@@ -148,6 +148,65 @@
          "trackType" : null,
          "type" : "FeatureTrack",
          "urlTemplate" : "tracks/Eufriesea_mexicana_v1.2/{refseq}/trackData.json"
+      },
+      {
+         "category" : "RNA-Seq/Mapped Reads",
+         "key" : "Eufmex_ASM148370v1_RNA-Seq-alignments_2021-06-14",
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diff --git a/organisms/stage/Euglossa_dilemma/trackList.json b/organisms/stage/Euglossa_dilemma/trackList.json
index 5a673cb..4f15480 100644
--- a/organisms/stage/Euglossa_dilemma/trackList.json
+++ b/organisms/stage/Euglossa_dilemma/trackList.json
@@ -1,161 +1,214 @@
 {
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+   "formatVersion" : 1,
+   "names" : {
+      "type" : "Hash",
+      "url" : "names/"
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-   "favicon" : "./plugins/WebApollo/img/webapollo_favicon.ico",
-   "alwaysOnTracks" : "DNA,Annotations",
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diff --git a/organisms/stage/Eurytemora_affinis/trackList.json b/organisms/stage/Eurytemora_affinis/trackList.json
index 457a731..16316c2 100644
--- a/organisms/stage/Eurytemora_affinis/trackList.json
+++ b/organisms/stage/Eurytemora_affinis/trackList.json
@@ -1,1801 +1,1795 @@
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+      "key": "protein2genome_Nematomorpha",
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+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
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+      "key": "protein2genome_Onychophora",
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+      "label": "protein2genome_Parazoa",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
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+        "Track legend": "Results from Protein2genome alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline."
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+      "key": "protein2genome_Placozoa",
+      "label": "protein2genome_Placozoa",
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+      "key": "protein2genome_Platyhelminthes",
+      "label": "protein2genome_Platyhelminthes",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
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+      "key": "protein2genome_Priapulida",
+      "label": "protein2genome_Priapulida",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
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+      "key": "protein2genome_Tardigrada",
+      "label": "protein2genome_Tardigrada",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
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+      "urlTemplate": "tracks/protein2genome_Tardigrada/{refseq}/trackData.json"
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+      "key": "protein2genome_Tunicata",
+      "label": "protein2genome_Tunicata",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
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+      "key": "repeatmasker",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
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+        "arrowheadClass": "webapollo-arrowhead",
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+      "key": "repeatrunner",
+      "label": "repeatrunner",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published - please cite doi: 10.1093/molbev/msx147",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
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diff --git a/organisms/stage/Eurytemora_affinis_-_training/trackList.json b/organisms/stage/Eurytemora_affinis_-_training/trackList.json
index 457a731..16316c2 100644
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+      "key": "protein2genome_Nematomorpha",
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+      "key": "protein2genome_Onychophora",
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+      "key": "protein2genome_Parazoa",
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+      "key": "protein2genome_Placozoa",
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+      "key": "protein2genome_Platyhelminthes",
+      "label": "protein2genome_Platyhelminthes",
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+      "key": "protein2genome_Priapulida",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
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+      "key": "repeatmasker",
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+      "urlTemplate": "user_contributed_data/jmunro/march_2016/VAJU/accepted_hits.bam"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Transcriptome/Coverage Plots (BigWig)",
+      "key": "VAJU_accepted_hits (Coverage Plot)",
+      "label": "VAJU_accepted_hits (Coverage Plot)",
+      "metadata": {
+        "Analysis method": "TopHat v2.0.2",
+        "File provider": "Joana C. Silva , Institute for Genome Sciences, University of Maryland School of Medicine",
+        "Publication status": "Published - please cite doi: 10.1093/molbev/msx147",
+        "Sequencing platform and version": "Illumina Hi-Seq 200 bp",
+        "Sex": "pooled",
+        "Tissues included": "whole animal homogenate",
+        "Track legend": "This track represents an RNA-Seq coverage plot."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "pos_color": "#00BFFF"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "user_contributed_data/jmunro/march_2016/VAJU/accepted_hits.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Transcriptome/Coverage Plots (BigWig)",
+      "key": "UMA_accepted_hits (Coverage Plot)",
+      "label": "UMA_accepted_hits (Coverage Plot)",
+      "metadata": {
+        "Analysis method": "TopHat v2.0.2",
+        "File provider": "Joana C. Silva , Institute for Genome Sciences, University of Maryland School of Medicine",
+        "Publication status": "Published - please cite doi: 10.1093/molbev/msx147",
+        "Sequencing platform and version": "Illumina Hi-Seq 200 bp",
+        "Sex": "pooled",
+        "Tissues included": "whole animal homogenate",
+        "Track legend": "This track represents an RNA-Seq coverage plot."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "pos_color": "#00BFFF"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "user_contributed_data/jmunro/march_2016/UMA/accepted_hits.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Transcriptome/Coverage Plots (BigWig)",
+      "key": "TM_accepted_hits (Coverage Plot)",
+      "label": "TM_accepted_hits (Coverage Plot)",
+      "metadata": {
+        "Analysis method": "TopHat v2.0.2",
+        "File provider": "Joana C. Silva , Institute for Genome Sciences, University of Maryland School of Medicine",
+        "Publication status": "Published - please cite doi: 10.1093/molbev/msx147",
+        "Sequencing platform and version": "Illumina Hi-Seq 200 bp",
+        "Sex": "male",
+        "Tissues included": "whole animal homogenate",
+        "Track legend": "This track represents an RNA-Seq coverage plot."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "pos_color": "#00BFFF"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "user_contributed_data/jmunro/march_2016/TM/accepted_hits.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Transcriptome/Coverage Plots (BigWig)",
+      "key": "VAF_accepted_hits (Coverage Plot)",
+      "label": "VAF_accepted_hits (Coverage Plot)",
+      "metadata": {
+        "Analysis method": "TopHat v2.0.2",
+        "File provider": "Joana C. Silva , Institute for Genome Sciences, University of Maryland School of Medicine",
+        "Publication status": "Published - please cite doi: 10.1093/molbev/msx147",
+        "Sequencing platform and version": "Illumina Hi-Seq 200 bp",
+        "Sex": "female",
+        "Tissues included": "whole animal homogenate",
+        "Track legend": "This track represents an RNA-Seq coverage plot."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "pos_color": "#00BFFF"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "user_contributed_data/jmunro/march_2016/VAF/accepted_hits.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Transcriptome/Coverage Plots (BigWig)",
+      "key": "VAM__accepted_hits (Coverage Plot)",
+      "label": "VAM__accepted_hits (Coverage Plot)",
+      "metadata": {
+        "Analysis method": "TopHat v2.0.2",
+        "File provider": "Joana C. Silva , Institute for Genome Sciences, University of Maryland School of Medicine",
+        "Publication status": "Published - please cite doi: 10.1093/molbev/msx147",
+        "Sequencing platform and version": "Illumina Hi-Seq 200 bp",
+        "Sex": "male",
+        "Tissues included": "whole animal homogenate",
+        "Track legend": "This track represents an RNA-Seq coverage plot."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "pos_color": "#00BFFF"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "user_contributed_data/jmunro/march_2016/VAM/accepted_hits.bigwig"
+    },
+    {
+      "category": "Transcriptome/Assembly",
+      "compress": 0,
+      "key": "075_zz91_transcriptome",
+      "label": "075_zz91_transcriptome",
+      "metadata": {
+        "Analysis method": "GMAP",
+        "File provider": "Joana C. Silva , Institute for Genome Sciences, University of Maryland School of Medicine",
+        "Publication status": "Published - please cite doi: 10.1093/molbev/msx147",
+        "Sequencing platform and version": "Illumina Hi-Seq 200 bp",
+        "Sex": "female",
+        "Tissues included": "whole animal homogenate"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "CDS": "transcriptome-cds",
+          "UTR": "transcriptome-utr",
+          "exon": "container-100pct",
+          "wholeCDS": null
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/075_zz91_transcriptome/{refseq}/trackData.json"
+    },
+    {
+      "category": "Transcriptome/Mapped Reads",
+      "key": "TF1_accepted_hits",
+      "label": "TF1_accepted_hits",
+      "metadata": {
+        "Analysis method": "TopHat v2.0.2",
+        "File provider": "Joana C. Silva , Institute for Genome Sciences, University of Maryland School of Medicine",
+        "Publication status": "Published - please cite doi: 10.1093/molbev/msx147",
+        "Sequencing platform and version": "Illumina Hi-Seq 200 bp",
+        "Sex": "female",
+        "Tissues included": "whole animal homogenate"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "user_contributed_data/jmunro/april_2016/TF_1 accepted_hits.bam"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Transcriptome/Coverage Plots (BigWig)",
+      "key": "TF1_accepted_hits (Coverage Plot)",
+      "label": "TF1_accepted_hits (Coverage Plot)",
+      "metadata": {
+        "Analysis method": "TopHat v2.0.2",
+        "File provider": "Joana C. Silva , Institute for Genome Sciences, University of Maryland School of Medicine",
+        "Publication status": "Published - please cite doi: 10.1093/molbev/msx147",
+        "Sequencing platform and version": "Illumina Hi-Seq 200 bp",
+        "Sex": "female",
+        "Tissues included": "whole animal homogenate"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "pos_color": "#00BFFF"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "user_contributed_data/jmunro/april_2016/TF_1-accepted_hits.bigwig"
+    },
+    {
+      "category": "Transcriptome/Splice Junctions",
+      "compress": 0,
+      "key": "TF1_tophat_junctions",
+      "label": "TF1_tophat_junctions",
+      "metadata": {
+        "Analysis method": "TopHat v2.0.2",
+        "File provider": "Joana C. Silva , Institute for Genome Sciences, University of Maryland School of Medicine",
+        "Publication status": "Published - please cite doi: 10.1093/molbev/msx147",
+        "Sequencing platform and version": "Illumina Hi-Seq 200 bp",
+        "Sex": "female",
+        "Tissues included": "whole animal homogenate"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "CDS": "junction-cds",
+          "UTR": "webapollo-UTR",
+          "exon": "container-100pct",
+          "wholeCDS": null
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/TF1_tophat_junctions/{refseq}/trackData.json"
+    }
+  ]
 }
diff --git a/organisms/stage/Fopius_arisanus/trackList.json b/organisms/stage/Fopius_arisanus/trackList.json
index 88122bd..ca97e03 100644
--- a/organisms/stage/Fopius_arisanus/trackList.json
+++ b/organisms/stage/Fopius_arisanus/trackList.json
@@ -1,432 +1,481 @@
 {
-   "css" : "./plugins/NAL_CSS/css/contrib_styles.css",
+   "alwaysOnTracks" : "DNA,Annotations",
+   "css" : "./plugins/NAL_CSS/css/main.css",
+   "favicon" : "./plugins/WebApollo/img/webapollo_favicon.ico",
+   "formatVersion" : 1,
    "share_link" : 0,
-   "plugins" : [
-      {
-         "location" : "./plugins/WebApollo",
-         "name" : "WebApollo"
-      }
-   ],
    "tracks" : [
       {
-         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
+         "category" : "Reference sequence",
          "chunkSize" : 20000,
-         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-",
+         "key" : "Reference sequence",
          "label" : "DNA",
+         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
          "type" : "SequenceTrack",
-         "category" : "Reference sequence",
-         "key" : "Reference sequence"
+         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-"
       },
       {
          "autocomplete" : "none",
+         "compress" : 0,
+         "key" : "User-created Annotations",
+         "label" : "Annotations",
+         "phase" : 0,
+         "storeClass" : "WebApollo/Store/SeqFeature/ScratchPad",
          "style" : {
-            "className" : "annot",
-            "renderClassName" : "annot-render",
-            "subfeatureClasses" : {
-               "non_canonical_three_prime_splice_site" : "noncanonical-splice-site",
-               "wholeCDS" : null,
-               "exon" : "container-100pct",
-               "CDS" : "annot-CDS",
-               "non_canonical_five_prime_splice_site" : "noncanonical-splice-site",
-               "UTR" : "annot-UTR"
-            },
-            "arrowheadClass" : "annot-arrowhead",
             "alternateClasses" : {
-               "transposable_element" : {
-                  "renderClassName" : "blue-ibeam-render",
-                  "className" : "blue-ibeam"
+               "miRNA" : {
+                  "className" : "brightgreen-80pct",
+                  "renderClassName" : "gray-center-30pct"
                },
-               "pseudogene" : {
-                  "renderClassName" : "gray-center-30pct",
-                  "className" : "light-purple-80pct"
+               "ncRNA" : {
+                  "className" : "brightgreen-80pct",
+                  "renderClassName" : "gray-center-30pct"
                },
-               "snRNA" : {
-                  "renderClassName" : "gray-center-30pct",
-                  "className" : "brightgreen-80pct"
+               "pseudogene" : {
+                  "className" : "light-purple-80pct",
+                  "renderClassName" : "gray-center-30pct"
                },
                "rRNA" : {
-                  "renderClassName" : "gray-center-30pct",
-                  "className" : "brightgreen-80pct"
-               },
-               "snoRNA" : {
-                  "renderClassName" : "gray-center-30pct",
-                  "className" : "brightgreen-80pct"
+                  "className" : "brightgreen-80pct",
+                  "renderClassName" : "gray-center-30pct"
                },
                "repeat_region" : {
                   "className" : "magenta-80pct"
                },
-               "ncRNA" : {
-                  "renderClassName" : "gray-center-30pct",
-                  "className" : "brightgreen-80pct"
+               "snRNA" : {
+                  "className" : "brightgreen-80pct",
+                  "renderClassName" : "gray-center-30pct"
                },
-               "miRNA" : {
-                  "renderClassName" : "gray-center-30pct",
-                  "className" : "brightgreen-80pct"
+               "snoRNA" : {
+                  "className" : "brightgreen-80pct",
+                  "renderClassName" : "gray-center-30pct"
                },
                "tRNA" : {
-                  "renderClassName" : "gray-center-30pct",
-                  "className" : "brightgreen-80pct"
+                  "className" : "brightgreen-80pct",
+                  "renderClassName" : "gray-center-30pct"
+               },
+               "transposable_element" : {
+                  "className" : "blue-ibeam",
+                  "renderClassName" : "blue-ibeam-render"
                }
             },
-            "uniqueIdField" : "id",
+            "arrowheadClass" : "annot-arrowhead",
             "centerSubFeature" : {
-               "non_canonical_three_prime_splice_site" : false,
-               "non_canonical_five_prime_splice_site" : false
-            }
+               "non_canonical_five_prime_splice_site" : false,
+               "non_canonical_three_prime_splice_site" : false
+            },
+            "className" : "annot",
+            "renderClassName" : "annot-render",
+            "subfeatureClasses" : {
+               "CDS" : "annot-CDS",
+               "UTR" : "annot-UTR",
+               "exon" : "container-100pct",
+               "non_canonical_five_prime_splice_site" : "noncanonical-splice-site",
+               "non_canonical_three_prime_splice_site" : "noncanonical-splice-site",
+               "wholeCDS" : null
+            },
+            "uniqueIdField" : "id"
          },
-         "key" : "User-created Annotations",
-         "storeClass" : "WebApollo/Store/SeqFeature/ScratchPad",
-         "phase" : 0,
-         "compress" : 0,
-         "label" : "Annotations",
-         "type" : "WebApollo/View/Track/AnnotTrack",
-         "subfeatures" : 1
+         "subfeatures" : 1,
+         "type" : "WebApollo/View/Track/AnnotTrack"
       },
       {
-         "style" : {
-            "pos_color" : "black",
-            "neg_color" : "white"
-         },
-         "bicolor_pivot" : "zero",
          "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Reference Assembly",
          "key" : "Gaps in assembly",
-         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
-         "urlTemplate" : "bigwig/64838_ref_ASM80636v1_chrUn_refseq_IDS.fa.gaps.bigwig",
          "label" : "Gaps in assembly",
-         "category" : "Reference Assembly",
          "metadata" : {
-            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank",
+            "Track contact" : "The i5k workspace@NAL",
             "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
-            "Track contact" : "The i5k workspace@NAL"
+            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
          },
-         "type" : "JBrowse/View/Track/Wiggle/Density"
-      },
-      {
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
          "style" : {
-            "neg_color" : "rgba(255,255,0,50)",
-            "pos_color" : "rgba(0,0,255,50)"
+            "neg_color" : "white",
+            "pos_color" : "black"
          },
-         "bicolor_pivot" : "0.5",
-         "key" : "GC Content",
-         "scoreType": "avgScore",
+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/64838_ref_ASM80636v1_chrUn_refseq_IDS.fa.gaps.bigwig"
+      },
+      {
          "autoscale" : "local",
-         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
-         "urlTemplate" : "bigwig/64838_ref_ASM80636v1_chrUn_refseq_IDS.fa.gc.bigwig",
+         "bicolor_pivot" : "0.5",
          "category" : "Reference Assembly",
+         "key" : "GC Content",
          "label" : "GC Content",
          "metadata" : {
-            "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track.",
+            "Track contact" : "The i5k workspace@NAL",
             "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
-            "Track contact" : "The i5k workspace@NAL"
+            "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
          },
-         "type" : "JBrowse/View/Track/Wiggle/Density"
-      },
-      {
+         "scoreType" : "avgScore",
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
          "style" : {
-            "className" : "container-16px",
-            "subfeatureClasses" : {
-               "wholeCDS" : null,
-               "exon" : "container-100pct",
-               "CDS" : "gnomon_CDS",
-               "UTR" : "gnomon_UTR"
-            },
-            "arrowheadClass" : "trellis-arrowhead"
+            "neg_color" : "rgba(255,255,0,50)",
+            "pos_color" : "rgba(0,0,255,50)"
          },
-         "key" : "NCBI Predicted protein coding genes, Annotation Release 100",
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
-         "trackType" : null,
-         "urlTemplate" : "tracks/RefSeq_Protein_Coding/{refseq}/trackData.json",
+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/64838_ref_ASM80636v1_chrUn_refseq_IDS.fa.gc.bigwig"
+      },
+      {
+         "category" : "NCBI-RefSeq Annotation Release 100/1. Gene Sets/Protein Coding",
          "compress" : 0,
+         "key" : "NCBI Predicted protein coding genes, Annotation Release 100",
+         "label" : "RefSeq_Protein_Coding",
          "metadata" : {
-            "Data source" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Fopius_arisanus/GFF/ref_ASM80636v1_scaffolds.gff3.gz",
-            "Method" : "http://www.ncbi.nlm.nih.gov/genome/guide/gnomon.shtml; http://www.ncbi.nlm.nih.gov/refseq/about/",
+            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Fopius_arisanus/README_CURRENT_RELEASE",
             "Data provider" : "NCBI",
-            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Fopius_arisanus/README_CURRENT_RELEASE"
+            "Data source" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Fopius_arisanus/GFF/ref_ASM80636v1_scaffolds.gff3.gz",
+            "Method" : "http://www.ncbi.nlm.nih.gov/genome/guide/gnomon.shtml; http://www.ncbi.nlm.nih.gov/refseq/about/"
          },
-         "type" : "FeatureTrack",
-         "category" : "NCBI-RefSeq Annotation Release 100/1. Gene Sets/Protein Coding",
-         "label" : "RefSeq_Protein_Coding"
-      },
-      {
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "className" : "container-16px",
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "{type}",
             "subfeatureClasses" : {
-               "wholeCDS" : null,
-               "exon" : "container-100pct",
                "CDS" : "gnomon_CDS",
-               "UTR" : "gnomon_UTR"
-            },
-            "arrowheadClass" : "trellis-arrowhead"
+               "UTR" : "gnomon_UTR",
+               "exon" : "container-100pct",
+               "wholeCDS" : null
+            }
          },
-         "key" : "NCBI Predicted low-quality protein coding genes, Annotation Release 100",
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "trackType" : null,
-         "urlTemplate" : "tracks/RefSeq_Low_Quality_Protein_Coding/{refseq}/trackData.json",
-         "compress" : 0,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/RefSeq_Protein_Coding/{refseq}/trackData.json"
+      },
+      {
          "category" : "NCBI-RefSeq Annotation Release 100/1. Gene Sets/Protein Coding",
+         "compress" : 0,
+         "key" : "NCBI Predicted low-quality protein coding genes, Annotation Release 100",
          "label" : "RefSeq_Low_Quality_Protein_Coding",
-         "type" : "FeatureTrack",
          "metadata" : {
-            "Method" : "http://www.ncbi.nlm.nih.gov/genome/guide/gnomon.shtml; http://www.ncbi.nlm.nih.gov/refseq/about/",
-            "Data source" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Fopius_arisanus/GFF/ref_ASM80636v1_scaffolds.gff3.gz",
+            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Fopius_arisanus/README_CURRENT_RELEASE",
             "Data provider" : "NCBI",
-            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Fopius_arisanus/README_CURRENT_RELEASE"
-         }
-      },
-      {
+            "Data source" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Fopius_arisanus/GFF/ref_ASM80636v1_scaffolds.gff3.gz",
+            "Method" : "http://www.ncbi.nlm.nih.gov/genome/guide/gnomon.shtml; http://www.ncbi.nlm.nih.gov/refseq/about/"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "className" : "container-16px",
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "{type}",
             "subfeatureClasses" : {
-               "wholeCDS" : null,
-               "exon" : "container-100pct",
                "CDS" : "gnomon_CDS",
-               "UTR" : "gnomon_UTR"
-            },
-            "arrowheadClass" : "trellis-arrowhead"
+               "UTR" : "gnomon_UTR",
+               "exon" : "container-100pct",
+               "wholeCDS" : null
+            }
          },
-         "key" : "NCBI Predicted noncoding RNA, Annotation Release 100",
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "trackType" : null,
-         "urlTemplate" : "tracks/RefSeq_Noncoding_RNA/{refseq}/trackData.json",
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+            "Publication status" : "Published. Calla et al. Transcriptome of the egg parasitoid Fopius arisanus: an important biocontrol tool for Tephritid fruit fly suppression, Gigascience,  2015, 4:36   doi:10.1186/s13742-015-0075-4 (http://www.gigasciencejournal.com/content/4/1/36)",
+            "Sequencing platform and version" : "Illumina HiSeq2000, 2x100 bp PE",
+            "Sex " : "Pool",
+            "Strain" : "Fari_Bdor",
+            "Tissues included" : "Pooled Pupae"
+         },
          "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
-         "urlTemplate" : "user_contributed_data/sgeib/Fari_i5k/pupae_accepted_hits_refSeq_IDs.bigwig",
-
-"category" : "Transcriptome/Coverage Plots (BigWig)",
-"metadata" : {
-	"Geographical location of specimen collection":"Fari Lab colony Bdor adapted, USDA-ARS Pacific Basin Agricultural Research Center, Hilo, HI",
-	"Tissues included":"Pooled Pupae",
-	"Sex ":"Pool",
-	"Strain":"Fari_Bdor",
-	"Other notes":"See publication and NCBI Bioproject for sample details",
-	"NCBI SRA accession #":"SRA: SRX689038",
-	"Sequencing platform and version":"Illumina HiSeq2000, 2x100 bp PE",
-	"Data source URL":"http://www.ncbi.nlm.nih.gov/bioproject/259571",
-	"Publication status":"Published. Calla et al. Transcriptome of the egg parasitoid Fopius arisanus: an important biocontrol tool for Tephritid fruit fly suppression, Gigascience,  2015, 4:36   doi:10.1186/s13742-015-0075-4 (http://www.gigasciencejournal.com/content/4/1/36)",
-	"File provider":"Scott Geib, USDA-ARS-PBARC",
-	"Analysis method":"TopHat v2.0.13",
-	"Date completed":"12/2/15"
-},
          "style" : {
             "pos_color" : "#00BFFF"
          },
-         "label" : "Fari_RNAseq_pupae (Coverage Plot)",
          "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/sgeib/Fari_i5k/pupae_accepted_hits_refSeq_IDs.bigwig"
+      },
+      {
+         "category" : "RNA-Seq/Mapped Reads",
+         "key" : "Fopari_ASM80636v1_RNA-Seq-alignments_2021-06-14",
+         "label" : "Fopari_ASM80636v1_RNA-Seq-alignments_2021-06-14",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR1560653'>SRR1560653</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR1560649'>SRR1560649</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR1560651'>SRR1560651</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR1560650'>SRR1560650</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Dark red alignments: Mapped portion of read aligned to forward strand<br>Light red alignments: Spliced portion of read aligned to forward strand<br>Dark blue alignments: Mapped portion of read aligned to reverse strand<br>Light blue alignments: Spliced portion of read aligned to reverse strand<br>Red marking - deletion in the read relative to the reference<br>Green marking - insertion in the read relative to the reference<br>Yellow marking  - mismatch (hover over the mismatch to see what the snp is)"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "unsafePopup" : true,
+         "urlTemplate" : "analyses/Fopius-arisanus-RNA-Seq_2021-06-14_v1.0/Fopari_ASM80636v1_RNA-Seq-alignments_2021-06-14.bam"
+      },
+      {
+         "autoscale" : "local",
          "bicolor_pivot" : "zero",
-         "key" : "Fari_RNAseq_pupae (Coverage Plot)",
-         "autoscale" : "local"
+         "category" : "RNA-Seq/Coverage Plots",
+         "key" : "Fopari_ASM80636v1_RNA-Seq-alignments_2021-06-14_coverage",
+         "label" : "Fopari_ASM80636v1_RNA-Seq-alignments_2021-06-14_coverage",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR1560653'>SRR1560653</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR1560649'>SRR1560649</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR1560651'>SRR1560651</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR1560650'>SRR1560650</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "unsafePopup" : true,
+         "urlTemplate" : "analyses/Fopius-arisanus-RNA-Seq_2021-06-14_v1.0/Fopari_ASM80636v1_RNA-Seq-alignments_2021-06-14.bigwig"
+      },
+      {
+         "category" : "RNA-Seq/Splice junctions",
+         "compress" : 0,
+         "key" : "Fopari_ASM80636v1_RNA-Seq-alignments_2021-06-14_junctions",
+         "label" : "Fopari_ASM80636v1_RNA-Seq-alignments_2021-06-14_junctions",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR1560653'>SRR1560653</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR1560649'>SRR1560649</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR1560651'>SRR1560651</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR1560650'>SRR1560650</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Junction reads generated by Hisat2 aligner and regtools. The number of alignments supporting the junction read is listed in blue."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "className" : "feature",
+            "description" : "score"
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "unsafePopup" : true,
+         "urlTemplate" : "tracks/Fopari_ASM80636v1_RNA-Seq-alignments_2021-06-14_junctions/{refseq}/trackData.json"
       }
-   ],
-   "favicon" : "./plugins/WebApollo/img/webapollo_favicon.ico",
-   "alwaysOnTracks" : "DNA,Annotations",
-   "formatVersion" : 1
+   ]
 }
diff --git a/organisms/stage/Frankliniella_occidentalis/trackList.json b/organisms/stage/Frankliniella_occidentalis/trackList.json
index bf5ef5e..a21f779 100644
--- a/organisms/stage/Frankliniella_occidentalis/trackList.json
+++ b/organisms/stage/Frankliniella_occidentalis/trackList.json
@@ -45,6 +45,7 @@
             "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
             "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
          },
+         "scoreType" : "avgScore",
          "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
          "style" : {
             "neg_color" : "rgba(255,255,0,50)",
@@ -66,9 +67,9 @@
             {
                "action" : "newWindow",
                "iconClass" : "dijitIconDatabase",
-               "label" : "function(track,feature){ return 'Open gene page for '+feature.get('id').replace(/-R./, '')}",
-               "title" : "function(track,feature){ return 'Open gene page for '+feature.get('id').replace(/-R./, '')}",
-               "url" : "function(track,feature){ return 'https://i5k.nal.usda.gov/'+feature.get('id').replace(/-R./, '')}"
+               "label" : "function(track,feature){ return 'Find NCBI record for '+feature.get('id').replace(/-R./, '')}",
+               "title" : "function(track,feature){ return 'Find NCBI record for '+feature.get('id').replace(/-R./, '')}",
+               "url" : "function(track,feature){ return 'https://www.ncbi.nlm.nih.gov/protein/'+feature.get('id').replace(/-R./, '')}"
             }
          ],
          "metadata" : {
@@ -80,7 +81,7 @@
          "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
             "arrowheadClass" : "trellis-arrowhead",
-            "className" : "container-16px",
+            "className" : "{type}",
             "description" : "product, note, description",
             "subfeatureClasses" : {
                "CDS" : "gnomon_CDS",
@@ -89,8 +90,8 @@
                "wholeCDS" : null
             }
          },
-         "trackType" : "ColorByType/View/Track/ColorByTypeDraggable",
-         "type" : "ColorByType/View/Track/ColorByTypeDraggable",
+         "trackType" : "HTMLFeatures",
+         "type" : "HTMLFeatures",
          "urlTemplate" : "tracks/fraocc_current_models/{refseq}/trackData.json"
       },
       {
@@ -215,18 +216,77 @@
          },
          "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "className" : "container-16px",
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "{type}",
             "subfeatureClasses" : {
-               "wholeCDS" : null,
-               "exon" : "container-100pct",
                "CDS" : "transcriptome-cds",
-               "UTR" : "transcriptome-utr"
-            },
-            "arrowheadClass" : "trellis-arrowhead"
+               "UTR" : "transcriptome-utr",
+               "exon" : "container-100pct",
+               "wholeCDS" : null
+            }
          },
          "trackType" : "null",
          "type" : "FeatureTrack",
          "urlTemplate" : "tracks/KSU_Cufflinks/{refseq}/trackData.json"
+      },
+      {
+         "category" : "RNA-Seq/Mapped Reads",
+         "key" : "Fraocc_Focc_3.0_RNA-Seq-alignments_2021-06-16",
+         "label" : "Fraocc_Focc_3.0_RNA-Seq-alignments_2021-06-16",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR7255049'>SRR7255049</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR1713042'>SRR1713042</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR7140917'>SRR7140917</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR1153459'>SRR1153459</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR1153463'>SRR1153463</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR1821972'>SRR1821972</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR13254810'>SRR13254810</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR1826955'>SRR1826955</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR1151394'>SRR1151394</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR1153466'>SRR1153466</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Dark red alignments: Mapped portion of read aligned to forward strand<br>Light red alignments: Spliced portion of read aligned to forward strand<br>Dark blue alignments: Mapped portion of read aligned to reverse strand<br>Light blue alignments: Spliced portion of read aligned to reverse strand<br>Red marking - deletion in the read relative to the reference<br>Green marking - insertion in the read relative to the reference<br>Yellow marking  - mismatch (hover over the mismatch to see what the snp is)"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "unsafePopup" : true,
+         "urlTemplate" : "analyses/Frankliniella-occidentalis-RNA-Seq_2021-06-16_v1.0/Fraocc_Focc_3.0_RNA-Seq-alignments_2021-06-16.bam"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "RNA-Seq/Coverage Plots",
+         "key" : "Fraocc_Focc_3.0_RNA-Seq-alignments_2021-06-16_coverage",
+         "label" : "Fraocc_Focc_3.0_RNA-Seq-alignments_2021-06-16_coverage",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR7255049'>SRR7255049</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR1713042'>SRR1713042</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR7140917'>SRR7140917</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR1153459'>SRR1153459</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR1153463'>SRR1153463</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR1821972'>SRR1821972</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR13254810'>SRR13254810</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR1826955'>SRR1826955</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR1151394'>SRR1151394</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR1153466'>SRR1153466</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "unsafePopup" : true,
+         "urlTemplate" : "analyses/Frankliniella-occidentalis-RNA-Seq_2021-06-16_v1.0/Fraocc_Focc_3.0_RNA-Seq-alignments_2021-06-16.bigwig"
+      },
+      {
+         "category" : "RNA-Seq/Splice junctions",
+         "compress" : 0,
+         "key" : "Fraocc_Focc_3.0_RNA-Seq-alignments_2021-06-16_junctions",
+         "label" : "Fraocc_Focc_3.0_RNA-Seq-alignments_2021-06-16_junctions",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR7255049'>SRR7255049</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR1713042'>SRR1713042</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR7140917'>SRR7140917</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR1153459'>SRR1153459</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR1153463'>SRR1153463</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR1821972'>SRR1821972</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR13254810'>SRR13254810</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR1826955'>SRR1826955</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR1151394'>SRR1151394</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR1153466'>SRR1153466</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Junction reads generated by Hisat2 aligner and regtools. The number of alignments supporting the junction read is listed in blue."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "className" : "feature",
+            "description" : "score"
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "unsafePopup" : true,
+         "urlTemplate" : "tracks/Fraocc_Focc_3.0_RNA-Seq-alignments_2021-06-16_junctions/{refseq}/trackData.json"
       }
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 }
diff --git a/organisms/stage/Galleria_mellonella/trackList.json b/organisms/stage/Galleria_mellonella/trackList.json
index 5a544d1..dfc68a2 100644
--- a/organisms/stage/Galleria_mellonella/trackList.json
+++ b/organisms/stage/Galleria_mellonella/trackList.json
@@ -45,6 +45,7 @@
             "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
             "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
          },
+         "scoreType" : "avgScore",
          "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
          "style" : {
             "neg_color" : "rgba(255,255,0,50)",
@@ -58,35 +59,28 @@
          "compress" : 0,
          "key" : "NCBI_Annotation_Release_101_Gene",
          "label" : "galmel_current_models",
+         "menuTemplate" : [
+            {
+               "label" : "View details"
+            },
+            {
+               "action" : "newWindow",
+               "iconClass" : "dijitIconDatabase",
+               "label" : "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
+               "title" : "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
+               "url" : "function(track,feature){ return 'https://www.ncbi.nlm.nih.gov/nuccore/'+feature.get('name')}"
+            }
+         ],
          "metadata" : {
             "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Galleria_mellonella/README_CURRENT_RELEASE",
             "Data provider" : "NCBI",
             "Data source" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/640/425/GCF_003640425.2_ASM364042v2/GCF_003640425.2_ASM364042v2_genomic.gff.gz",
             "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
          },
-          "menuTemplate" : [
-             {
-                "label" : "View details",
-             },
-             {
-              "label": "function(track,feature){ return 'Find i5k Workspace gene page for '+feature.get('name')}",
-              "title": "function(track,feature){ return 'Find i5k Workspace gene page for '+feature.get('name')}",
-              "iconClass" : "dijitIconDatabase",
-              "action": "newWindow",
-              "url" : "function(track,feature){ return 'https://i5k.nal.usda.gov/search/site/'+feature.get('name')}",
-              },
-             {
-              "label": "function(track,feature){ return 'Go to NCBI gene page for '+feature.get('name')}",
-              "title": "function(track,feature){ return 'Go to NCBI gene page for '+feature.get('name')}",
-              "iconClass" : "dijitIconDatabase",
-              "action": "newWindow",
-              "url" : "function(track,feature){ return 'https://www.ncbi.nlm.nih.gov/nuccore/'+feature.get('name')}",
-              }
-        ],
          "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
             "arrowheadClass" : "trellis-arrowhead",
-            "className" : "container-16px",
+            "className" : "{type}",
             "description" : "product, note, description",
             "subfeatureClasses" : {
                "CDS" : "gnomon_CDS",
@@ -95,8 +89,8 @@
                "wholeCDS" : null
             }
          },
-         "trackType" : "ColorByType/View/Track/ColorByTypeDraggable",
-         "type" : "ColorByType/View/Track/ColorByTypeDraggable",
+         "trackType" : "HTMLFeatures",
+         "type" : "HTMLFeatures",
          "urlTemplate" : "tracks/galmel_current_models/{refseq}/trackData.json"
       },
       {
@@ -113,7 +107,7 @@
          "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
             "arrowheadClass" : "trellis-arrowhead",
-            "className" : "container-16px",
+            "className" : "{type}",
             "description" : "product, note, description",
             "subfeatureClasses" : {
                "CDS" : "gnomon_CDS",
@@ -125,6 +119,65 @@
          "trackType" : "HTMLFeatures",
          "type" : "HTMLFeatures",
          "urlTemplate" : "tracks/NCBI_Annotation_Release_101_Pseudogene/{refseq}/trackData.json"
+      },
+      {
+         "category" : "RNA-Seq/Mapped Reads",
+         "key" : "Galmel_ASM364042v2_RNA-Seq-alignments_2021-07-03",
+         "label" : "Galmel_ASM364042v2_RNA-Seq-alignments_2021-07-03",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR5590482'>SRR5590482</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR5590491'>SRR5590491</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR8307568'>SRR8307568</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11446320'>SRR11446320</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR5590472'>SRR5590472</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR12236965'>SRR12236965</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR12236963'>SRR12236963</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR12236970'>SRR12236970</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR5590492'>SRR5590492</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR6365216'>SRR6365216</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Dark red alignments: Mapped portion of read aligned to forward strand<br>Light red alignments: Spliced portion of read aligned to forward strand<br>Dark blue alignments: Mapped portion of read aligned to reverse strand<br>Light blue alignments: Spliced portion of read aligned to reverse strand<br>Red marking - deletion in the read relative to the reference<br>Green marking - insertion in the read relative to the reference<br>Yellow marking  - mismatch (hover over the mismatch to see what the snp is)"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
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+         "unsafePopup" : true,
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diff --git a/organisms/stage/Gerris_buenoi/trackList.json b/organisms/stage/Gerris_buenoi/trackList.json
index dbf8b57..ffb36c7 100644
--- a/organisms/stage/Gerris_buenoi/trackList.json
+++ b/organisms/stage/Gerris_buenoi/trackList.json
@@ -1,1416 +1,1311 @@
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-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
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-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
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+      "label": "blastx_Cephalochordata",
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+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Blastx alignments of a set of Cephalochordata proteins as part of the MAKER automated annotation pipeline."
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+        "arrowheadClass": "webapollo-arrowhead",
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-        "Track legend" : "Results from Blastx alignments of a set of Crustacea proteins as part of the MAKER automated annotation pipeline.", 
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-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
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+      "key": "blastx_Chelicerata",
+      "label": "blastx_Chelicerata",
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+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Blastx alignments of a set of Chelicerata proteins as part of the MAKER automated annotation pipeline."
+      },
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     },
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-        "Track legend" : "Results from Blastx alignments of a set of Echinodermata proteins as part of the MAKER automated annotation pipeline.", 
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-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
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+      "key": "blastx_Cnidaria",
+      "label": "blastx_Cnidaria",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Blastx alignments of a set of Cnidaria proteins as part of the MAKER automated annotation pipeline."
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     },
-         "key" : "blastx_Echinodermata",
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-
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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-         "urlTemplate" : "tracks/blastx_Echinodermata/{refseq}/trackData.json",
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-      },
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-               "match_part" : "blastx"
-            },
-            "arrowheadClass" : "webapollo-arrowhead"
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-        "Track legend" : "Results from Blastx alignments of a set of Mollusca proteins as part of the MAKER automated annotation pipeline.", 
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
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-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
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+      "category": "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX",
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+      "key": "blastx_Craniata",
+      "label": "blastx_Craniata",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Blastx alignments of a set of Craniata proteins as part of the MAKER automated annotation pipeline."
+      },
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     },
-         "key" : "blastx_Mollusca",
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-
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
-         "trackType" : null,
-         "urlTemplate" : "tracks/blastx_Mollusca/{refseq}/trackData.json",
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-      {
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-            "subfeatureClasses" : {
-               "match_part" : "blastx"
-            },
-            "arrowheadClass" : "webapollo-arrowhead"
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-	         "metadata" : {
-        "Track legend" : "Results from Blastx alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline.", 
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-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
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+      "category": "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX",
+      "compress": 0,
+      "key": "blastx_Crustacea",
+      "label": "blastx_Crustacea",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Blastx alignments of a set of Crustacea proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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+          "match_part": "blastx"
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+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/blastx_Crustacea/{refseq}/trackData.json"
     },
-         "key" : "blastx_Nemata",
-
-
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
-         "trackType" : null,
-         "urlTemplate" : "tracks/blastx_Nemata/{refseq}/trackData.json",
-         "compress" : 0,
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-         "label" : "blastx_Nemata"
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-               "match_part" : "blastx"
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-            "arrowheadClass" : "webapollo-arrowhead"
-         },
-	 "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX",
-	         "metadata" : {
-        "Track legend" : "Results from Blastx alignments of a set of Nematomorpha proteins as part of the MAKER automated annotation pipeline.", 
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
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+      "category": "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX",
+      "compress": 0,
+      "key": "blastx_Echinodermata",
+      "label": "blastx_Echinodermata",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Blastx alignments of a set of Echinodermata proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
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+        "arrowheadClass": "webapollo-arrowhead",
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+          "match_part": "blastx"
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+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/blastx_Echinodermata/{refseq}/trackData.json"
     },
-         "key" : "blastx_Nematomorpha",
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-
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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-         "urlTemplate" : "tracks/blastx_Nematomorpha/{refseq}/trackData.json",
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-         "type" : "FeatureTrack",
-         "label" : "blastx_Nematomorpha"
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-               "match_part" : "blastx"
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-            "arrowheadClass" : "webapollo-arrowhead"
-         },
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-        "Track legend" : "Results from Blastx alignments of a set of Onychophora proteins as part of the MAKER automated annotation pipeline.", 
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
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+      "category": "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX",
+      "compress": 0,
+      "key": "blastx_Mollusca",
+      "label": "blastx_Mollusca",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Blastx alignments of a set of Mollusca proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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+          "match_part": "blastx"
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+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/blastx_Mollusca/{refseq}/trackData.json"
     },
-         "key" : "blastx_Onychophora",
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-
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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-         "urlTemplate" : "tracks/blastx_Onychophora/{refseq}/trackData.json",
-         "compress" : 0,
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-         "label" : "blastx_Onychophora"
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-               "match_part" : "blastx"
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-            "arrowheadClass" : "webapollo-arrowhead"
-         },
-	 "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX",
-	         "metadata" : {
-        "Track legend" : "Results from Blastx alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline.", 
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
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+      "category": "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX",
+      "compress": 0,
+      "key": "blastx_Nemata",
+      "label": "blastx_Nemata",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Blastx alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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+          "match_part": "blastx"
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+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/blastx_Nemata/{refseq}/trackData.json"
     },
-         "key" : "blastx_Parazoa",
-
-
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
-         "trackType" : null,
-         "urlTemplate" : "tracks/blastx_Parazoa/{refseq}/trackData.json",
-         "compress" : 0,
-         "type" : "FeatureTrack",
-         "label" : "blastx_Parazoa"
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-      {
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-               "match_part" : "blastx"
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-         },
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-	         "metadata" : {
-        "Track legend" : "Results from Blastx alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline.", 
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
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+      "key": "blastx_Nematomorpha",
+      "label": "blastx_Nematomorpha",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Blastx alignments of a set of Nematomorpha proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
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+        "arrowheadClass": "webapollo-arrowhead",
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+      "type": "FeatureTrack",
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     },
-         "key" : "blastx_Placozoa",
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-
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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-         "urlTemplate" : "tracks/blastx_Placozoa/{refseq}/trackData.json",
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-         "label" : "blastx_Placozoa"
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-               "match_part" : "blastx"
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-            "arrowheadClass" : "webapollo-arrowhead"
-         },
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-	         "metadata" : {
-        "Track legend" : "Results from Blastx alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline.", 
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
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+      "category": "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX",
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+      "key": "blastx_Onychophora",
+      "label": "blastx_Onychophora",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Blastx alignments of a set of Onychophora proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
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+        "arrowheadClass": "webapollo-arrowhead",
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+          "match_part": "blastx"
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+      },
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/blastx_Onychophora/{refseq}/trackData.json"
     },
-         "key" : "blastx_Platyhelminthes",
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-
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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-         "urlTemplate" : "tracks/blastx_Platyhelminthes/{refseq}/trackData.json",
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+        "Track legend": "Results from Blastx alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline."
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+      "key": "protein2genome_Arthropoda",
+      "label": "protein2genome_Arthropoda",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Arthropoda proteins as part of the MAKER automated annotation pipeline."
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-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
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-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
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+      "key": "protein2genome_Atelocerata",
+      "label": "protein2genome_Atelocerata",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Atelocerata proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
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+        "arrowheadClass": "webapollo-arrowhead",
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-        "Track legend" : "Results from Protein2genome alignments of a set of Crustacea proteins as part of the MAKER automated annotation pipeline.",
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
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+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+      "key": "protein2genome_Cephalochordata",
+      "label": "protein2genome_Cephalochordata",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Cephalochordata proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
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+        "arrowheadClass": "webapollo-arrowhead",
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-               "match_part" : "protein2genome"
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-	 "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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-        "Track legend" : "Results from Protein2genome alignments of a set of Echinodermata proteins as part of the MAKER automated annotation pipeline.",
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
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+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Chelicerata",
+      "label": "protein2genome_Chelicerata",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Chelicerata proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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+          "match_part": "protein2genome"
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+      "type": "FeatureTrack",
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     },
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-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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-         "urlTemplate" : "tracks/protein2genome_Echinodermata/{refseq}/trackData.json",
-         "compress" : 0,
-         "type" : "FeatureTrack",
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-            "subfeatureClasses" : {
-               "match_part" : "protein2genome"
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-            "arrowheadClass" : "webapollo-arrowhead"
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-	 "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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-        "Track legend" : "Results from Protein2genome alignments of a set of Mollusca proteins as part of the MAKER automated annotation pipeline.",
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
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+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Cnidaria",
+      "label": "protein2genome_Cnidaria",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Cnidaria proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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+          "match_part": "protein2genome"
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+      "type": "FeatureTrack",
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-               "match_part" : "protein2genome"
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-            "arrowheadClass" : "webapollo-arrowhead"
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-	 "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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-        "Track legend" : "Results from Protein2genome alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline.",
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
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+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+      "key": "protein2genome_Craniata",
+      "label": "protein2genome_Craniata",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Craniata proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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+          "match_part": "protein2genome"
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+      "type": "FeatureTrack",
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-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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-         "urlTemplate" : "tracks/protein2genome_Nemata/{refseq}/trackData.json",
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-      {
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-            "subfeatureClasses" : {
-               "match_part" : "protein2genome"
-            },
-            "arrowheadClass" : "webapollo-arrowhead"
-         },
-	 "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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-        "Track legend" : "Results from Protein2genome alignments of a set of Nematomorpha proteins as part of the MAKER automated annotation pipeline.",
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
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+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Crustacea",
+      "label": "protein2genome_Crustacea",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Crustacea proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
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+          "match_part": "protein2genome"
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+      },
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Crustacea/{refseq}/trackData.json"
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-               "match_part" : "protein2genome"
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-        "Track legend" : "Results from Protein2genome alignments of a set of Onychophora proteins as part of the MAKER automated annotation pipeline.",
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
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+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Echinodermata",
+      "label": "protein2genome_Echinodermata",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Echinodermata proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Echinodermata/{refseq}/trackData.json"
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-               "match_part" : "protein2genome"
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-            "arrowheadClass" : "webapollo-arrowhead"
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-	 "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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-        "Track legend" : "Results from Protein2genome alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline.",
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
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+      "compress": 0,
+      "key": "protein2genome_Mollusca",
+      "label": "protein2genome_Mollusca",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Mollusca proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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+          "match_part": "protein2genome"
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+      "type": "FeatureTrack",
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     },
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-               "match_part" : "protein2genome"
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-	 "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
-	         "metadata" : {
-        "Track legend" : "Results from Protein2genome alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline.",
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
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+      "key": "protein2genome_Nemata",
+      "label": "protein2genome_Nemata",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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+          "match_part": "protein2genome"
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-               "match_part" : "protein2genome"
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-            "arrowheadClass" : "webapollo-arrowhead"
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-	 "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
-	         "metadata" : {
-        "Track legend" : "Results from Protein2genome alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline.",
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
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+      "key": "protein2genome_Nematomorpha",
+      "label": "protein2genome_Nematomorpha",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Nematomorpha proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
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     },
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-               "match_part" : "protein2genome"
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-         },
-	 "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
-	         "metadata" : {
-        "Track legend" : "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline.",
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Onychophora",
+      "label": "protein2genome_Onychophora",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Onychophora proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Onychophora/{refseq}/trackData.json"
     },
-         "key" : "protein2genome_Priapulida",
-
-
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
-         "trackType" : null,
-         "urlTemplate" : "tracks/protein2genome_Priapulida/{refseq}/trackData.json",
-         "compress" : 0,
-         "type" : "FeatureTrack",
-         "label" : "protein2genome_Priapulida"
-      },
-      {
-         "style" : {
-            "className" : "container-10px",
-            "subfeatureClasses" : {
-               "match_part" : "protein2genome"
-            },
-            "arrowheadClass" : "webapollo-arrowhead"
-         },
-	 "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
-	         "metadata" : {
-        "Track legend" : "Results from Protein2genome alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline.",
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Parazoa",
+      "label": "protein2genome_Parazoa",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Parazoa/{refseq}/trackData.json"
     },
-         "key" : "protein2genome_Tardigrada",
-
-
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
-         "trackType" : null,
-         "urlTemplate" : "tracks/protein2genome_Tardigrada/{refseq}/trackData.json",
-         "compress" : 0,
-         "type" : "FeatureTrack",
-         "label" : "protein2genome_Tardigrada"
-      },
-      {
-         "style" : {
-            "className" : "container-10px",
-            "subfeatureClasses" : {
-               "match_part" : "protein2genome"
-            },
-            "arrowheadClass" : "webapollo-arrowhead"
-         },
-	 "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
-	         "metadata" : {
-        "Track legend" : "Results from Protein2genome alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline.",
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Placozoa",
+      "label": "protein2genome_Placozoa",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Placozoa/{refseq}/trackData.json"
     },
-         "key" : "protein2genome_Tunicata",
-
-
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
-         "trackType" : null,
-         "urlTemplate" : "tracks/protein2genome_Tunicata/{refseq}/trackData.json",
-         "compress" : 0,
-         "type" : "FeatureTrack",
-         "label" : "protein2genome_Tunicata"
-      },
-      {
-         "style" : {
-            "className" : "container-10px",
-            "subfeatureClasses" : {
-               "match_part" : "protein2genome"
-            },
-            "arrowheadClass" : "webapollo-arrowhead"
-         },
-	 "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
-	         "metadata" : {
-        "Track legend" : "Results from Protein2genome alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline.",
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Platyhelminthes",
+      "label": "protein2genome_Platyhelminthes",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Platyhelminthes/{refseq}/trackData.json"
     },
-         "key" : "protein2genome_UNCATEGORISED",
-
-
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
-         "trackType" : null,
-         "urlTemplate" : "tracks/protein2genome_UNCATEGORISED/{refseq}/trackData.json",
-         "compress" : 0,
-         "type" : "FeatureTrack",
-         "label" : "protein2genome_UNCATEGORISED"
-      },
-      {
-         "style" : {
-            "className" : "container-10px",
-            "subfeatureClasses" : {
-               "match_part" : "repeat"
-            },
-            "arrowheadClass" : "webapollo-arrowhead"
-         },
-	 "category" : "BCM_v0.5.3/2. Evidence/Repeats",
-	        "metadata" : {
-        "Track legend" : "Results from RepeatMasker as part of the MAKER automated annotation pipeline.",
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Priapulida",
+      "label": "protein2genome_Priapulida",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Priapulida/{refseq}/trackData.json"
     },
-         "key" : "repeatmasker",
-
-
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
-         "trackType" : null,
-         "urlTemplate" : "tracks/repeatmasker/{refseq}/trackData.json",
-         "compress" : 0,
-         "type" : "FeatureTrack",
-         "label" : "repeatmasker"
-      },
-      {
-         "style" : {
-            "className" : "container-10px",
-            "subfeatureClasses" : {
-               "match_part" : "repeat"
-            },
-            "arrowheadClass" : "webapollo-arrowhead"
-         },
-	 "category" : "BCM_v0.5.3/2. Evidence/Repeats",
-	        "metadata" : {
-        "Track legend" : "Results from Repeatrunner as part of the MAKER automated annotation pipeline.",
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Tardigrada",
+      "label": "protein2genome_Tardigrada",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Tardigrada/{refseq}/trackData.json"
     },
-         "key" : "repeatrunner",
-
-
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
-         "trackType" : null,
-         "urlTemplate" : "tracks/repeatrunner/{refseq}/trackData.json",
-         "compress" : 0,
-         "type" : "FeatureTrack",
-         "label" : "repeatrunner"
-      },
-      {
-         "style" : {
-            "className" : "container-10px",
-            "subfeatureClasses" : {
-               "match_part" : "snap"
-            },
-            "arrowheadClass" : "webapollo-arrowhead"
-         },
-	 "category" : "BCM_v0.5.3/1. Gene Sets/Supplementary Gene Predictions",
-	        "metadata" : {
-        "Track legend" : "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline.",
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Tunicata",
+      "label": "protein2genome_Tunicata",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Tunicata/{refseq}/trackData.json"
     },
-         "key" : "snap_masked",
-
-
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
-         "trackType" : null,
-         "urlTemplate" : "tracks/snap_masked/{refseq}/trackData.json",
-         "compress" : 0,
-         "type" : "FeatureTrack",
-         "label" : "snap_masked"
-      },
-      {
-         "style" : {
-            "pos_color" : "black",
-            "neg_color" : "white"
-         },
-         "bicolor_pivot" : "zero",
-         "autoscale" : "local",
-	 "category" : "Reference Assembly",
-	        "metadata" : {
-        "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank",
-        "Track contact" : "The i5k workspace@NAL",
-        "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
-},
-         "key" : "Gaps in assembly",
-
-
-         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
-         "urlTemplate" : "bigwig/Gbue.scaffolds.50.fa.gaps.bigwig",
-         "label" : "Gaps in assembly",
-         "type" : "JBrowse/View/Track/Wiggle/Density"
-      },
-      {
-         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
-         "urlTemplate" : "bam/darmisen/Gbue_ICD_GBi5AK.bam",
-         "metadata" : {
-            "Track legend" : "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)",
-            "Data source 1" : "http://de.iplantcollaborative.org/dl/d/0058E2C3-0661-4F81-9AF3-E0DC790885DD/Gbue_ICD_GBi5AK.T7-mix-emb-ny-1M-1F-cross-2-1_1pA_D2FUUACXX-3-ID10_1_sequence.txt",
-            "Data source 2" : "http://de.iplantcollaborative.org/dl/d/F5E1D612-1F2F-48DA-88FF-9F321A4988AD/Gbue_ICD_GBi5AK.T7-mix-emb-ny-1M-1F-cross-2-1_1pA_D2FUUACXX-3-ID10_2_sequence.txt",
-            "File provider" : "David Armisen, Institut de genomique fonctionelle de Lyon",
-            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
-            "Alignment method" : "Tophat 2.0.9, in iPlant Discovery Enviroment",
-	    	       "Alignment parameters": "--align_reads 'serial' --mate-inner-dist '50' --file_query 'Gbue_ICD_GBi5AK.T7-mix-emb-ny-1M-1F-cross-2-1_1pA_D2FUUACXX-3-ID10_1_sequence.txt' --file_query2 'Gbue_ICD_GBi5AK.T7-mix-emb-ny-1M-1F-cross-2-1_1pA_D2FUUACXX-3-ID10_2_sequence.txt' --library-type  'fr-unstranded' --min-anchor-length  '8' --splice-mismatches  '0' --min-intron-length  '70' --max-intron-length  '50000' --min-isoform-fraction  '0.15' --max-multihits  '20' --min-segment-intron  '50' --max-segment-intron  '500000' --segment-mismatches  '2' --segment-length  '20' --num-threads  '6' --user_database 'Gbue.scaffolds.50.fa' --b2-sensitive  --tophat_version '2.0.9' --bowtie_version '2.1.0'"
-         },
-         "category" : "Transcriptome/Mapped Reads",
-         "type" : "WebApollo/View/Track/DraggableAlignments",
-         "label" : "PE_reads_i5k_RNA-Seq",
-         "key" : "PE reads i5k - RNA-Seq"
-      },
-      {
-         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
-         "urlTemplate" : "bigwig/darmisen/Gbue_ICD_GBi5AK.bigwig",
-         "style" : {
-            "clip_marker_color": "red",
-            "height": 75,
-            "bg_color": "rgba(230,230,230,0.6)",
-            "neg_color" : "#0086B3",
-            "pos_color" : "#00BFFF"
-         },
-         "metadata" : {
-            "Track legend" : "This track represents an X-Y plot plot of RNA-Seq coverage. Secondary and supplementary alignments, as well as optical PCR duplicates and alignments failing QC are not included in the coverage calculations.",
-            "Data source 1" : "http://de.iplantcollaborative.org/dl/d/0058E2C3-0661-4F81-9AF3-E0DC790885DD/Gbue_ICD_GBi5AK.T7-mix-emb-ny-1M-1F-cross-2-1_1pA_D2FUUACXX-3-ID10_1_sequence.txt",
-            "Data source 2" : "http://de.iplantcollaborative.org/dl/d/F5E1D612-1F2F-48DA-88FF-9F321A4988AD/Gbue_ICD_GBi5AK.T7-mix-emb-ny-1M-1F-cross-2-1_1pA_D2FUUACXX-3-ID10_2_sequence.txt",
-            "File provider" : "David Armisen, Institut de genomique fonctionelle de Lyon",
-            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
-            "Alignment method" : "Tophat 2.0.9, in iPlant Discovery Enviroment",
-	    	       "Alignment parameters": "--align_reads 'serial' --mate-inner-dist '50' --file_query 'Gbue_ICD_GBi5AK.T7-mix-emb-ny-1M-1F-cross-2-1_1pA_D2FUUACXX-3-ID10_1_sequence.txt' --file_query2 'Gbue_ICD_GBi5AK.T7-mix-emb-ny-1M-1F-cross-2-1_1pA_D2FUUACXX-3-ID10_2_sequence.txt' --library-type  'fr-unstranded' --min-anchor-length  '8' --splice-mismatches  '0' --min-intron-length  '70' --max-intron-length  '50000' --min-isoform-fraction  '0.15' --max-multihits  '20' --min-segment-intron  '50' --max-segment-intron  '500000' --segment-mismatches  '2' --segment-length  '20' --num-threads  '6' --user_database 'Gbue.scaffolds.50.fa' --b2-sensitive  --tophat_version '2.0.9' --bowtie_version '2.1.0'"
-         },
-           "category": "Transcriptome/Coverage plots (BigWig)",
-           "label" : "PE reads i5k - RNA-Seq coverage",
-           "type" : "JBrowse/View/Track/Wiggle/XYPlot",
-           "bicolor_pivot" : "zero",
-           "key" : "PE reads i5k - RNA-Seq coverage",
-           "autoscale" : "local"
-      },
-      {
-         "category" : "Official Gene Set v1.0/1. Gene Sets/Protein Coding",
-         "compress" : 0,
-         "key" : "Gerris buenoi Official Gene Set v1.0, protein-coding genes",
-         "label" : "gerbue_current_models",
-         "metadata" : {
-            "Data description" : "https://doi.org/10.1101/242230",
-            "Data provider" : "The i5k Workspace@NAL",
-            "Data source" : "https://doi.org/10.15482/USDA.ADC/1423873",
-            "Method" : "https://github.com/NAL-i5K/GFF3toolkit",
-            "publication status" : "Published, please cite https://doi.org/10.1101/242230 or https://doi.org/10.15482/USDA.ADC/1423873"
-         },
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
-         "style" : {
-            "arrowheadClass" : "trellis-arrowhead",
-            "className" : "container-16px",
-            "subfeatureClasses" : {
-               "CDS" : "ogs-cds",
-               "UTR" : "ogs-utr",
-               "exon" : "container-100pct",
-               "five_prime_utr" : "ogs-utr",
-               "three_prime_utr" : "ogs-utr",
-               "wholeCDS" : null
-            }
-         },
-         "trackType" : null,
-         "type" : "FeatureTrack",
-         "urlTemplate" : "tracks/gerbue_current_models/{refseq}/trackData.json"
-      },
-     {
-         "category" : "Official Gene Set v1.0/1. Gene Sets/Protein Coding",
-         "compress" : 0,
-         "key" : "Gerris buenoi Official Gene Set v1.0, pseudogenes",
-         "label" : "GBUE_OGSv10_pseudogenes",
-         "metadata" : {
-            "Data description" : "https://doi.org/10.1101/242230",
-            "Data provider" : "The i5k Workspace@NAL",
-            "Data source" : "https://doi.org/10.15482/USDA.ADC/1423873",
-            "Method" : "https://github.com/NAL-i5K/GFF3toolkit",
-            "publication status" : "Published, please cite https://doi.org/10.1101/242230 or https://doi.org/10.15482/USDA.ADC/1423873"
-         },
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
-         "style" : {
-            "arrowheadClass" : "trellis-arrowhead",
-            "className" : "container-16px",
-            "subfeatureClasses" : {
-               "CDS" : "ogs-cds",
-               "UTR" : "ogs-utr",
-               "five_prime_utr" : "ogs-utr",
-               "pseudogenic_exon" : "ogs-utr",
-               "three_prime_utr" : "ogs-utr",
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-         "autoscale" : "local"
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-   "favicon" : "./plugins/WebApollo/img/webapollo_favicon.ico",
-   "formatVersion" : 1,
-   "alwaysOnTracks" : "DNA,Annotations"
+    {
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+        "Track legend": "Results from Protein2genome alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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+        "subfeatureClasses": {
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+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_UNCATEGORISED/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/2. Evidence/Repeats",
+      "compress": 0,
+      "key": "repeatmasker",
+      "label": "repeatmasker",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from RepeatMasker as part of the MAKER automated annotation pipeline."
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+      "urlTemplate": "tracks/repeatmasker/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/2. Evidence/Repeats",
+      "compress": 0,
+      "key": "repeatrunner",
+      "label": "repeatrunner",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Repeatrunner as part of the MAKER automated annotation pipeline."
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+        "arrowheadClass": "webapollo-arrowhead",
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+        "subfeatureClasses": {
+          "match_part": "repeat"
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+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/repeatrunner/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/1. Gene Sets/Supplementary Gene Predictions",
+      "compress": 0,
+      "key": "snap_masked",
+      "label": "snap_masked",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "snap"
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+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/snap_masked/{refseq}/trackData.json"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Reference Assembly",
+      "key": "Gaps in assembly",
+      "label": "Gaps in assembly",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "white",
+        "pos_color": "black"
+      },
+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "bigwig/Gbue.scaffolds.50.fa.gaps.bigwig"
+    },
+    {
+      "category": "Transcriptome/Mapped Reads",
+      "key": "PE reads i5k - RNA-Seq",
+      "label": "PE_reads_i5k_RNA-Seq",
+      "metadata": {
+        "Alignment method": "Tophat 2.0.9, in iPlant Discovery Enviroment",
+        "Alignment parameters": "--align_reads 'serial' --mate-inner-dist '50' --file_query 'Gbue_ICD_GBi5AK.T7-mix-emb-ny-1M-1F-cross-2-1_1pA_D2FUUACXX-3-ID10_1_sequence.txt' --file_query2 'Gbue_ICD_GBi5AK.T7-mix-emb-ny-1M-1F-cross-2-1_1pA_D2FUUACXX-3-ID10_2_sequence.txt' --library-type  'fr-unstranded' --min-anchor-length  '8' --splice-mismatches  '0' --min-intron-length  '70' --max-intron-length  '50000' --min-isoform-fraction  '0.15' --max-multihits  '20' --min-segment-intron  '50' --max-segment-intron  '500000' --segment-mismatches  '2' --segment-length  '20' --num-threads  '6' --user_database 'Gbue.scaffolds.50.fa' --b2-sensitive  --tophat_version '2.0.9' --bowtie_version '2.1.0'",
+        "Data source 1": "http://de.iplantcollaborative.org/dl/d/0058E2C3-0661-4F81-9AF3-E0DC790885DD/Gbue_ICD_GBi5AK.T7-mix-emb-ny-1M-1F-cross-2-1_1pA_D2FUUACXX-3-ID10_1_sequence.txt",
+        "Data source 2": "http://de.iplantcollaborative.org/dl/d/F5E1D612-1F2F-48DA-88FF-9F321A4988AD/Gbue_ICD_GBi5AK.T7-mix-emb-ny-1M-1F-cross-2-1_1pA_D2FUUACXX-3-ID10_2_sequence.txt",
+        "File provider": "David Armisen, Institut de genomique fonctionelle de Lyon",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "bam/darmisen/Gbue_ICD_GBi5AK.bam"
+    },
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+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Transcriptome/Coverage plots (BigWig)",
+      "key": "PE reads i5k - RNA-Seq coverage",
+      "label": "PE reads i5k - RNA-Seq coverage",
+      "metadata": {
+        "Alignment method": "Tophat 2.0.9, in iPlant Discovery Enviroment",
+        "Alignment parameters": "--align_reads 'serial' --mate-inner-dist '50' --file_query 'Gbue_ICD_GBi5AK.T7-mix-emb-ny-1M-1F-cross-2-1_1pA_D2FUUACXX-3-ID10_1_sequence.txt' --file_query2 'Gbue_ICD_GBi5AK.T7-mix-emb-ny-1M-1F-cross-2-1_1pA_D2FUUACXX-3-ID10_2_sequence.txt' --library-type  'fr-unstranded' --min-anchor-length  '8' --splice-mismatches  '0' --min-intron-length  '70' --max-intron-length  '50000' --min-isoform-fraction  '0.15' --max-multihits  '20' --min-segment-intron  '50' --max-segment-intron  '500000' --segment-mismatches  '2' --segment-length  '20' --num-threads  '6' --user_database 'Gbue.scaffolds.50.fa' --b2-sensitive  --tophat_version '2.0.9' --bowtie_version '2.1.0'",
+        "Data source 1": "http://de.iplantcollaborative.org/dl/d/0058E2C3-0661-4F81-9AF3-E0DC790885DD/Gbue_ICD_GBi5AK.T7-mix-emb-ny-1M-1F-cross-2-1_1pA_D2FUUACXX-3-ID10_1_sequence.txt",
+        "Data source 2": "http://de.iplantcollaborative.org/dl/d/F5E1D612-1F2F-48DA-88FF-9F321A4988AD/Gbue_ICD_GBi5AK.T7-mix-emb-ny-1M-1F-cross-2-1_1pA_D2FUUACXX-3-ID10_2_sequence.txt",
+        "File provider": "David Armisen, Institut de genomique fonctionelle de Lyon",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "This track represents an X-Y plot plot of RNA-Seq coverage. Secondary and supplementary alignments, as well as optical PCR duplicates and alignments failing QC are not included in the coverage calculations."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "bg_color": "rgba(230,230,230,0.6)",
+        "clip_marker_color": "red",
+        "height": 75,
+        "neg_color": "#0086B3",
+        "pos_color": "#00BFFF"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "bigwig/darmisen/Gbue_ICD_GBi5AK.bigwig"
+    },
+    {
+      "category": "Official Gene Set v1.0/1. Gene Sets/Protein Coding",
+      "compress": 0,
+      "key": "Gerris buenoi Official Gene Set v1.0, protein-coding genes",
+      "label": "gerbue_current_models",
+      "metadata": {
+        "Data description": "https://doi.org/10.1101/242230",
+        "Data provider": "The i5k Workspace@NAL",
+        "Data source": "https://doi.org/10.15482/USDA.ADC/1423873",
+        "Method": "https://github.com/NAL-i5K/GFF3toolkit",
+        "publication status": "Published, please cite https://doi.org/10.1101/242230 or https://doi.org/10.15482/USDA.ADC/1423873"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "CDS": "ogs-cds",
+          "UTR": "ogs-utr",
+          "exon": "container-100pct",
+          "five_prime_utr": "ogs-utr",
+          "three_prime_utr": "ogs-utr",
+          "wholeCDS": null
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/gerbue_current_models/{refseq}/trackData.json"
+    },
+    {
+      "category": "Official Gene Set v1.0/1. Gene Sets/Protein Coding",
+      "compress": 0,
+      "key": "Gerris buenoi Official Gene Set v1.0, pseudogenes",
+      "label": "GBUE_OGSv10_pseudogenes",
+      "metadata": {
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+        "Data provider": "The i5k Workspace@NAL",
+        "Data source": "https://doi.org/10.15482/USDA.ADC/1423873",
+        "Method": "https://github.com/NAL-i5K/GFF3toolkit",
+        "publication status": "Published, please cite https://doi.org/10.1101/242230 or https://doi.org/10.15482/USDA.ADC/1423873"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "CDS": "ogs-cds",
+          "UTR": "ogs-utr",
+          "five_prime_utr": "ogs-utr",
+          "pseudogenic_exon": "ogs-utr",
+          "three_prime_utr": "ogs-utr",
+          "wholeCDS": null
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/GBUE_OGSv10_pseudogenes/{refseq}/trackData.json"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "0.5",
+      "category": "Reference Assembly",
+      "key": "GC Content",
+      "label": "GC Content",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+      },
+      "scoreType": "avgScore",
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "rgba(255,255,0,50)",
+        "pos_color": "rgba(0,0,255,50)"
+      },
+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "bigwig/Gbue.scaffolds.50.fa.gc.bigwig"
+    }
+  ]
 }
diff --git a/organisms/stage/Habropoda_laboriosa/trackList.json b/organisms/stage/Habropoda_laboriosa/trackList.json
index ae1bea3..9660934 100644
--- a/organisms/stage/Habropoda_laboriosa/trackList.json
+++ b/organisms/stage/Habropoda_laboriosa/trackList.json
@@ -1,176 +1,229 @@
 {
+   "alwaysOnTracks" : "DNA,Annotations",
+   "css" : "./plugins/NAL_CSS/css/main.css",
+   "favicon" : "./plugins/WebApollo/img/webapollo_favicon.ico",
+   "formatVersion" : 1,
+   "names" : {
+      "type" : "Hash",
+      "url" : "names/"
+   },
    "share_link" : 0,
-   "css" : "./plugins/NAL_CSS/css/contrib_styles.css",
    "tracks" : [
       {
+         "category" : "Reference sequence",
          "chunkSize" : 20000,
+         "key" : "Reference sequence",
+         "label" : "DNA",
          "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
-         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-",
-         "category" : "Reference sequence",
          "type" : "SequenceTrack",
-         "label" : "DNA",
-         "key" : "Reference sequence"
+         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-"
       },
       {
          "autocomplete" : "none",
+         "compress" : 0,
+         "key" : "User-created Annotations",
+         "label" : "Annotations",
+         "phase" : 0,
+         "storeClass" : "WebApollo/Store/SeqFeature/ScratchPad",
          "style" : {
-            "renderClassName" : "annot-render",
-            "className" : "annot",
-            "subfeatureClasses" : {
-               "wholeCDS" : null,
-               "non_canonical_three_prime_splice_site" : "noncanonical-splice-site",
-               "exon" : "container-100pct",
-               "CDS" : "annot-CDS",
-               "UTR" : "annot-UTR",
-               "non_canonical_five_prime_splice_site" : "noncanonical-splice-site"
-            },
             "alternateClasses" : {
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-                  "renderClassName" : "blue-ibeam-render"
-               },
-               "pseudogene" : {
-                  "className" : "light-purple-80pct",
+               "miRNA" : {
+                  "className" : "brightgreen-80pct",
                   "renderClassName" : "gray-center-30pct"
                },
-               "snRNA" : {
+               "ncRNA" : {
                   "className" : "brightgreen-80pct",
                   "renderClassName" : "gray-center-30pct"
                },
-               "rRNA" : {
-                  "className" : "brightgreen-80pct",
+               "pseudogene" : {
+                  "className" : "light-purple-80pct",
                   "renderClassName" : "gray-center-30pct"
                },
-               "snoRNA" : {
+               "rRNA" : {
                   "className" : "brightgreen-80pct",
                   "renderClassName" : "gray-center-30pct"
                },
                "repeat_region" : {
                   "className" : "magenta-80pct"
                },
-               "ncRNA" : {
+               "snRNA" : {
                   "className" : "brightgreen-80pct",
                   "renderClassName" : "gray-center-30pct"
                },
-               "miRNA" : {
+               "snoRNA" : {
                   "className" : "brightgreen-80pct",
                   "renderClassName" : "gray-center-30pct"
                },
                "tRNA" : {
                   "className" : "brightgreen-80pct",
                   "renderClassName" : "gray-center-30pct"
+               },
+               "transposable_element" : {
+                  "className" : "blue-ibeam",
+                  "renderClassName" : "blue-ibeam-render"
                }
             },
             "arrowheadClass" : "annot-arrowhead",
-            "uniqueIdField" : "id",
             "centerSubFeature" : {
-               "non_canonical_three_prime_splice_site" : false,
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-            }
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-         "storeClass" : "WebApollo/Store/SeqFeature/ScratchPad",
-         "phase" : 0,
-         "compress" : 0,
-         "label" : "Annotations",
-         "type" : "WebApollo/View/Track/AnnotTrack",
-         "subfeatures" : 1
-      },
-      {
-         "style" : {
-            "className" : "container-16px",
+               "non_canonical_five_prime_splice_site" : false,
+               "non_canonical_three_prime_splice_site" : false
+            },
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+            "renderClassName" : "annot-render",
             "subfeatureClasses" : {
-               "wholeCDS" : null,
+               "CDS" : "annot-CDS",
+               "UTR" : "annot-UTR",
                "exon" : "container-100pct",
-               "CDS" : "primary_gene_set-cds",
-               "UTR" : "primary_gene_set-utr"
+               "non_canonical_five_prime_splice_site" : "noncanonical-splice-site",
+               "non_canonical_three_prime_splice_site" : "noncanonical-splice-site",
+               "wholeCDS" : null
             },
-            "arrowheadClass" : "trellis-arrowhead"
+            "uniqueIdField" : "id"
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-         "key" : "GenBank Annotations, protein-coding",
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
-         "trackType" : null,
-         "urlTemplate" : "tracks/hablab_current_models/{refseq}/trackData.json",
+         "subfeatures" : 1,
+         "type" : "WebApollo/View/Track/AnnotTrack"
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          "compress" : 0,
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          "metadata" : {
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             "Data provider" : "NCBI/GenBank",
-            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_001263275.1_ASM126327v1/README.txt"
+            "Data source" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_001263275.1_ASM126327v1/GCA_001263275.1_ASM126327v1_genomic.gff.gz"
          },
-         "category" : "GenBank Annotations/1. Gene Sets/Protein Coding",
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "{type}",
+            "subfeatureClasses" : {
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+            }
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          "type" : "FeatureTrack",
-         "label" : "hablab_current_models"
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       },
       {
-         "style" : {
-            "neg_color" : "white",
-            "pos_color" : "black"
-         },
+         "autoscale" : "local",
          "bicolor_pivot" : "zero",
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          "key" : "Gaps in assembly",
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-         "type" : "JBrowse/View/Track/Wiggle/Density",
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          "metadata" : {
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+            "Track contact" : "The i5k workspace@NAL",
             "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
-            "Track contact" : "The i5k workspace@NAL"
+            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
          },
-         "label" : "Gaps in assembly",
-         "category" : "Reference Assembly"
-      },
-      {
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
          "style" : {
-            "pos_color" : "rgba(0,0,255,50)",
-            "neg_color" : "rgba(255,255,0,50)"
+            "neg_color" : "white",
+            "pos_color" : "black"
          },
-         "bicolor_pivot" : "0.5",
+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/GCA_001263275.1_ASM126327v1_genomic.fna.gaps.bigwig"
+      },
+      {
          "autoscale" : "local",
+         "bicolor_pivot" : "0.5",
+         "category" : "Reference Assembly",
          "key" : "GC Content",
-         "scoreType": "avgScore",
-         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
-         "urlTemplate" : "bigwig/GCA_001263275.1_ASM126327v1_genomic.fna.gc.bigwig",
+         "label" : "GC Content",
          "metadata" : {
-            "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track.",
+            "Track contact" : "The i5k workspace@NAL",
             "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
-            "Track contact" : "The i5k workspace@NAL"
+            "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+         },
+         "scoreType" : "avgScore",
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "rgba(255,255,0,50)",
+            "pos_color" : "rgba(0,0,255,50)"
          },
-         "label" : "GC Content",
          "type" : "JBrowse/View/Track/Wiggle/Density",
-         "category" : "Reference Assembly"
+         "urlTemplate" : "bigwig/GCA_001263275.1_ASM126327v1_genomic.fna.gc.bigwig"
       },
       {
-         "style" : {
-            "className" : "container-16px",
-            "arrowheadClass" : "trellis-arrowhead"
-         },
-         "key" : "GenBank Annotations, pseudogenes",
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
-         "trackType" : null,
-         "urlTemplate" : "tracks/GenBank_Annotations_Pseudogene/{refseq}/trackData.json",
+         "category" : "GenBank Annotations/1. Gene Sets/Pseudogenes",
          "compress" : 0,
+         "key" : "GenBank Annotations, pseudogenes",
          "label" : "GenBank_Annotations_Pseudogene",
-         "category" : "GenBank Annotations/1. Gene Sets/Pseudogenes",
          "metadata" : {
             "Data Description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_001263275.1_ASM126327v1/README.txt",
-            "Data source" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_001263275.1_ASM126327v1/GCA_001263275.1_ASM126327v1_genomic.gff.gz",
-            "Data provider" : "NCBI/GenBank"
+            "Data provider" : "NCBI/GenBank",
+            "Data source" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_001263275.1_ASM126327v1/GCA_001263275.1_ASM126327v1_genomic.gff.gz"
          },
-         "type" : "FeatureTrack"
-      }
-   ],
-   "plugins" : [
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "{type}"
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/GenBank_Annotations_Pseudogene/{refseq}/trackData.json"
+      },
+      {
+         "category" : "RNA-Seq/Mapped Reads",
+         "key" : "Hablab_ASM126327v1_RNA-Seq-alignments_2021-06-15",
+         "label" : "Hablab_ASM126327v1_RNA-Seq-alignments_2021-06-15",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR2001612'>SRR2001612</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Dark red alignments: Mapped portion of read aligned to forward strand<br>Light red alignments: Spliced portion of read aligned to forward strand<br>Dark blue alignments: Mapped portion of read aligned to reverse strand<br>Light blue alignments: Spliced portion of read aligned to reverse strand<br>Red marking - deletion in the read relative to the reference<br>Green marking - insertion in the read relative to the reference<br>Yellow marking  - mismatch (hover over the mismatch to see what the snp is)"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "unsafePopup" : true,
+         "urlTemplate" : "analyses/Habropoda-laboriosa-RNA-Seq_2021-06-15_v1.0/Hablab_ASM126327v1_RNA-Seq-alignments_2021-06-15.bam"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "RNA-Seq/Coverage Plots",
+         "key" : "Hablab_ASM126327v1_RNA-Seq-alignments_2021-06-15_coverage",
+         "label" : "Hablab_ASM126327v1_RNA-Seq-alignments_2021-06-15_coverage",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR2001612'>SRR2001612</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "unsafePopup" : true,
+         "urlTemplate" : "analyses/Habropoda-laboriosa-RNA-Seq_2021-06-15_v1.0/Hablab_ASM126327v1_RNA-Seq-alignments_2021-06-15.bigwig"
+      },
       {
-         "location" : "./plugins/WebApollo",
-         "name" : "WebApollo"
+         "category" : "RNA-Seq/Splice junctions",
+         "compress" : 0,
+         "key" : "Hablab_ASM126327v1_RNA-Seq-alignments_2021-06-15_junctions",
+         "label" : "Hablab_ASM126327v1_RNA-Seq-alignments_2021-06-15_junctions",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR2001612'>SRR2001612</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Junction reads generated by Hisat2 aligner and regtools. The number of alignments supporting the junction read is listed in blue."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "className" : "feature",
+            "description" : "score"
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "unsafePopup" : true,
+         "urlTemplate" : "tracks/Hablab_ASM126327v1_RNA-Seq-alignments_2021-06-15_junctions/{refseq}/trackData.json"
       }
-   ],
-   "names" : {
-      "url" : "names/",
-      "type" : "Hash"
-   },
-   "favicon" : "./plugins/WebApollo/img/webapollo_favicon.ico",
-   "formatVersion" : 1,
-   "alwaysOnTracks" : "DNA,Annotations"
+   ]
 }
diff --git a/organisms/stage/Halyomorpha_halys/trackList.json b/organisms/stage/Halyomorpha_halys/trackList.json
index cf691ed..d518f5f 100644
--- a/organisms/stage/Halyomorpha_halys/trackList.json
+++ b/organisms/stage/Halyomorpha_halys/trackList.json
@@ -45,6 +45,7 @@
             "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
             "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
          },
+         "scoreType" : "avgScore",
          "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
          "style" : {
             "neg_color" : "rgba(255,255,0,50)",
@@ -402,17 +403,28 @@
          "compress" : 0,
          "key" : "OGSv1.2 Gene",
          "label" : "halhal_current_models",
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
-	 "menuTemplate" : [ { "label" : "View details", }, { "label": "function(track,feature){ return 'Find gene page for '+feature.get('id')}", "title": "function(track,feature){ return 'Find gene page for '+feature.get('id')}", "iconClass" : "dijitIconDatabase", "action": "newWindow", "url" : "function(track,feature){ return 'https://i5k.nal.usda.gov/search/site/'+feature.get('id')}", }, ],
+         "menuTemplate" : [
+            {
+               "label" : "View details"
+            },
+            {
+               "action" : "newWindow",
+               "iconClass" : "dijitIconDatabase",
+               "label" : "function(track,feature){ return 'Find NCBI record for '+feature.get('id')}",
+               "title" : "function(track,feature){ return 'Find NCBI record for '+feature.get('id')}",
+               "url" : "function(track,feature){ return 'https://www.ncbi.nlm.nih.gov/protein/'+feature.get('id')}"
+            }
+         ],
          "metadata" : {
-                    "Data source" : "https://data.nal.usda.gov/dataset/halyomorpha-halys-official-gene-set-v12",
-                    "Materials and Methods" : "Halyomorpha halys Official Gene Set halhal_OGSv1.2 is an integration of automatic gene predictions from NCBI's eukaryotic annotation pipeline, NCBI Halyomorpha halys Annotation Release 100 (https://www.ncbi.nlm.nih.gov/genome/annotation_euk/Halyomorpha_halys/100/; ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/696/795/GCF_000696795.1_Hhal_1.0), with manual annotations by the research community (performed via the Apollo manual curation software, http://genomearchitect.org/). OGSv1.2 was updated from OGSv1.1 (https://doi.org/10.15482/USDA.ADC/1504240) to the coordinates of genome assembly GCA_000696795.3 (https://www.ncbi.nlm.nih.gov/assembly/GCA_000696795.3) using https://github.com/NAL-i5K/coordinates_conversion/.",
-                    "Publication status" : "In review",
-                    "Data provider" : "Michael Sparks, USDA-ARS"
+            "Data provider" : "Michael Sparks, USDA-ARS",
+            "Data source" : "https://data.nal.usda.gov/dataset/halyomorpha-halys-official-gene-set-v12",
+            "Materials and Methods" : "Halyomorpha halys Official Gene Set halhal_OGSv1.2 is an integration of automatic gene predictions from NCBI's eukaryotic annotation pipeline, NCBI Halyomorpha halys Annotation Release 100 (https://www.ncbi.nlm.nih.gov/genome/annotation_euk/Halyomorpha_halys/100/; ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/696/795/GCF_000696795.1_Hhal_1.0), with manual annotations by the research community (performed via the Apollo manual curation software, http://genomearchitect.org/). OGSv1.2 was updated from OGSv1.1 (https://doi.org/10.15482/USDA.ADC/1504240) to the coordinates of genome assembly GCA_000696795.3 (https://www.ncbi.nlm.nih.gov/assembly/GCA_000696795.3) using https://github.com/NAL-i5K/coordinates_conversion/.",
+            "Publication status" : "In review"
          },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
             "arrowheadClass" : "trellis-arrowhead",
-            "className" : "container-16px",
+            "className" : "{type}",
             "description" : "product, note, description",
             "subfeatureClasses" : {
                "CDS" : "gnomon_CDS",
@@ -421,9 +433,68 @@
                "wholeCDS" : null
             }
          },
-         "trackType" : "ColorByType/View/Track/ColorByTypeDraggable",
-         "type" : "ColorByType/View/Track/ColorByTypeDraggable",
+         "trackType" : "HTMLFeatures",
+         "type" : "HTMLFeatures",
          "urlTemplate" : "tracks/halhal_current_models/{refseq}/trackData.json"
+      },
+      {
+         "category" : "RNA-Seq/Mapped Reads",
+         "key" : "Halhal_Hhal_1.1_RNA-Seq-alignments_2021-06-15",
+         "label" : "Halhal_Hhal_1.1_RNA-Seq-alignments_2021-06-15",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR1207183'>SRR1207183</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR1207182'>SRR1207182</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR12286915'>SRR12286915</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11747758'>SRR11747758</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR1301985'>SRR1301985</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR1207181'>SRR1207181</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR9969962'>SRR9969962</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR1206311'>SRR1206311</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR1611187'>SRR1611187</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR12286914'>SRR12286914</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Dark red alignments: Mapped portion of read aligned to forward strand<br>Light red alignments: Spliced portion of read aligned to forward strand<br>Dark blue alignments: Mapped portion of read aligned to reverse strand<br>Light blue alignments: Spliced portion of read aligned to reverse strand<br>Red marking - deletion in the read relative to the reference<br>Green marking - insertion in the read relative to the reference<br>Yellow marking  - mismatch (hover over the mismatch to see what the snp is)"
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+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "unsafePopup" : true,
+         "urlTemplate" : "analyses/Halyomorpha-halys-RNA-Seq_2021-06-15_v1.0/Halhal_Hhal_1.1_RNA-Seq-alignments_2021-06-15.bam"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "RNA-Seq/Coverage Plots",
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+         "label" : "Halhal_Hhal_1.1_RNA-Seq-alignments_2021-06-15_coverage",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
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+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
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+         "urlTemplate" : "analyses/Halyomorpha-halys-RNA-Seq_2021-06-15_v1.0/Halhal_Hhal_1.1_RNA-Seq-alignments_2021-06-15.bigwig"
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+         "metadata" : {
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+            "Track legend" : "Junction reads generated by Hisat2 aligner and regtools. The number of alignments supporting the junction read is listed in blue."
+         },
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+         "style" : {
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+         "urlTemplate" : "tracks/Halhal_Hhal_1.1_RNA-Seq-alignments_2021-06-15_junctions/{refseq}/trackData.json"
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 }
diff --git a/organisms/stage/Helicoverpa_zea/trackList.json b/organisms/stage/Helicoverpa_zea/trackList.json
new file mode 100755
index 0000000..94e5b67
--- /dev/null
+++ b/organisms/stage/Helicoverpa_zea/trackList.json
@@ -0,0 +1,183 @@
+{
+   "formatVersion" : 1,
+   "names" : {
+      "type" : "Hash",
+      "url" : "names/"
+   },
+   "tracks" : [
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+         "chunkSize" : 20000,
+         "key" : "Reference sequence",
+         "label" : "DNA",
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+         "type" : "SequenceTrack",
+         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-"
+      },
+      {
+         "category" : "NCBI Annotation Release 100",
+         "compress" : 0,
+         "key" : "NCBI_Annotation_Release_100_Gene",
+         "label" : "helzea_current_models",
+         "menuTemplate" : [
+            {
+               "label" : "View details"
+            },
+            {
+               "action" : "newWindow",
+               "iconClass" : "dijitIconDatabase",
+               "label" : "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
+               "title" : "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
+               "url" : "function(track,feature){ return 'https://www.ncbi.nlm.nih.gov/nuccore/'+feature.get('name')}"
+            }
+         ],
+         "metadata" : {
+            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Helicoverpa_zea/README_CURRENT_RELEASE",
+            "Data provider" : "NCBI",
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+               "UTR" : "gnomon_UTR",
+               "exon" : "container-100pct",
+               "wholeCDS" : null
+            }
+         },
+         "trackType" : "HTMLFeatures",
+         "type" : "HTMLFeatures",
+         "urlTemplate" : "tracks/helzea_current_models/{refseq}/trackData.json"
+      },
+      {
+         "category" : "NCBI Annotation Release 100",
+         "compress" : 0,
+         "key" : "NCBI_Annotation_Release_100_Pseudogene",
+         "label" : "NCBI_Annotation_Release_100_Pseudogene",
+         "metadata" : {
+            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Helicoverpa_zea/README_CURRENT_RELEASE",
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+         "style" : {
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+            "className" : "container-16px",
+            "description" : "product, note, description",
+            "subfeatureClasses" : {
+               "CDS" : "gnomon_CDS",
+               "UTR" : "gnomon_UTR",
+               "exon" : "container-100pct",
+               "wholeCDS" : null
+            }
+         },
+         "trackType" : "HTMLFeatures",
+         "type" : "HTMLFeatures",
+         "urlTemplate" : "tracks/NCBI_Annotation_Release_100_Pseudogene/{refseq}/trackData.json"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Reference Assembly",
+         "key" : "Gaps in assembly",
+         "label" : "Gaps in assembly",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "white",
+            "pos_color" : "black"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/GCF_022581195.2_ilHelZeax1.1_genomic.fna.gaps.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "0.5",
+         "category" : "Reference Assembly",
+         "key" : "GC Content",
+         "label" : "GC Content",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+         },
+         "scoreType" : "avgScore",
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "rgba(255,255,0,50)",
+            "pos_color" : "rgba(0,0,255,50)"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/GCF_022581195.2_ilHelZeax1.1_genomic.fna.gc.bigwig"
+      },
+      {
+         "category" : "RNA-Seq/Mapped Reads",
+         "key" : "Helzea_ilHelZeax1.1_RNA-Seq-alignments_2022-04-07",
+         "label" : "Helzea_ilHelZeax1.1_RNA-Seq-alignments_2022-04-07",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR8987512'>SRR8987512</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR16121636'>SRR16121636</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR16121655'>SRR16121655</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR16121646'>SRR16121646</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR10493559'>SRR10493559</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR16121660'>SRR16121660</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR16121653'>SRR16121653</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR16121658'>SRR16121658</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR10493553'>SRR10493553</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR8987510'>SRR8987510</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Dark red alignments: Mapped portion of read aligned to forward strand<br>Light red alignments: Spliced portion of read aligned to forward strand<br>Dark blue alignments: Mapped portion of read aligned to reverse strand<br>Light blue alignments: Spliced portion of read aligned to reverse strand<br>Red marking - deletion in the read relative to the reference<br>Green marking - insertion in the read relative to the reference<br>Yellow marking  - mismatch (hover over the mismatch to see what the snp is)"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "unsafePopup" : true,
+         "urlTemplate" : "analyses/Helicoverpa-zea-RNA-Seq_2022-04-07_v1.0/Helzea_ilHelZeax1.1_RNA-Seq-alignments_2022-04-07.bam"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "RNA-Seq/Coverage Plots",
+         "key" : "Helzea_ilHelZeax1.1_RNA-Seq-alignments_2022-04-07_coverage",
+         "label" : "Helzea_ilHelZeax1.1_RNA-Seq-alignments_2022-04-07_coverage",
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "unsafePopup" : true,
+        "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR8987512'>SRR8987512</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR16121636'>SRR16121636</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR16121655'>SRR16121655</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR16121646'>SRR16121646</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR10493559'>SRR10493559</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR16121660'>SRR16121660</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR16121653'>SRR16121653</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR16121658'>SRR16121658</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR10493553'>SRR10493553</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR8987510'>SRR8987510</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage."
+         },
+         "style" : {
+            "pos_color" : "#00BFFF"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "analyses/Helicoverpa-zea-RNA-Seq_2022-04-07_v1.0/Helzea_ilHelZeax1.1_RNA-Seq-alignments_2022-04-07.bigwig"
+      },
+      {
+         "category" : "RNA-Seq/Splice junctions",
+         "compress" : 0,
+         "key" : "Helzea_ilHelZeax1.1_RNA-Seq-alignments_2022-04-07_junctions",
+         "label" : "Helzea_ilHelZeax1.1_RNA-Seq-alignments_2022-04-07_junctions",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR8987512'>SRR8987512</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR16121636'>SRR16121636</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR16121655'>SRR16121655</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR16121646'>SRR16121646</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR10493559'>SRR10493559</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR16121660'>SRR16121660</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR16121653'>SRR16121653</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR16121658'>SRR16121658</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR10493553'>SRR10493553</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR8987510'>SRR8987510</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Junction reads generated by Hisat2 aligner and regtools. The number of alignments supporting the junction read is listed in blue."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "className" : "feature",
+            "description" : "score"
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "unsafePopup" : true,
+         "urlTemplate" : "tracks/Helzea_ilHelZeax1.1_RNA-Seq-alignments_2022-04-07_junctions/{refseq}/trackData.json"
+      }
+   ]
+}
diff --git a/organisms/stage/Heliothis_virescens/trackList.json b/organisms/stage/Heliothis_virescens/trackList.json
index 64b500d..c9bbd31 100644
--- a/organisms/stage/Heliothis_virescens/trackList.json
+++ b/organisms/stage/Heliothis_virescens/trackList.json
@@ -1,18 +1,12 @@
 {
    "alwaysOnTracks" : "DNA,Annotations",
-   "css" : "data/contrib_styles.css",
+   "css" : "./plugins/NAL_CSS/css/main.css",
    "favicon" : "./plugins/WebApollo/img/webapollo_favicon.ico",
    "formatVersion" : 1,
    "names" : {
       "type" : "Hash",
       "url" : "names/"
    },
-   "plugins" : [
-      {
-         "location" : "./plugins/WebApollo",
-         "name" : "WebApollo"
-      }
-   ],
    "share_link" : 0,
    "tracks" : [
       {
@@ -119,6 +113,7 @@
             "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
             "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
          },
+         "scoreType" : "avgScore",
          "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
          "style" : {
             "neg_color" : "rgba(255,255,0,50)",
@@ -439,7 +434,7 @@
          "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
             "arrowheadClass" : "trellis-arrowhead",
-            "className" : "container-16px"
+            "className" : "{type}"
          },
          "trackType" : null,
          "type" : "FeatureTrack",
@@ -461,7 +456,7 @@
          "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
             "arrowheadClass" : "trellis-arrowhead",
-            "className" : "container-16px"
+            "className" : "{type}"
          },
          "trackType" : null,
          "type" : "FeatureTrack",
@@ -483,7 +478,7 @@
          "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
             "arrowheadClass" : "trellis-arrowhead",
-            "className" : "container-16px"
+            "className" : "{type}"
          },
          "trackType" : null,
          "type" : "FeatureTrack",
@@ -505,7 +500,7 @@
          "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
             "arrowheadClass" : "trellis-arrowhead",
-            "className" : "container-16px"
+            "className" : "{type}"
          },
          "trackType" : null,
          "type" : "FeatureTrack",
@@ -527,7 +522,7 @@
          "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
             "arrowheadClass" : "trellis-arrowhead",
-            "className" : "container-16px"
+            "className" : "{type}"
          },
          "trackType" : null,
          "type" : "FeatureTrack",
@@ -549,7 +544,7 @@
          "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
             "arrowheadClass" : "trellis-arrowhead",
-            "className" : "container-16px"
+            "className" : "{type}"
          },
          "trackType" : null,
          "type" : "FeatureTrack",
@@ -571,7 +566,7 @@
          "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
             "arrowheadClass" : "trellis-arrowhead",
-            "className" : "container-16px"
+            "className" : "{type}"
          },
          "trackType" : null,
          "type" : "FeatureTrack",
@@ -593,27 +588,27 @@
          "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
             "arrowheadClass" : "trellis-arrowhead",
-            "className" : "container-16px"
+            "className" : "{type}"
          },
          "trackType" : null,
          "type" : "FeatureTrack",
          "urlTemplate" : "tracks/HVI-AF_GKW-21/{refseq}/trackData.json"
       },
       {
+         "category" : "H. virescens Official Gene Set v1/1. Gene Sets/Protein Coding",
          "compress" : 0,
+         "key" : "H_virescens_OGS1",
+         "label" : "helvir_current_models",
          "metadata" : {
             "Data provider" : "Alexie Papanicolaou, Hawkesbury Institute for the Environment Richmond NSW Australia",
             "Data source" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/002/382/865/GCA_002382865.1_K63_refined_pacbio",
             "Method" : "JAMg version RC1, http://jamg.sourceforge.net/",
             "Publication status" : "Published - please cite http://onlinelibrary.wiley.com/doi/10.1111/mec.14430/abstract"
          },
-         "category" : "H. virescens Official Gene Set v1/1. Gene Sets/Protein Coding",
-         "key" : "H_virescens_OGS1",
-         "label" : "helvir_current_models",
          "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
             "arrowheadClass" : "trellis-arrowhead",
-            "className" : "container-16px",
+            "className" : "{type}",
             "description" : "id, description",
             "label" : "Dbxref,name",
             "subfeatureClasses" : {
@@ -626,6 +621,65 @@
          "trackType" : null,
          "type" : "FeatureTrack",
          "urlTemplate" : "tracks/helvir_current_models/{refseq}/trackData.json"
+      },
+      {
+         "category" : "RNA-Seq/Mapped Reads",
+         "key" : "Helvir_K63_refined_pacbio_RNA-Seq-alignments_2021-06-15",
+         "label" : "Helvir_K63_refined_pacbio_RNA-Seq-alignments_2021-06-15",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR1867807'>SRR1867807</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=ERR1855015'>ERR1855015</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR1867809'>SRR1867809</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=ERR1855018'>ERR1855018</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR2912076'>SRR2912076</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR6417880'>SRR6417880</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR2176142'>SRR2176142</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=ERR1855016'>ERR1855016</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=ERR1855020'>ERR1855020</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=ERR1855019'>ERR1855019</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Dark red alignments: Mapped portion of read aligned to forward strand<br>Light red alignments: Spliced portion of read aligned to forward strand<br>Dark blue alignments: Mapped portion of read aligned to reverse strand<br>Light blue alignments: Spliced portion of read aligned to reverse strand<br>Red marking - deletion in the read relative to the reference<br>Green marking - insertion in the read relative to the reference<br>Yellow marking  - mismatch (hover over the mismatch to see what the snp is)"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "unsafePopup" : true,
+         "urlTemplate" : "analyses/Heliothis-virescens-RNA-Seq_2021-06-15_v1.0/Helvir_K63_refined_pacbio_RNA-Seq-alignments_2021-06-15.bam"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "RNA-Seq/Coverage Plots",
+         "key" : "Helvir_K63_refined_pacbio_RNA-Seq-alignments_2021-06-15_coverage",
+         "label" : "Helvir_K63_refined_pacbio_RNA-Seq-alignments_2021-06-15_coverage",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR1867807'>SRR1867807</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=ERR1855015'>ERR1855015</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR1867809'>SRR1867809</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=ERR1855018'>ERR1855018</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR2912076'>SRR2912076</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR6417880'>SRR6417880</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR2176142'>SRR2176142</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=ERR1855016'>ERR1855016</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=ERR1855020'>ERR1855020</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=ERR1855019'>ERR1855019</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "unsafePopup" : true,
+         "urlTemplate" : "analyses/Heliothis-virescens-RNA-Seq_2021-06-15_v1.0/Helvir_K63_refined_pacbio_RNA-Seq-alignments_2021-06-15.bigwig"
+      },
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+         "key" : "Helvir_K63_refined_pacbio_RNA-Seq-alignments_2021-06-15_junctions",
+         "label" : "Helvir_K63_refined_pacbio_RNA-Seq-alignments_2021-06-15_junctions",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR1867807'>SRR1867807</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=ERR1855015'>ERR1855015</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR1867809'>SRR1867809</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=ERR1855018'>ERR1855018</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR2912076'>SRR2912076</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR6417880'>SRR6417880</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR2176142'>SRR2176142</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=ERR1855016'>ERR1855016</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=ERR1855020'>ERR1855020</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=ERR1855019'>ERR1855019</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Junction reads generated by Hisat2 aligner and regtools. The number of alignments supporting the junction read is listed in blue."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "className" : "feature",
+            "description" : "score"
+         },
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+         "type" : "FeatureTrack",
+         "unsafePopup" : true,
+         "urlTemplate" : "tracks/Helvir_K63_refined_pacbio_RNA-Seq-alignments_2021-06-15_junctions/{refseq}/trackData.json"
       }
    ]
 }
diff --git a/organisms/stage/Holacanthella_duospinosa/trackList.json b/organisms/stage/Holacanthella_duospinosa/trackList.json
index 13fc6ce..ae31341 100644
--- a/organisms/stage/Holacanthella_duospinosa/trackList.json
+++ b/organisms/stage/Holacanthella_duospinosa/trackList.json
@@ -1,85 +1,144 @@
 {
+   "formatVersion" : 1,
+   "names" : {
+      "type" : "Hash",
+      "url" : "names/"
+   },
    "tracks" : [
       {
-         "seqType" : "dna",
+         "category" : "Reference sequence",
+         "faiUrlTemplate" : "seq/GCA_002738285.1_ASM273828v1_genomic.fna.fai",
          "key" : "Reference sequence",
-         "useAsRefSeqStore" : 1,
+         "label" : "DNA",
+         "seqType" : "dna",
          "storeClass" : "JBrowse/Store/Sequence/IndexedFasta",
-         "urlTemplate" : "seq/GCA_002738285.1_ASM273828v1_genomic.fna",
          "type" : "SequenceTrack",
-         "label" : "DNA",
-         "category" : "Reference sequence",
-         "faiUrlTemplate" : "seq/GCA_002738285.1_ASM273828v1_genomic.fna.fai"
+         "urlTemplate" : "seq/GCA_002738285.1_ASM273828v1_genomic.fna",
+         "useAsRefSeqStore" : 1
       },
       {
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
-         "trackType" : null,
-         "urlTemplate" : "tracks/holduo_current_models/{refseq}/trackData.json",
+         "category" : "Holacanthella duospinosa annotations v1.0/1. Gene Sets/Protein Coding",
          "compress" : 0,
-	 "category":"Holacanthella duospinosa annotations v1.0/1. Gene Sets/Protein Coding",
-	 "metadata":{
-		"Data provider":"Chen Wu, Plant and Food New Zealand",
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+         "label" : "holduo_current_models",
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+            "Data source" : "https://i5k.nal.usda.gov/annotations/739261/",
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diff --git a/organisms/stage/Homalodisca_vitripennis/trackList.json b/organisms/stage/Homalodisca_vitripennis/trackList.json
index cd94e4b..6e20893 100644
--- a/organisms/stage/Homalodisca_vitripennis/trackList.json
+++ b/organisms/stage/Homalodisca_vitripennis/trackList.json
@@ -1,1343 +1,1335 @@
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+        "Data description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Data provider": "Daniel Hughes, Baylor College of Medicine",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Platyhelminthes/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Priapulida",
+      "label": "protein2genome_Priapulida",
+      "metadata": {
+        "Data description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Data provider": "Daniel Hughes, Baylor College of Medicine",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Priapulida/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Tardigrada",
+      "label": "protein2genome_Tardigrada",
+      "metadata": {
+        "Data description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Data provider": "Daniel Hughes, Baylor College of Medicine",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Tardigrada/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Tunicata",
+      "label": "protein2genome_Tunicata",
+      "metadata": {
+        "Data description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Data provider": "Daniel Hughes, Baylor College of Medicine",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Tunicata/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_UNCATEGORISED",
+      "label": "protein2genome_UNCATEGORISED",
+      "metadata": {
+        "Data description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Data provider": "Daniel Hughes, Baylor College of Medicine",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_UNCATEGORISED/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/1. Gene Sets/Supplementary Gene Predictions",
+      "compress": 0,
+      "key": "SNAP gene predictions",
+      "label": "snap_masked",
+      "metadata": {
+        "Data description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Data provider": "Daniel Hughes, Baylor College of Medicine",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "snap"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/snap_masked/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/2. Evidence/Repeats",
+      "compress": 0,
+      "key": "repeatmasker",
+      "label": "repeatmasker",
+      "metadata": {
+        "Data description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Data provider": "Daniel Hughes, Baylor College of Medicine",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from RepeatMasker as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "repeat"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/repeatmasker/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/2. Evidence/Repeats",
+      "compress": 0,
+      "key": "repeatrunner",
+      "label": "repeatrunner",
+      "metadata": {
+        "Data description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Data provider": "Daniel Hughes, Baylor College of Medicine",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Repeatrunner as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "repeat"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/repeatrunner/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/4. Transcriptome /Splice Junctions",
+      "compress": 0,
+      "key": "Hvit_female_RNAseq junction reads",
+      "label": "Hvit_female_RNAseq_junction-reads",
+      "metadata": {
+        "Alignment summary": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Glassy-winged_sharpshooter/RNA_sequence/tophat_female_Nvit_RNAseq_alignments/align_summary.txt",
+        "Analysis method": "TopHat v2.0.13",
+        "File provider": "Stephen Richards, Baylor College of Medicine",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Sex": "female"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "CDS": "junction-cds",
+          "UTR": "webapollo-UTR",
+          "exon": "container-100pct",
+          "wholeCDS": null
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/Hvit_female_RNAseq_junction-reads/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/4. Transcriptome /Splice Junctions",
+      "compress": 0,
+      "key": "Hvit_male_RNAseq junction reads",
+      "label": "Hvit_male_RNAseq_junction-reads",
+      "metadata": {
+        "Alignment summary": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Glassy-winged_sharpshooter/RNA_sequence/tophat_male_Hvit_RNAseq_alignments/align_summary.txt",
+        "Analysis method": "TopHat v2.0.13",
+        "File provider": "Stephen Richards, Baylor College of Medicine",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Sex": "male"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "CDS": "junction-cds",
+          "UTR": "webapollo-UTR",
+          "exon": "container-100pct",
+          "wholeCDS": null
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/Hvit_male_RNAseq_junction-reads/{refseq}/trackData.json"
+    },
+    {
+      "autocomplete": "none",
+      "compress": 0,
+      "key": "User-created Annotations",
+      "label": "Annotations",
+      "phase": 0,
+      "storeClass": "WebApollo/Store/SeqFeature/ScratchPad",
+      "style": {
+        "alternateClasses": {
+          "miRNA": {
+            "className": "brightgreen-80pct",
+            "renderClassName": "gray-center-30pct"
+          },
+          "ncRNA": {
+            "className": "brightgreen-80pct",
+            "renderClassName": "gray-center-30pct"
+          },
+          "pseudogene": {
+            "className": "light-purple-80pct",
+            "renderClassName": "gray-center-30pct"
+          },
+          "rRNA": {
+            "className": "brightgreen-80pct",
+            "renderClassName": "gray-center-30pct"
+          },
+          "repeat_region": {
+            "className": "magenta-80pct"
+          },
+          "snRNA": {
+            "className": "brightgreen-80pct",
+            "renderClassName": "gray-center-30pct"
+          },
+          "snoRNA": {
+            "className": "brightgreen-80pct",
+            "renderClassName": "gray-center-30pct"
+          },
+          "tRNA": {
+            "className": "brightgreen-80pct",
+            "renderClassName": "gray-center-30pct"
+          },
+          "transposable_element": {
+            "className": "blue-ibeam",
+            "renderClassName": "blue-ibeam-render"
+          }
+        },
+        "arrowheadClass": "annot-arrowhead",
+        "centerSubFeature": {
+          "non_canonical_five_prime_splice_site": false,
+          "non_canonical_three_prime_splice_site": false
+        },
+        "className": "annot",
+        "renderClassName": "annot-render",
+        "subfeatureClasses": {
+          "CDS": "annot-CDS",
+          "UTR": "annot-UTR",
+          "exon": "container-100pct",
+          "non_canonical_five_prime_splice_site": "noncanonical-splice-site",
+          "non_canonical_three_prime_splice_site": "noncanonical-splice-site",
+          "wholeCDS": null
+        },
+        "uniqueIdField": "id"
+      },
+      "subfeatures": 1,
+      "type": "WebApollo/View/Track/AnnotTrack"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Reference Assembly",
+      "key": "Gaps in assembly",
+      "label": "Gaps in assembly",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "white",
+        "pos_color": "black"
+      },
+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "bigwig/GCA_000696855.1_Hvit_1.0_genomic.fna.gaps.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "0.5",
+      "category": "Reference Assembly",
+      "key": "GC Content",
+      "label": "GC Content",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+      },
+      "scoreType": "avgScore",
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "rgba(255,255,0,50)",
+        "pos_color": "rgba(0,0,255,50)"
+      },
+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "bigwig/GCA_000696855.1_Hvit_1.0_genomic.fna.gc.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "BCM_v0.5.3/4. Transcriptome /Coverage Plots (BigWig)",
+      "key": "Hvit_female_RNAseq (Coverage Plot)",
+      "label": "Hvit_female_RNAseq (Coverage Plot)",
+      "metadata": {
+        "Alignment summary": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Glassy-winged_sharpshooter/RNA_sequence/tophat_female_Nvit_RNAseq_alignments/align_summary.txt",
+        "Analysis method": "TopHat v2.0.13",
+        "File provider": "Stephen Richards, Baylor College of Medicine",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Sex": "female"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "pos_color": "#00BFFF"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "user_contributed_data/srichards/male-female/female_Nvit_RNAseq_alignments_accepted_hits_GCA_000696855.1.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "BCM_v0.5.3/4. Transcriptome /Coverage Plots (BigWig)",
+      "key": "Hvit_male_RNAseq (Coverage Plot)",
+      "label": "Hvit_male_RNAseq (Coverage Plot)",
+      "metadata": {
+        "Alignment summary": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Glassy-winged_sharpshooter/RNA_sequence/tophat_male_Hvit_RNAseq_alignments/align_summary.txt",
+        "Analysis method": "TopHat v2.0.13",
+        "File provider": "Stephen Richards, Baylor College of Medicine",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Sex": "male"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "pos_color": "#00BFFF"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "user_contributed_data/srichards/male-female/male_Nvit_RNAseq_alignments_accepted_hits_GCA_000696855.1.bigwig"
+    },
+    {
+      "category": "BCM_v0.5.3/4. Transcriptome /Mapped Reads",
+      "key": "Hvit_female_RNAseq",
+      "label": "Hvit_female_RNAseq",
+      "metadata": {
+        "Alignment summary": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Glassy-winged_sharpshooter/RNA_sequence/tophat_female_Nvit_RNAseq_alignments/align_summary.txt",
+        "Analysis method": "TopHat v2.0.13",
+        "File provider": "Stephen Richards, Baylor College of Medicine",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Sex": "female"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "user_contributed_data/srichards/male-female/female_Nvit_RNAseq_alignments_accepted_hits_GCA_000696855.1.bam"
+    },
+    {
+      "category": "BCM_v0.5.3/4. Transcriptome /Mapped Reads",
+      "key": "Hvit_male_RNAseq",
+      "label": "Hvit_male_RNAseq",
+      "metadata": {
+        "Alignment summary": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Glassy-winged_sharpshooter/RNA_sequence/tophat_male_Hvit_RNAseq_alignments/align_summary.txt",
+        "Analysis method": "TopHat v2.0.13",
+        "File provider": "Stephen Richards, Baylor College of Medicine",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Sex": "male"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "user_contributed_data/srichards/male-female/male_Nvit_RNAseq_alignments_accepted_hits_GCA_000696855.1.bam"
+    }
+  ]
 }
diff --git a/organisms/stage/Hyalella_azteca/trackList.json b/organisms/stage/Hyalella_azteca/trackList.json
index 38b4efe..153aae8 100644
--- a/organisms/stage/Hyalella_azteca/trackList.json
+++ b/organisms/stage/Hyalella_azteca/trackList.json
@@ -45,6 +45,7 @@
             "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
             "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
          },
+         "scoreType" : "avgScore",
          "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
          "style" : {
             "neg_color" : "rgba(255,255,0,50)",
@@ -56,12 +57,31 @@
       {
          "category" : "Official Gene Set",
          "compress" : 0,
+         "fmtDetailValue_Id" : "function (id, feature) {  var name2 = id.replace(/-R./, '');  if(feature.get('type')=='mRNA') {    return '<a target=_blank href=https://i5k.nal.usda.gov/'+name2+'>'+id+'</a>';} else { return id;}}",
          "key" : "OGSv1.2 Gene",
          "label" : "hyaazt_current_models",
+         "menuTemplate" : [
+            {
+               "label" : "View details"
+            },
+            {
+               "action" : "newWindow",
+               "iconClass" : "dijitIconDatabase",
+               "label" : "function(track,feature){ return 'Find NCBI record for '+feature.get('id').replace(/-R./, '')}",
+               "title" : "function(track,feature){ return 'Find NCBI record for '+feature.get('id').replace(/-R./, '')}",
+               "url" : "function(track,feature){ return 'https://www.ncbi.nlm.nih.gov/protein/'+feature.get('id').replace(/-R./, '')}"
+            }
+         ],
+         "metadata" : {
+            "Data provider" : "Helen Poynton; Li-Mei Chiang; Monica Poelchau",
+            "Data source" : "https://data.nal.usda.gov/dataset/hyalella-azteca-official-gene-set-v12",
+            "Materials and Methods" : "The Hyalella azteca Official Gene Set v1.0, originally generated from assembly Hyalella azteca Genome Assembly 1.0 (10.15482/USDA.ADC/1415994) was lifted over to Hazt_2.0 using the NCBI's remap service, the CrossMap software (http://crossmap.sourceforge.net/), and remap_gff3 (https://github.com/NAL-i5K/remap-gff3). This resulted in the unreleased OGSv1.1. OGSv1.1 received additional QA/QC during NCBI submission, generating Hyalella azteca OGSv1.2.",
+            "Publication status" : "Published, please cite https://doi.org/10.1021/acs.est.8b00837"
+         },
          "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
             "arrowheadClass" : "trellis-arrowhead",
-            "className" : "container-16px",
+            "className" : "{type}",
             "description" : "product, note, description",
             "subfeatureClasses" : {
                "CDS" : "gnomon_CDS",
@@ -70,17 +90,68 @@
                "wholeCDS" : null
             }
          },
-         "trackType" : "ColorByType/View/Track/ColorByTypeDraggable",
-         "type" : "ColorByType/View/Track/ColorByTypeDraggable",
-         "urlTemplate" : "tracks/hyaazt_current_models/{refseq}/trackData.json",
-	 "fmtDetailValue_Id": "function (id, feature) {  var name2 = id.replace(/\-R./, '');  if(feature.get('type')=='mRNA') {    return '<a target=_blank href=https://i5k.nal.usda.gov/'+name2+'>'+id+'</a>';} else { return id;}}", 
-	 "menuTemplate" : [ { "label" : "View details", }, { "label": "function(track,feature){ return 'Open gene page for '+feature.get('id').replace(/\-R./, '')}", "title": "function(track,feature){ return 'Open gene page for '+feature.get('id').replace(/\-R./, '')}", "iconClass" : "dijitIconDatabase", "action": "newWindow", "url" : "function(track,feature){ return 'https://i5k.nal.usda.gov/'+feature.get('id').replace(/\-R./, '')}", }, ],
+         "trackType" : "HTMLFeatures",
+         "type" : "HTMLFeatures",
+         "urlTemplate" : "tracks/hyaazt_current_models/{refseq}/trackData.json"
+      },
+      {
+         "category" : "RNA-Seq/Mapped Reads",
+         "key" : "Hyaazt_Hazt_2.0.1_RNA-Seq-alignments_2021-07-03",
+         "label" : "Hyaazt_Hazt_2.0.1_RNA-Seq-alignments_2021-07-03",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR3532635'>SRR3532635</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR3532639'>SRR3532639</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR3532640'>SRR3532640</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR3532636'>SRR3532636</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR3532634'>SRR3532634</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR3532644'>SRR3532644</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR3532645'>SRR3532645</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR3532638'>SRR3532638</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR3532633'>SRR3532633</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR3532641'>SRR3532641</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Dark red alignments: Mapped portion of read aligned to forward strand<br>Light red alignments: Spliced portion of read aligned to forward strand<br>Dark blue alignments: Mapped portion of read aligned to reverse strand<br>Light blue alignments: Spliced portion of read aligned to reverse strand<br>Red marking - deletion in the read relative to the reference<br>Green marking - insertion in the read relative to the reference<br>Yellow marking  - mismatch (hover over the mismatch to see what the snp is)"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "unsafePopup" : true,
+         "urlTemplate" : "analyses/Hyalella-azteca-RNA-Seq_2021-07-03_v1.0/Hyaazt_Hazt_2.0.1_RNA-Seq-alignments_2021-07-03.bam"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "RNA-Seq/Coverage Plots",
+         "key" : "Hyaazt_Hazt_2.0.1_RNA-Seq-alignments_2021-07-03_coverage",
+         "label" : "Hyaazt_Hazt_2.0.1_RNA-Seq-alignments_2021-07-03_coverage",
          "metadata" : {
-                    "Data source" : "https://data.nal.usda.gov/dataset/hyalella-azteca-official-gene-set-v12",
-                    "Materials and Methods" : "The Hyalella azteca Official Gene Set v1.0, originally generated from assembly Hyalella azteca Genome Assembly 1.0 (10.15482/USDA.ADC/1415994) was lifted over to Hazt_2.0 using the NCBI's remap service, the CrossMap software (http://crossmap.sourceforge.net/), and remap_gff3 (https://github.com/NAL-i5K/remap-gff3). This resulted in the unreleased OGSv1.1. OGSv1.1 received additional QA/QC during NCBI submission, generating Hyalella azteca OGSv1.2.",
-                    "Publication status" : "Published, please cite https://doi.org/10.1021/acs.est.8b00837",
-                    "Data provider" : "Helen Poynton; Li-Mei Chiang; Monica Poelchau"
-         }
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR3532635'>SRR3532635</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR3532639'>SRR3532639</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR3532640'>SRR3532640</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR3532636'>SRR3532636</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR3532634'>SRR3532634</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR3532644'>SRR3532644</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR3532645'>SRR3532645</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR3532638'>SRR3532638</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR3532633'>SRR3532633</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR3532641'>SRR3532641</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "unsafePopup" : true,
+         "urlTemplate" : "analyses/Hyalella-azteca-RNA-Seq_2021-07-03_v1.0/Hyaazt_Hazt_2.0.1_RNA-Seq-alignments_2021-07-03.bigwig"
+      },
+      {
+         "category" : "RNA-Seq/Splice junctions",
+         "compress" : 0,
+         "key" : "Hyaazt_Hazt_2.0.1_RNA-Seq-alignments_2021-07-03_junctions",
+         "label" : "Hyaazt_Hazt_2.0.1_RNA-Seq-alignments_2021-07-03_junctions",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR3532635'>SRR3532635</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR3532639'>SRR3532639</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR3532640'>SRR3532640</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR3532636'>SRR3532636</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR3532634'>SRR3532634</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR3532644'>SRR3532644</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR3532645'>SRR3532645</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR3532638'>SRR3532638</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR3532633'>SRR3532633</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR3532641'>SRR3532641</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Junction reads generated by Hisat2 aligner and regtools. The number of alignments supporting the junction read is listed in blue."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "className" : "feature",
+            "description" : "score"
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "unsafePopup" : true,
+         "urlTemplate" : "tracks/Hyaazt_Hazt_2.0.1_RNA-Seq-alignments_2021-07-03_junctions/{refseq}/trackData.json"
       }
    ]
 }
diff --git a/organisms/stage/Ladona_fulva/trackList.json b/organisms/stage/Ladona_fulva/trackList.json
new file mode 100644
index 0000000..bf5a17d
--- /dev/null
+++ b/organisms/stage/Ladona_fulva/trackList.json
@@ -0,0 +1,153 @@
+{
+   "formatVersion" : 1,
+   "names" : {
+      "type" : "Hash",
+      "url" : "names/"
+   },
+   "tracks" : [
+      {
+         "category" : "Reference sequence",
+         "chunkSize" : 20000,
+         "key" : "Reference sequence",
+         "label" : "DNA",
+         "seqType" : "dna",
+         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
+         "type" : "SequenceTrack",
+         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-"
+      },
+      {
+         "category" : "Official Gene Set",
+         "compress" : 0,
+         "key" : "Ladona fulva ladful_OGSv1.0 Gene",
+         "label" : "ladful_current_models",
+         "metadata" : {
+            "Data description" : "https://doi.org/10.15482/USDA.ADC/1520869",
+            "Data provider" : "National Agricultural Library",
+            "Data source" : "https://doi.org/10.15482/USDA.ADC/1520869",
+            "Method" : "https://doi.org/10.15482/USDA.ADC/1520869"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "menuTemplate" : [
+             {
+                "label" : "View details"
+             },
+             {
+              "label": "function(track,feature){ return 'Find NCBI record for '+feature.get('id')}",
+              "title": "function(track,feature){ return 'Find NCBI record for '+feature.get('id')}",
+              "iconClass" : "dijitIconDatabase",
+              "action": "newWindow",
+              "url" : "function(track,feature){ return 'https://www.ncbi.nlm.nih.gov/protein/'+feature.get('id')}"
+              }
+        ],
+         "style" : {
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "container-16px",
+            "description" : "product, note, description",
+            "subfeatureClasses" : {
+               "CDS" : "gnomon_CDS",
+               "UTR" : "gnomon_UTR",
+               "exon" : "container-100pct",
+               "wholeCDS" : null
+            }
+         },
+         "trackType" : "HTMLFeatures",
+         "type" : "HTMLFeatures",
+         "urlTemplate" : "tracks/ladful_current_models/{refseq}/trackData.json"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Reference Assembly",
+         "key" : "Gaps in assembly",
+         "label" : "Gaps in assembly",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "white",
+            "pos_color" : "black"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/GCA_000376725.2_Lful_2.0_genomic.fna.gaps.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "0.5",
+         "category" : "Reference Assembly",
+         "key" : "GC Content",
+         "label" : "GC Content",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+         },
+         "scoreType" : "avgScore",
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "rgba(255,255,0,50)",
+            "pos_color" : "rgba(0,0,255,50)"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/GCA_000376725.2_Lful_2.0_genomic.fna.gc.bigwig"
+      },
+      {
+         "category" : "RNA-Seq/Mapped Reads",
+         "key" : "Ladful_Lful_2.0_RNA-Seq-alignments_2021-10-05",
+         "label" : "Ladful_Lful_2.0_RNA-Seq-alignments_2021-10-05",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR1850403'>SRR1850403</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Dark red alignments: Mapped portion of read aligned to forward strand<br>Light red alignments: Spliced portion of read aligned to forward strand<br>Dark blue alignments: Mapped portion of read aligned to reverse strand<br>Light blue alignments: Spliced portion of read aligned to reverse strand<br>Red marking - deletion in the read relative to the reference<br>Green marking - insertion in the read relative to the reference<br>Yellow marking  - mismatch (hover over the mismatch to see what the snp is)"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "analyses/Ladona-fulva-RNA-Seq_2021-10-05_v1.0/Ladful_Lful_2.0_RNA-Seq-alignments_2021-10-05.bam"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "RNA-Seq/Coverage Plots",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR1850403'>SRR1850403</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage."
+         },
+         "key" : "Ladful_Lful_2.0_RNA-Seq-alignments_2021-10-05_coverage",
+         "label" : "Ladful_Lful_2.0_RNA-Seq-alignments_2021-10-05_coverage",
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "analyses/Ladona-fulva-RNA-Seq_2021-10-05_v1.0/Ladful_Lful_2.0_RNA-Seq-alignments_2021-10-05.bigwig"
+      },
+      {
+         "category" : "RNA-Seq/Splice junctions",
+         "compress" : 0,
+         "key" : "Ladful_Lful_2.0_RNA-Seq-alignments_2021-10-05_junctions",
+         "label" : "Ladful_Lful_2.0_RNA-Seq-alignments_2021-10-05_junctions",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR1850403'>SRR1850403</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Junction reads generated by Hisat2 aligner and regtools. The number of alignments supporting the junction read is listed in blue."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+	     "description":"score",
+            "className" : "feature"
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/Ladful_Lful_2.0_RNA-Seq-alignments_2021-10-05_junctions/{refseq}/trackData.json"
+      }
+   ]
+}
diff --git a/organisms/stage/Laodelphax_striatellus/trackList.json b/organisms/stage/Laodelphax_striatellus/trackList.json
index 124931d..3f7ee9f 100755
--- a/organisms/stage/Laodelphax_striatellus/trackList.json
+++ b/organisms/stage/Laodelphax_striatellus/trackList.json
@@ -1,161 +1,162 @@
 {
-   "formatVersion" : 1,
-   "names" : {
-      "type" : "Hash",
-      "url" : "names/"
-   },
-   "refSeqs" : "seq/GCA_003335185.2_ASM333518v2_genomic.fna.fai",
-   "tracks" : [
-      {
-         "category" : "Reference sequence",
-         "chunkSize" : 20000,
-         "key" : "Reference sequence",
-         "label" : "DNA",
-         "seqType" : "dna",
-         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
-         "type" : "SequenceTrack",
-         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-"
+  "formatVersion": 1,
+  "names": {
+    "type": "Hash",
+    "url": "names/"
+  },
+  "refSeqs": "seq/GCA_003335185.2_ASM333518v2_genomic.fna.fai",
+  "tracks": [
+    {
+      "category": "Reference sequence",
+      "chunkSize": 20000,
+      "key": "Reference sequence",
+      "label": "DNA",
+      "seqType": "dna",
+      "storeClass": "JBrowse/Store/Sequence/StaticChunked",
+      "type": "SequenceTrack",
+      "urlTemplate": "seq/{refseq_dirpath}/{refseq}-"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Reference Assembly",
+      "key": "Gaps in assembly",
+      "label": "Gaps in assembly",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
       },
-      {
-         "autoscale" : "local",
-         "bicolor_pivot" : "zero",
-         "category" : "Reference Assembly",
-         "key" : "Gaps in assembly",
-         "label" : "Gaps in assembly",
-         "metadata" : {
-            "Track contact" : "The i5k workspace@NAL",
-            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
-            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
-         },
-         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
-         "style" : {
-            "neg_color" : "white",
-            "pos_color" : "black"
-         },
-         "type" : "JBrowse/View/Track/Wiggle/Density",
-         "urlTemplate" : "bigwig/GCA_003335185.2_ASM333518v2_genomic.fna.gaps.bigwig"
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "white",
+        "pos_color": "black"
       },
-      {
-         "autoscale" : "local",
-         "bicolor_pivot" : "0.5",
-         "category" : "Reference Assembly",
-         "key" : "GC Content",
-         "label" : "GC Content",
-         "metadata" : {
-            "Track contact" : "The i5k workspace@NAL",
-            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
-            "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
-         },
-         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
-         "style" : {
-            "neg_color" : "rgba(255,255,0,50)",
-            "pos_color" : "rgba(0,0,255,50)"
-         },
-         "type" : "JBrowse/View/Track/Wiggle/Density",
-         "urlTemplate" : "bigwig/GCA_003335185.2_ASM333518v2_genomic.fna.gc.bigwig"
+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "bigwig/GCA_003335185.2_ASM333518v2_genomic.fna.gaps.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "0.5",
+      "category": "Reference Assembly",
+      "key": "GC Content",
+      "label": "GC Content",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
       },
-      {
-         "category" : "DNA-Seq/Variant Information",
-         "key" : "ASM333518v2-variant-alignment_v1.1_4-5-2019",
-         "label" : "ASM333518v2-variant-alignment_v1.1_4-5-2019",
-         "metadata" : {
-            "Data provider" : "Junjie Zhu, Chinese Academy of Sciences",
-            "Data source" : "http://dx.doi.org/10.5524/100361",
-            "Materials and Methods" : "http://dx.doi.org/10.5524/100361",
-            "Publication status" : "Published, please cite http://dx.doi.org/10.5524/100361 and https://doi:10.1093/gigascience/gix109"
-         },
-         "storeClass" : "JBrowse/Store/SeqFeature/VCFTabix",
-         "type" : "JBrowse/View/Track/HTMLVariants",
-         "urlTemplate" : "ASM333518v2-variant-alignment_v1.1_4-5-2019/ASM333518v2-variant-alignment_v1.1_4-5-2019.vcf.gz"
+      "scoreType": "avgScore",
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "rgba(255,255,0,50)",
+        "pos_color": "rgba(0,0,255,50)"
       },
-      {
-         "category" : "Official Gene Set",
-         "compress" : 0,
-         "key" : "laostr_OGSv1.2 gene",
-         "label" : "laostr_current_models",
-         "fmtDetailValue_Id": "function (id, feature) {  var name2 = id.replace(/\-R./, '');  if(feature.get('type')=='mRNA') {    return '<a target=_blank href=https://i5k.nal.usda.gov/'+name2+'>'+id+'</a>';} else { return id;}}",
-         "menuTemplate" : [
-             {
-                "label" : "View details",
-             },
-             {
-              "label": "function(track,feature){ return 'Open gene page for '+feature.get('id').replace(/\-R./, '')}",
-              "title": "function(track,feature){ return 'Open gene page for '+feature.get('id').replace(/\-R./, '')}",
-              "iconClass" : "dijitIconDatabase",
-              "action": "newWindow",
-              "url" : "function(track,feature){ return 'https://i5k.nal.usda.gov/'+feature.get('id').replace(/\-R./, '')}",
-              },
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-            "Data source" : "http://dx.doi.org/10.5524/100361",
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-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
-         "style" : {
-            "arrowheadClass" : "trellis-arrowhead",
-            "className" : "container-16px",
-            "description" : "product, note, description",
-            "subfeatureClasses" : {
-               "CDS" : "gnomon_CDS",
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-            }
-         },
-         "trackType" : "ColorByType/View/Track/ColorByTypeDraggable",
-         "type" : "ColorByType/View/Track/ColorByTypeDraggable",
-         "urlTemplate" : "tracks/laostr_current_models/{refseq}/trackData.json"
+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "bigwig/GCA_003335185.2_ASM333518v2_genomic.fna.gc.bigwig"
+    },
+    {
+      "category": "DNA-Seq/Variant Information",
+      "key": "ASM333518v2-variant-alignment_v1.1_4-5-2019",
+      "label": "ASM333518v2-variant-alignment_v1.1_4-5-2019",
+      "metadata": {
+        "Data provider": "Junjie Zhu, Chinese Academy of Sciences",
+        "Data source": "http://dx.doi.org/10.5524/100361",
+        "Materials and Methods": "http://dx.doi.org/10.5524/100361",
+        "Publication status": "Published, please cite http://dx.doi.org/10.5524/100361 and https://doi:10.1093/gigascience/gix109"
       },
-      {
-         "category" : "Official Gene Set",
-         "compress" : 0,
-         "key" : "laostr_OGS_v1.2 pseudogene",
-         "label" : "laostr_OGS_v1.2_pseudogene",
-         "metadata" : {
-            "Data provider" : "Junjie Zhu, Chinese Academy of Sciences",
-            "Data source" : "http://dx.doi.org/10.5524/100361",
-            "Materials and Methods" : "http://dx.doi.org/10.5524/100361",
-            "Publication status" : "Published, please cite http://dx.doi.org/10.5524/100361 and https://doi:10.1093/gigascience/gix109"
-         },
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
-         "style" : {
-            "arrowheadClass" : "trellis-arrowhead",
-            "className" : "container-16px",
-            "description" : "product, note, description",
-            "subfeatureClasses" : {
-               "CDS" : "gnomon_CDS",
-               "UTR" : "gnomon_UTR",
-               "exon" : "container-100pct",
-               "wholeCDS" : null
-            }
-         },
-         "trackType" : "HTMLFeatures",
-         "type" : "HTMLFeatures",
-         "urlTemplate" : "tracks/laostr_OGS_v1.2_pseudogene/{refseq}/trackData.json"
+      "storeClass": "JBrowse/Store/SeqFeature/VCFTabix",
+      "type": "JBrowse/View/Track/HTMLVariants",
+      "urlTemplate": "ASM333518v2-variant-alignment_v1.1_4-5-2019/ASM333518v2-variant-alignment_v1.1_4-5-2019.vcf.gz"
+    },
+    {
+      "category": "Official Gene Set",
+      "compress": 0,
+      "fmtDetailValue_Id": "function (id, feature) {  var name2 = id.replace(/-R./, '');  if(feature.get('type')=='mRNA') {    return '<a target=_blank href=https://i5k.nal.usda.gov/'+name2+'>'+id+'</a>';} else { return id;}}",
+      "key": "laostr_OGSv1.2 gene",
+      "label": "laostr_current_models",
+      "menuTemplate": [
+        {
+          "label": "View details"
+        },
+        {
+          "action": "newWindow",
+          "iconClass": "dijitIconDatabase",
+          "label": "function(track,feature){ return 'Find NCBI record for '+feature.get('id').replace(/-R./, '')}",
+          "title": "function(track,feature){ return 'Find NCBI record for '+feature.get('id').replace(/-R./, '')}",
+          "url": "function(track,feature){ return 'https://www.ncbi.nlm.nih.gov/protein/'+feature.get('id').replace(/-R./, '')}"
+        }
+      ],
+      "metadata": {
+        "Data provider": "Junjie Zhu, Chinese Academy of Sciences",
+        "Data source": "http://dx.doi.org/10.5524/100361",
+        "Materials and Methods": "http://dx.doi.org/10.5524/100361",
+        "Publication status": "Published, please cite http://dx.doi.org/10.5524/100361 and https://doi:10.1093/gigascience/gix109"
       },
-      {
-         "category" : "Sequence composition calculation/RepeatMasker",
-         "compress" : 0,
-         "key" : "ASM333518v2_Laodelphax_striatellus.RepeatMasker_v1.1_4-5-2019",
-         "label" : "ASM333518v2_Laodelphax_striatellus.RepeatMasker_v1.1_4-5-2019",
-         "metadata" : {
-            "Data provider" : "Junjie Zhu, Chinese Academy of Sciences",
-            "Data source" : "http://dx.doi.org/10.5524/100361",
-            "Materials and Methods" : "http://dx.doi.org/10.5524/100361",
-            "Publication status" : "Published, please cite http://dx.doi.org/10.5524/100361 and https://doi:10.1093/gigascience/gix109"
-         },
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
-         "style" : {
-            "arrowheadClass" : "trellis-arrowhead",
-            "className" : "feature",
-            "description" : "target",
-            "renderClassName" : "repeat"
-         },
-         "trackType" : "HTMLFeatures",
-         "type" : "HTMLFeatures",
-         "urlTemplate" : "tracks/ASM333518v2_Laodelphax_striatellus.RepeatMasker_v1.1_4-5-2019/{refseq}/trackData.json"
-      }
-   ]
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "description": "product, note, description",
+        "subfeatureClasses": {
+          "CDS": "gnomon_CDS",
+          "UTR": "gnomon_UTR",
+          "exon": "container-100pct",
+          "wholeCDS": null
+        }
+      },
+      "trackType": "HTMLFeatures",
+      "type": "HTMLFeatures",
+      "urlTemplate": "tracks/laostr_current_models/{refseq}/trackData.json"
+    },
+    {
+      "category": "Official Gene Set",
+      "compress": 0,
+      "key": "laostr_OGS_v1.2 pseudogene",
+      "label": "laostr_OGS_v1.2_pseudogene",
+      "metadata": {
+        "Data provider": "Junjie Zhu, Chinese Academy of Sciences",
+        "Data source": "http://dx.doi.org/10.5524/100361",
+        "Materials and Methods": "http://dx.doi.org/10.5524/100361",
+        "Publication status": "Published, please cite http://dx.doi.org/10.5524/100361 and https://doi:10.1093/gigascience/gix109"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "description": "product, note, description",
+        "subfeatureClasses": {
+          "CDS": "gnomon_CDS",
+          "UTR": "gnomon_UTR",
+          "exon": "container-100pct",
+          "wholeCDS": null
+        }
+      },
+      "trackType": "HTMLFeatures",
+      "type": "HTMLFeatures",
+      "urlTemplate": "tracks/laostr_OGS_v1.2_pseudogene/{refseq}/trackData.json"
+    },
+    {
+      "category": "Sequence composition calculation/RepeatMasker",
+      "compress": 0,
+      "key": "ASM333518v2_Laodelphax_striatellus.RepeatMasker_v1.1_4-5-2019",
+      "label": "ASM333518v2_Laodelphax_striatellus.RepeatMasker_v1.1_4-5-2019",
+      "metadata": {
+        "Data provider": "Junjie Zhu, Chinese Academy of Sciences",
+        "Data source": "http://dx.doi.org/10.5524/100361",
+        "Materials and Methods": "http://dx.doi.org/10.5524/100361",
+        "Publication status": "Published, please cite http://dx.doi.org/10.5524/100361 and https://doi:10.1093/gigascience/gix109"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "feature",
+        "description": "target",
+        "renderClassName": "repeat"
+      },
+      "trackType": "HTMLFeatures",
+      "type": "HTMLFeatures",
+      "urlTemplate": "tracks/ASM333518v2_Laodelphax_striatellus.RepeatMasker_v1.1_4-5-2019/{refseq}/trackData.json"
+    }
+  ]
 }
diff --git a/organisms/stage/Lasioglossum_albipes/trackList.json b/organisms/stage/Lasioglossum_albipes/trackList.json
index 476668f..b1ff640 100644
--- a/organisms/stage/Lasioglossum_albipes/trackList.json
+++ b/organisms/stage/Lasioglossum_albipes/trackList.json
@@ -1,169 +1,223 @@
 {
-   "css" : "data/contrib_styles.css",
+   "alwaysOnTracks" : "DNA,Annotations",
+   "css" : "./plugins/NAL_CSS/css/main.css",
+   "favicon" : "./plugins/WebApollo/img/webapollo_favicon.ico",
+   "formatVersion" : 1,
+   "names" : {
+      "type" : "Hash",
+      "url" : "names/"
+   },
    "share_link" : 0,
-   "plugins" : [
-      {
-         "location" : "./plugins/WebApollo",
-         "name" : "WebApollo"
-      }
-   ],
    "tracks" : [
       {
-         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
+         "category" : "Reference sequence",
          "chunkSize" : 20000,
-         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-",
+         "key" : "Reference sequence",
          "label" : "DNA",
+         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
          "type" : "SequenceTrack",
-         "category" : "Reference sequence",
-         "key" : "Reference sequence"
+         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-"
       },
       {
          "autocomplete" : "none",
+         "compress" : 0,
+         "key" : "User-created Annotations",
+         "label" : "Annotations",
+         "phase" : 0,
+         "storeClass" : "WebApollo/Store/SeqFeature/ScratchPad",
          "style" : {
-            "className" : "annot",
-            "renderClassName" : "annot-render",
-            "subfeatureClasses" : {
-               "non_canonical_three_prime_splice_site" : "noncanonical-splice-site",
-               "wholeCDS" : null,
-               "exon" : "container-100pct",
-               "CDS" : "annot-CDS",
-               "non_canonical_five_prime_splice_site" : "noncanonical-splice-site",
-               "UTR" : "annot-UTR"
-            },
-            "arrowheadClass" : "annot-arrowhead",
             "alternateClasses" : {
-               "transposable_element" : {
-                  "renderClassName" : "blue-ibeam-render",
-                  "className" : "blue-ibeam"
+               "miRNA" : {
+                  "className" : "brightgreen-80pct",
+                  "renderClassName" : "gray-center-30pct"
                },
-               "pseudogene" : {
-                  "renderClassName" : "gray-center-30pct",
-                  "className" : "light-purple-80pct"
+               "ncRNA" : {
+                  "className" : "brightgreen-80pct",
+                  "renderClassName" : "gray-center-30pct"
                },
-               "snRNA" : {
-                  "renderClassName" : "gray-center-30pct",
-                  "className" : "brightgreen-80pct"
+               "pseudogene" : {
+                  "className" : "light-purple-80pct",
+                  "renderClassName" : "gray-center-30pct"
                },
                "rRNA" : {
-                  "renderClassName" : "gray-center-30pct",
-                  "className" : "brightgreen-80pct"
-               },
-               "snoRNA" : {
-                  "renderClassName" : "gray-center-30pct",
-                  "className" : "brightgreen-80pct"
+                  "className" : "brightgreen-80pct",
+                  "renderClassName" : "gray-center-30pct"
                },
                "repeat_region" : {
                   "className" : "magenta-80pct"
                },
-               "miRNA" : {
-                  "renderClassName" : "gray-center-30pct",
-                  "className" : "brightgreen-80pct"
+               "snRNA" : {
+                  "className" : "brightgreen-80pct",
+                  "renderClassName" : "gray-center-30pct"
+               },
+               "snoRNA" : {
+                  "className" : "brightgreen-80pct",
+                  "renderClassName" : "gray-center-30pct"
                },
                "tRNA" : {
-                  "renderClassName" : "gray-center-30pct",
-                  "className" : "brightgreen-80pct"
+                  "className" : "brightgreen-80pct",
+                  "renderClassName" : "gray-center-30pct"
                },
-               "ncRNA" : {
-                  "renderClassName" : "gray-center-30pct",
-                  "className" : "brightgreen-80pct"
+               "transposable_element" : {
+                  "className" : "blue-ibeam",
+                  "renderClassName" : "blue-ibeam-render"
                }
             },
-            "uniqueIdField" : "id",
+            "arrowheadClass" : "annot-arrowhead",
             "centerSubFeature" : {
-               "non_canonical_three_prime_splice_site" : false,
-               "non_canonical_five_prime_splice_site" : false
-            }
-         },
-         "key" : "User-created Annotations",
-         "storeClass" : "WebApollo/Store/SeqFeature/ScratchPad",
-         "phase" : 0,
-         "compress" : 0,
-         "label" : "Annotations",
-         "type" : "WebApollo/View/Track/AnnotTrack",
-         "subfeatures" : 1
-      },
-      {
-         "style" : {
-            "className" : "container-16px",
+               "non_canonical_five_prime_splice_site" : false,
+               "non_canonical_three_prime_splice_site" : false
+            },
+            "className" : "annot",
+            "renderClassName" : "annot-render",
             "subfeatureClasses" : {
-               "wholeCDS" : null,
+               "CDS" : "annot-CDS",
+               "UTR" : "annot-UTR",
                "exon" : "container-100pct",
-               "CDS" : "primary_gene_set-cds",
-               "UTR" : "primary_gene_set-utr"
+               "non_canonical_five_prime_splice_site" : "noncanonical-splice-site",
+               "non_canonical_three_prime_splice_site" : "noncanonical-splice-site",
+               "wholeCDS" : null
             },
-            "arrowheadClass" : "trellis-arrowhead"
+            "uniqueIdField" : "id"
          },
-         "key" : "Lalb_OGSv5.42",
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
-         "trackType" : null,
-         "urlTemplate" : "tracks/lasalb_current_models/{refseq}/trackData.json",
-         "compress" : 0,
-         "type" : "FeatureTrack",
+         "subfeatures" : 1,
+         "type" : "WebApollo/View/Track/AnnotTrack"
+      },
+      {
          "category" : "Lasioglossum albipes OGSv5.42/1. Gene Sets/Protein Coding",
+         "compress" : 0,
+         "key" : "Lalb_OGSv5.42",
+         "label" : "lasalb_current_models",
          "menuTemplate" : [
-             {
-                "label" : "View details",
-             },
-             {
-              "label": "function(track,feature){ return 'Search HymenopteraMine for '+feature.get('id')}",
-              "title": "function(track,feature){ return 'Search HymenopteraMine for '+feature.get('id')}",
-              "iconClass" : "dijitIconDatabase",
-              "action": "newWindow",
-              "url" : "function(track,feature){ return 'http://128.206.116.3:8080/hymenopteramine/keywordSearchResults.do?searchTerm='+feature.get('id')+'&searchSubmit=Search'}",
-              },
-        ],
+            {
+               "label" : "View details"
+            },
+            {
+               "action" : "newWindow",
+               "iconClass" : "dijitIconDatabase",
+               "label" : "function(track,feature){ return 'Search HymenopteraMine for '+feature.get('id')}",
+               "title" : "function(track,feature){ return 'Search HymenopteraMine for '+feature.get('id')}",
+               "url" : "function(track,feature){ return 'http://128.206.116.3:8080/hymenopteramine/keywordSearchResults.do?searchTerm='+feature.get('id')+'&searchSubmit=Search'}"
+            }
+         ],
          "metadata" : {
+            "Data provider" : "Kocher, SD. Harvard University",
             "Data source" : "http://hymenopteragenome.org/beebase/sites/hymenopteragenome.org.beebase/files/data/consortium_data/Lalb_OGS_v5.42.gff.gz",
             "Method" : "For full methods, see the associated publication, PMID 24359881",
-            "Data provider" : "Kocher, SD. Harvard University",
-	    "Other notes" : "The original file was transformed to GenBank coordinates by the NAL. Several gene models predicted on the original assembly were lost during the coordinate transformation due to changes in the assembly."
+            "Other notes" : "The original file was transformed to GenBank coordinates by the NAL. Several gene models predicted on the original assembly were lost during the coordinate transformation due to changes in the assembly."
          },
-         "label" : "lasalb_current_models"
-      },
-      {
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "pos_color" : "black",
-            "neg_color" : "white"
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "{type}",
+            "subfeatureClasses" : {
+               "CDS" : "primary_gene_set-cds",
+               "UTR" : "primary_gene_set-utr",
+               "exon" : "container-100pct",
+               "wholeCDS" : null
+            }
          },
-         "bicolor_pivot" : "zero",
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/lasalb_current_models/{refseq}/trackData.json"
+      },
+      {
          "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Reference Assembly",
          "key" : "Gaps in assembly",
-         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
-         "urlTemplate" : "bigwig/GCA_000346575.1_ASM34657v1_genomic_GenBankIDs.fna.gaps.bigwig",
          "label" : "Gaps in assembly",
-         "category" : "Reference Assembly",
          "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
             "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
-            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank",
-            "Track contact" : "The i5k workspace@NAL"
+            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "white",
+            "pos_color" : "black"
          },
-         "type" : "JBrowse/View/Track/Wiggle/Density"
+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/GCA_000346575.1_ASM34657v1_genomic_GenBankIDs.fna.gaps.bigwig"
       },
       {
+         "autoscale" : "local",
+         "bicolor_pivot" : "0.5",
+         "category" : "Reference Assembly",
+         "key" : "GC Content",
+         "label" : "GC Content",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+         },
+         "scoreType" : "avgScore",
          "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
-         "urlTemplate" : "bigwig/GCA_000346575.1_ASM34657v1_genomic_GenBankIDs.fna.gc.bigwig",
          "style" : {
             "neg_color" : "rgba(255,255,0,50)",
             "pos_color" : "rgba(0,0,255,50)"
          },
-         "label" : "GC Content",
          "type" : "JBrowse/View/Track/Wiggle/Density",
-         "bicolor_pivot" : "0.5",
-         "key" : "GC Content",
-         "category" : "Reference Assembly",
+         "urlTemplate" : "bigwig/GCA_000346575.1_ASM34657v1_genomic_GenBankIDs.fna.gc.bigwig"
+      },
+      {
+         "category" : "RNA-Seq/Mapped Reads",
+         "key" : "Lasalb_ASM34657v1_RNA-Seq-alignments_2021-06-16",
+         "label" : "Lasalb_ASM34657v1_RNA-Seq-alignments_2021-06-16",
          "metadata" : {
-            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
-            "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track.",
-            "Track contact" : "The i5k workspace@NAL"
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR578269'>SRR578269</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR12340134'>SRR12340134</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Dark red alignments: Mapped portion of read aligned to forward strand<br>Light red alignments: Spliced portion of read aligned to forward strand<br>Dark blue alignments: Mapped portion of read aligned to reverse strand<br>Light blue alignments: Spliced portion of read aligned to reverse strand<br>Red marking - deletion in the read relative to the reference<br>Green marking - insertion in the read relative to the reference<br>Yellow marking  - mismatch (hover over the mismatch to see what the snp is)"
          },
-         "autoscale" : "local"
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "unsafePopup" : true,
+         "urlTemplate" : "analyses/Lasioglossum-albipes-RNA-Seq_2021-06-16_v1.0/Lasalb_ASM34657v1_RNA-Seq-alignments_2021-06-16.bam"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "RNA-Seq/Coverage Plots",
+         "key" : "Lasalb_ASM34657v1_RNA-Seq-alignments_2021-06-16_coverage",
+         "label" : "Lasalb_ASM34657v1_RNA-Seq-alignments_2021-06-16_coverage",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR578269'>SRR578269</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR12340134'>SRR12340134</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "unsafePopup" : true,
+         "urlTemplate" : "analyses/Lasioglossum-albipes-RNA-Seq_2021-06-16_v1.0/Lasalb_ASM34657v1_RNA-Seq-alignments_2021-06-16.bigwig"
+      },
+      {
+         "category" : "RNA-Seq/Splice junctions",
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diff --git a/organisms/stage/Latrodectus_hesperus/trackList.json b/organisms/stage/Latrodectus_hesperus/trackList.json
index 60fb02e..b72b172 100755
--- a/organisms/stage/Latrodectus_hesperus/trackList.json
+++ b/organisms/stage/Latrodectus_hesperus/trackList.json
@@ -1,1217 +1,1211 @@
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+        "Track legend": "Results from Protein2genome alignments of a set of Echinodermata proteins as part of the MAKER automated annotation pipeline."
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+        "Data provider": "Daniel Hughes, Baylor College of Medicine",
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+        "Data provider": "Daniel Hughes, Baylor College of Medicine",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline."
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+      "key": "protein2genome_Placozoa",
+      "label": "protein2genome_Placozoa",
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+        "Data description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Data provider": "Daniel Hughes, Baylor College of Medicine",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline."
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+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
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+        "arrowheadClass": "webapollo-arrowhead",
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+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+      "key": "protein2genome_Platyhelminthes",
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+        "Data description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Data provider": "Daniel Hughes, Baylor College of Medicine",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline."
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+        "arrowheadClass": "webapollo-arrowhead",
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+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Priapulida",
+      "label": "protein2genome_Priapulida",
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+        "Data description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Data provider": "Daniel Hughes, Baylor College of Medicine",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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+          "match_part": "protein2genome"
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+      "urlTemplate": "tracks/protein2genome_Priapulida/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Tardigrada",
+      "label": "protein2genome_Tardigrada",
+      "metadata": {
+        "Data description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Data provider": "Daniel Hughes, Baylor College of Medicine",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
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+          "match_part": "protein2genome"
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Tardigrada/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Tunicata",
+      "label": "protein2genome_Tunicata",
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+        "Data description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Data provider": "Daniel Hughes, Baylor College of Medicine",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline."
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+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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+      "urlTemplate": "tracks/protein2genome_Tunicata/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_UNCATEGORISED",
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+        "Data description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Data provider": "Daniel Hughes, Baylor College of Medicine",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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+      "urlTemplate": "tracks/protein2genome_UNCATEGORISED/{refseq}/trackData.json"
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+      "category": "BCM_v0.5.3/2. Evidence/Repeats",
+      "compress": 0,
+      "key": "repeatmasker",
+      "label": "repeatmasker",
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+        "Data description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Data provider": "Daniel Hughes, Baylor College of Medicine",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from RepeatMasker as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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+    {
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+      "key": "repeatrunner",
+      "label": "repeatrunner",
+      "metadata": {
+        "Data description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Data provider": "Daniel Hughes, Baylor College of Medicine",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Repeatrunner as part of the MAKER automated annotation pipeline."
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+        "Data description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Data provider": "Daniel Hughes, Baylor College of Medicine",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline."
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+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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+      "key": "User-created Annotations",
+      "label": "Annotations",
+      "phase": 0,
+      "storeClass": "WebApollo/Store/SeqFeature/ScratchPad",
+      "style": {
+        "alternateClasses": {
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+            "renderClassName": "gray-center-30pct"
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+            "className": "brightgreen-80pct",
+            "renderClassName": "gray-center-30pct"
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+            "renderClassName": "gray-center-30pct"
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+            "renderClassName": "gray-center-30pct"
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+            "renderClassName": "gray-center-30pct"
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+            "renderClassName": "gray-center-30pct"
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+            "renderClassName": "gray-center-30pct"
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+        },
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+          "non_canonical_three_prime_splice_site": false
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+          "non_canonical_five_prime_splice_site": "noncanonical-splice-site",
+          "non_canonical_three_prime_splice_site": "noncanonical-splice-site",
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+        },
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+      "subfeatures": 1,
+      "type": "WebApollo/View/Track/AnnotTrack"
+    },
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+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Reference Assembly",
+      "key": "Gaps in assembly",
+      "label": "Gaps in assembly",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "white",
+        "pos_color": "black"
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+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "bigwig/GCA_000697925.1_Lhes_1.0_genomic.fna.gaps.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "0.5",
+      "category": "Reference Assembly",
+      "key": "GC Content",
+      "label": "GC Content",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+      },
+      "scoreType": "avgScore",
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "rgba(255,255,0,50)",
+        "pos_color": "rgba(0,0,255,50)"
+      },
+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "bigwig/GCA_000697925.1_Lhes_1.0_genomic.fna.gc.bigwig"
+    }
+  ]
 }
diff --git a/organisms/stage/Leptinotarsa_decemlineata/trackList.json b/organisms/stage/Leptinotarsa_decemlineata/trackList.json
index 46e7b84..ecd41fb 100644
--- a/organisms/stage/Leptinotarsa_decemlineata/trackList.json
+++ b/organisms/stage/Leptinotarsa_decemlineata/trackList.json
@@ -1,511 +1,571 @@
 {
+   "formatVersion" : 1,
+   "names" : {
+      "type" : "Hash",
+      "url" : "names/"
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    "tracks" : [
       {
-         "seqType" : "dna",
+         "category" : "Reference sequence",
+         "faiUrlTemplate" : "seq/GCF_000500325.1_Ldec_2.0_genomic.fna.fai",
          "key" : "Reference sequence",
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-         "urlTemplate" : "seq/GCF_000500325.1_Ldec_2.0_genomic.fna",
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-         "faiUrlTemplate" : "seq/GCF_000500325.1_Ldec_2.0_genomic.fna.fai"
+         "urlTemplate" : "seq/GCF_000500325.1_Ldec_2.0_genomic.fna",
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-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
-         "trackType" : null,
-         "urlTemplate" : "tracks/lepdec_current_models/{refseq}/trackData.json",
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          "compress" : 0,
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          "label" : "lepdec_current_models",
          "metadata" : {
+            "Data description" : "https://doi.org/10.1038/s41598-018-20154-1",
             "Data source" : "https://i5k.nal.usda.gov/node/739326/",
-            "Method" : "A MAKER2 gene set (https://i5k.nal.usda.gov/node/291080) was merged with Apollo-curated manual annotations and miRNA annotations using the GFF3toolkit software (https://github.com/NAL-i5K/GFF3toolkit/). This gene set, OGSv1.1 is described in doi:10.1038/s41598-018-20154-1. OGSv1.1 was mapped to the updated genome assembly Ldec2.0 (https://i5k.nal.usda.gov/node/739326/) using the program remap-gff3 (https://github.com/NAL-i5K/remap-gff3), resulting in OGSv1.2.",
-            "Data description" : "https://doi.org/10.1038/s41598-018-20154-1"
+            "Method" : "A MAKER2 gene set (https://i5k.nal.usda.gov/node/291080) was merged with Apollo-curated manual annotations and miRNA annotations using the GFF3toolkit software (https://github.com/NAL-i5K/GFF3toolkit/). This gene set, OGSv1.1 is described in doi:10.1038/s41598-018-20154-1. OGSv1.1 was mapped to the updated genome assembly Ldec2.0 (https://i5k.nal.usda.gov/node/739326/) using the program remap-gff3 (https://github.com/NAL-i5K/remap-gff3), resulting in OGSv1.2."
          },
-         "category" : "Official Gene Set v1.2/1. Gene Sets/Protein Coding",
-         "type" : "FeatureTrack"
-      },
-      {
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          "style" : {
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diff --git a/organisms/stage/Leptinotarsa_decemlineata_training/trackList.json b/organisms/stage/Leptinotarsa_decemlineata_training/trackList.json
index 5add448..9edadf2 100644
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+      "key": "protein2genome_Nematomorpha",
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+      "key": "protein2genome_Onychophora",
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+      "label": "protein2genome_Parazoa",
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+      "key": "protein2genome_Placozoa",
+      "label": "protein2genome_Placozoa",
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+      "key": "protein2genome_Platyhelminthes",
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+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
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+      "key": "protein2genome_Priapulida",
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+      "key": "repeatmasker",
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+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from RepeatMasker as part of the MAKER automated annotation pipeline."
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+      "key": "repeatrunner",
+      "label": "repeatrunner",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
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diff --git a/organisms/stage/Limnephilus_lunatus/trackList.json b/organisms/stage/Limnephilus_lunatus/trackList.json
index 3aaf1d2..3c75026 100644
--- a/organisms/stage/Limnephilus_lunatus/trackList.json
+++ b/organisms/stage/Limnephilus_lunatus/trackList.json
@@ -1,1348 +1,1244 @@
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+        "Track legend": "Results from Blastx alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline."
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+      "label": "blastx_Onychophora",
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+        "Track legend": "Results from Blastx alignments of a set of Onychophora proteins as part of the MAKER automated annotation pipeline."
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+        "Track legend": "Results from Blastx alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline."
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+        "Track legend": "Results from Blastx alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline."
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+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Blastx alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline."
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+      "key": "cegma",
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+      "key": "est_gff:cufflinks_i5k",
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+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from EST alignments resulting from the Cufflinks software as part of the MAKER automated annotation pipeline."
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+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline."
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+      "label": "protein2genome_Platyhelminthes",
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+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline."
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-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
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+      "key": "protein2genome_Priapulida",
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+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline."
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-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
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+      "key": "protein2genome_Tardigrada",
+      "label": "protein2genome_Tardigrada",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline."
+      },
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-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
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+      "key": "protein2genome_Tunicata",
+      "label": "protein2genome_Tunicata",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline."
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-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
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+      "key": "protein2genome_UNCATEGORISED",
+      "label": "protein2genome_UNCATEGORISED",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline."
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+        "arrowheadClass": "webapollo-arrowhead",
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-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
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+      "category": "BCM_v0.5.3/2. Evidence/Repeats",
+      "compress": 0,
+      "key": "repeatmasker",
+      "label": "repeatmasker",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from RepeatMasker as part of the MAKER automated annotation pipeline."
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+        "arrowheadClass": "webapollo-arrowhead",
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-        "Track legend" : "Results from RepeatMasker as part of the MAKER automated annotation pipeline.",
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-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
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+      "key": "repeatrunner",
+      "label": "repeatrunner",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Repeatrunner as part of the MAKER automated annotation pipeline."
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-        "Track legend" : "Results from Repeatrunner as part of the MAKER automated annotation pipeline.",
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
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-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
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+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline."
+      },
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+        "arrowheadClass": "webapollo-arrowhead",
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-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
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+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Reference Assembly",
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+        "Track contact": "The i5k workspace@NAL",
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+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
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index a1a46a3..d54fd3c 100644
--- a/organisms/stage/Locusta_migratoria/trackList.json
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diff --git a/organisms/stage/Loxosceles_reclusa/trackList.json b/organisms/stage/Loxosceles_reclusa/trackList.json
index add4941..5d4419d 100644
--- a/organisms/stage/Loxosceles_reclusa/trackList.json
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+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from RepeatMasker as part of the MAKER automated annotation pipeline."
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+      "key": "repeatrunner",
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+        "Data provider": "Daniel Hughes, Baylor College of Medicine",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Repeatrunner as part of the MAKER automated annotation pipeline."
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+      "compress": 0,
+      "key": "SNAP gene predictions",
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+        "Data provider": "Daniel Hughes, Baylor College of Medicine",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline."
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+      "key": "User-created Annotations",
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+      "phase": 0,
+      "storeClass": "WebApollo/Store/SeqFeature/ScratchPad",
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+          "transposable_element": {
+            "className": "blue-ibeam",
+            "renderClassName": "blue-ibeam-render"
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         },
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-        	    "Track contact" : "The i5k workspace@NAL",
-        	    "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance."
+        "arrowheadClass": "annot-arrowhead",
+        "centerSubFeature": {
+          "non_canonical_five_prime_splice_site": false,
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         },
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-   ],
-   "favicon" : "./plugins/WebApollo/img/webapollo_favicon.ico",
-   "alwaysOnTracks" : "DNA,Annotations",
-   "formatVersion" : 1
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+          "non_canonical_three_prime_splice_site": "noncanonical-splice-site",
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+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+      },
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+      "style": {
+        "neg_color": "white",
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+      "urlTemplate": "bigwig/GCA_001188405.1_Lrec_1.0_genomic.fna.gaps.bigwig"
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+      "category": "Reference Assembly",
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+      "label": "GC Content",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+      },
+      "scoreType": "avgScore",
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
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+        "pos_color": "rgba(0,0,255,50)"
+      },
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+      "urlTemplate": "bigwig/GCA_001188405.1_Lrec_1.0_genomic.fna.gc.bigwig"
+    }
+  ]
 }
diff --git a/organisms/stage/Lucilia_sericata/trackList.json b/organisms/stage/Lucilia_sericata/trackList.json
new file mode 100644
index 0000000..99bf39f
--- /dev/null
+++ b/organisms/stage/Lucilia_sericata/trackList.json
@@ -0,0 +1,154 @@
+{
+   "formatVersion" : 1,
+   "names" : {
+      "type" : "Hash",
+      "url" : "names/"
+   },
+   "tracks" : [
+      {
+         "category" : "Reference sequence",
+         "chunkSize" : 20000,
+         "key" : "Reference sequence",
+         "label" : "DNA",
+         "seqType" : "dna",
+         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
+         "type" : "SequenceTrack",
+         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-"
+      },
+      {
+         "category" : "NCBI Annotation Release 100",
+         "compress" : 0,
+         "key" : "NCBI_Annotation_Release_100_Gene",
+         "label" : "lucser_current_models",
+         "menuTemplate" : [
+             {
+                "label" : "View details"
+             },
+             {
+              "label": "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
+              "title": "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
+              "iconClass" : "dijitIconDatabase",
+              "action": "newWindow",
+              "url" : "function(track,feature){ return 'https://www.ncbi.nlm.nih.gov/nuccore/'+feature.get('name')}"
+              }
+        ],
+         "metadata" : {
+            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Lucilia_sericata/README_CURRENT_RELEASE",
+            "Data provider" : "NCBI",
+            "Data source" : "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/015/586/225/GCF_015586225.1_ASM1558622v1/GCF_015586225.1_ASM1558622v1_genomic.gff.gz",
+            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "container-16px",
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+            }
+         },
+         "trackType" : "HTMLFeatures",
+         "type" : "HTMLFeatures",
+         "urlTemplate" : "tracks/lucser_current_models/{refseq}/trackData.json"
+      },
+      {
+         "category" : "NCBI Annotation Release 100",
+         "compress" : 0,
+         "key" : "NCBI_Annotation_Release_100_Pseudogene",
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+         "metadata" : {
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+            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
+         },
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+         "style" : {
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+            "className" : "container-16px",
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+         },
+         "trackType" : "HTMLFeatures",
+         "type" : "HTMLFeatures",
+         "urlTemplate" : "tracks/NCBI_Annotation_Release_100_Pseudogene/{refseq}/trackData.json"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "0.5",
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+         "key" : "GC Content",
+         "label" : "GC Content",
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+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+         },
+         "scoreType" : "avgScore",
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "rgba(255,255,0,50)",
+            "pos_color" : "rgba(0,0,255,50)"
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+         "urlTemplate" : "bigwig/GCF_015586225.1_ASM1558622v1_genomic.fna.gc.bigwig"
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+         "label" : "Lucser_ASM1558622v1_RNA-Seq-alignments_2021-08-11",
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+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR14883001'>SRR14883001</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11814677'>SRR11814677</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR14883004'>SRR14883004</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11814669'>SRR11814669</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR14882999'>SRR14882999</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR350015'>SRR350015</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR14882997'>SRR14882997</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=ERR658157'>ERR658157</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11814676'>SRR11814676</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR14882996'>SRR14882996</a>",
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+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "analyses/Lucilia-sericata-RNA-Seq_2021-08-11_v1.0/Lucser_ASM1558622v1_RNA-Seq-alignments_2021-08-11.bam"
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+         "category" : "RNA-Seq/Splice junctions",
+         "compress" : 0,
+         "key" : "Lucser_ASM1558622v1_RNA-Seq-alignments_2021-08-11_junctions",
+         "label" : "Lucser_ASM1558622v1_RNA-Seq-alignments_2021-08-11_junctions",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR14883001'>SRR14883001</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11814677'>SRR11814677</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR14883004'>SRR14883004</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11814669'>SRR11814669</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR14882999'>SRR14882999</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR350015'>SRR350015</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR14882997'>SRR14882997</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=ERR658157'>ERR658157</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11814676'>SRR11814676</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR14882996'>SRR14882996</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Junction reads generated by Hisat2 aligner and regtools. The number of alignments supporting the junction read is listed in blue."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "className" : "feature",
+	    "description" : "score"
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/Lucser_ASM1558622v1_RNA-Seq-alignments_2021-08-11_junctions/{refseq}/trackData.json"
+      }
+   ]
+}
diff --git a/organisms/stage/Mamestra_configurata/trackList.json b/organisms/stage/Mamestra_configurata/trackList.json
index c03d97e..2420965 100644
--- a/organisms/stage/Mamestra_configurata/trackList.json
+++ b/organisms/stage/Mamestra_configurata/trackList.json
@@ -1,164 +1,163 @@
 {
-   "tracks" : [
-      {
-         "seqType" : "dna",
-         "key" : "Reference sequence",
-         "useAsRefSeqStore" : 1,
-         "storeClass" : "JBrowse/Store/Sequence/IndexedFasta",
-         "urlTemplate" : "seq/GCA_002192655.1_ASM219265v1_genomic.fna",
-         "type" : "SequenceTrack",
-         "label" : "DNA",
-         "category" : "Reference sequence",
-         "faiUrlTemplate" : "seq/GCA_002192655.1_ASM219265v1_genomic.fna.fai"
+  "formatVersion": 1,
+  "names": {
+    "type": "Hash",
+    "url": "names/"
+  },
+  "tracks": [
+    {
+      "category": "Reference sequence",
+      "faiUrlTemplate": "seq/GCA_002192655.1_ASM219265v1_genomic.fna.fai",
+      "key": "Reference sequence",
+      "label": "DNA",
+      "seqType": "dna",
+      "storeClass": "JBrowse/Store/Sequence/IndexedFasta",
+      "type": "SequenceTrack",
+      "urlTemplate": "seq/GCA_002192655.1_ASM219265v1_genomic.fna",
+      "useAsRefSeqStore": 1
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Reference Assembly",
+      "key": "Gaps in assembly",
+      "label": "Gaps in assembly",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
       },
-      {
-         "style" : {
-            "pos_color" : "black",
-            "neg_color" : "white"
-         },
-         "bicolor_pivot" : "zero",
-         "autoscale" : "local",
-         "key" : "Gaps in assembly",
-         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
-         "urlTemplate" : "bigwig/GCA_002192655.1_ASM219265v1_genomic.fna.gaps.bigwig",
-         "label" : "Gaps in assembly",
-         "category" : "Reference Assembly",
-         "metadata" : {
-            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
-            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank",
-            "Track contact" : "The i5k workspace@NAL"
-         },
-         "type" : "JBrowse/View/Track/Wiggle/Density"
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "white",
+        "pos_color": "black"
       },
-      {
-         "scoreType" : "avgScore",
-         "style" : {
-            "neg_color" : "rgba(255,255,0,50)",
-            "pos_color" : "rgba(0,0,255,50)"
-         },
-         "bicolor_pivot" : "0.5",
-         "key" : "GC Content",
-         "autoscale" : "local",
-         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
-         "urlTemplate" : "bigwig/GCA_002192655.1_ASM219265v1_genomic.fna.gc.bigwig",
-         "type" : "JBrowse/View/Track/Wiggle/Density",
-         "category" : "Reference Assembly",
-         "label" : "GC Content",
-         "metadata" : {
-            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
-            "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track.",
-            "Track contact" : "The i5k workspace@NAL"
-         }
+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "bigwig/GCA_002192655.1_ASM219265v1_genomic.fna.gaps.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "0.5",
+      "category": "Reference Assembly",
+      "key": "GC Content",
+      "label": "GC Content",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
       },
-      {
-         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
-         "urlTemplate" : "bam/BAW_454_and_Sanger.bam",
-         "histograms" : {
-            "color" : "#00BFFF",
-            "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
-            "urlTemplate" : "bigwig/BAW_454_and_Sanger.bw",
-            "height" : 75
-         },
-         "metadata" : {
-            "Track legend" : "Blue glyphs represent reads mapped to the forward strand, and red glyphs represent reads mapped to the reverse strand. If a read is discontinuously mapped (e.g. representing a splice junction), mapped segments are connected with a thinner black line. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)",
-            "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
-            "Tissues/Life stage included" : "larval midgut and adult head",
-            "Sequencing method" : "illumina",
-            "Alignment method" : "CLC genomics workbench",
-            "Geographic location (latitude and longitude)" : "52.133560, -106.635252",
-            "Read cleaning method" : "None",
-            "Data Provider" : "Cathy Coutu"
-         },
-         "type" : "WebApollo/View/Track/DraggableAlignments",
-  	 "category": "5. Transcriptome/Mapped Reads",
-         "label" : "long_read_RNA_mapped_to_genome",
-         "key" : "long_read_RNA_mapped_to_genome"
+      "scoreType": "avgScore",
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "rgba(255,255,0,50)",
+        "pos_color": "rgba(0,0,255,50)"
       },
-      {
-         "histograms" : {
-            "color" : "#00BFFF",
-            "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
-            "urlTemplate" : "bigwig/merged.reduced-coverage-RGmod.bw",
-            "height" : 75
-         },
-         "featureScale" : 0.005,
-         "key" : "Short_read_RNA_mapped_to_genome",
-         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
-         "urlTemplate" : "bam/merged.reduced-coverage-RGmod.bam",
-         "maxFeatureScreenDensity" : 0.08,
-         "type" : "WebApollo/View/Track/DraggableAlignments",
-         "metadata" : {
-            "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
-            "Track legend" : "Blue glyphs represent reads mapped to the forward strand, and red glyphs represent reads mapped to the reverse strand. If a read is discontinuously mapped (e.g. representing a splice junction), mapped segments are connected with a thinner black line. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)",
-		"Tissues/Life stage included" : "larval midgut and adult head",
-            "Sequencing method" : "illumina",
-            "Data provider" : "Cathy Coutu",
-            "Alignment method" : "CLC genomics workbench Version 10",
-            "Geographic location (latitude and longitude)" : "52.133560, -106.635252"
-         },
-  	 "category": "5. Transcriptome/Mapped Reads",
-         "label" : "Short_read_RNA_mapped_to_genome"
+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "bigwig/GCA_002192655.1_ASM219265v1_genomic.fna.gc.bigwig"
+    },
+    {
+      "category": "5. Transcriptome/Mapped Reads",
+      "histograms": {
+        "color": "#00BFFF",
+        "height": 75,
+        "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+        "urlTemplate": "bigwig/BAW_454_and_Sanger.bw"
       },
-      {
-         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
-         "urlTemplate" : "bigwig/BAW_454_and_Sanger.bw",
-         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
-         "label" : "long_read_RNA_mapped_to_genome_coverage",
-         "bicolor_pivot" : "zero",
-	 "style": {
-    	   "pos_color": "#FFA600",
-    	   "neg_color": "#005EFF",
-    	   "origin_color": "#888",
-    	   "variance_band_color": "rgba(0,0,0,0.3)",
-    	   "clip_marker_color": "red",
-    	   "height": 50
-	 },
-  	 "category": "5. Transcriptome/Coverage Plots (BigWig)",
-         "metadata" : {
-"Track legend" : "This track represents an X-Y plot of RNA-Seq coverage.",
-            "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
-	    "Tissues/Life stage included" : "larval midgut and adult head",
-            "Sequencing method" : "illumina",
-            "Alignment method" : "CLC genomics workbench",
-            "Geographic location (latitude and longitude)" : "52.133560, -106.635252",
-            "Read cleaning method" : "None",
-            "Data Provider" : "Cathy Coutu"
-         },
-
-         "autoscale" : "local",
-         "key" : "long_read_RNA_mapped_to_genome_coverage"
+      "key": "long_read_RNA_mapped_to_genome",
+      "label": "long_read_RNA_mapped_to_genome",
+      "metadata": {
+        "Alignment method": "CLC genomics workbench",
+        "Data Provider": "Cathy Coutu",
+        "Geographic location (latitude and longitude)": "52.133560, -106.635252",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Read cleaning method": "None",
+        "Sequencing method": "illumina",
+        "Tissues/Life stage included": "larval midgut and adult head",
+        "Track legend": "Blue glyphs represent reads mapped to the forward strand, and red glyphs represent reads mapped to the reverse strand. If a read is discontinuously mapped (e.g. representing a splice junction), mapped segments are connected with a thinner black line. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)"
       },
-      {
-         "category": "5. Transcriptome/Coverage Plots (BigWig)",
-         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
-         "urlTemplate" : "bigwig/merged.reduced-coverage-RGmod.bw",
-         "label" : "Short_read_RNA_mapped_to_genome_coverage",
-         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
-	 "style": {
-    	   "pos_color": "#FFA600",
-    	   "neg_color": "#005EFF",
-    	   "origin_color": "#888",
-    	   "variance_band_color": "rgba(0,0,0,0.3)",
-    	   "clip_marker_color": "red",
-    	   "height": 50
-	 },
-         "metadata" : {
-"Track legend" : "This track represents an X-Y plot of RNA-Seq coverage.",
-            "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
-            "Tissues/Life stage included" : "larval midgut and adult head",
-            "Sequencing method" : "illumina",
-            "Data provider" : "Cathy Coutu",
-            "Alignment method" : "CLC genomics workbench Version 10",
-            "Geographic location (latitude and longitude)" : "52.133560, -106.635252"
-         },
-         "bicolor_pivot" : "zero",
-         "key" : "Short_read_RNA_mapped_to_genome_coverage",
-         "autoscale" : "local"
-      }
-   ],
-   "names" : {
-      "url" : "names/",
-      "type" : "Hash"
-   },
-   "formatVersion" : 1
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "bam/BAW_454_and_Sanger.bam"
+    },
+    {
+      "category": "5. Transcriptome/Mapped Reads",
+      "featureScale": 0.005,
+      "histograms": {
+        "color": "#00BFFF",
+        "height": 75,
+        "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+        "urlTemplate": "bigwig/merged.reduced-coverage-RGmod.bw"
+      },
+      "key": "Short_read_RNA_mapped_to_genome",
+      "label": "Short_read_RNA_mapped_to_genome",
+      "maxFeatureScreenDensity": 0.08,
+      "metadata": {
+        "Alignment method": "CLC genomics workbench Version 10",
+        "Data provider": "Cathy Coutu",
+        "Geographic location (latitude and longitude)": "52.133560, -106.635252",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Sequencing method": "illumina",
+        "Tissues/Life stage included": "larval midgut and adult head",
+        "Track legend": "Blue glyphs represent reads mapped to the forward strand, and red glyphs represent reads mapped to the reverse strand. If a read is discontinuously mapped (e.g. representing a splice junction), mapped segments are connected with a thinner black line. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "bam/merged.reduced-coverage-RGmod.bam"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "5. Transcriptome/Coverage Plots (BigWig)",
+      "key": "long_read_RNA_mapped_to_genome_coverage",
+      "label": "long_read_RNA_mapped_to_genome_coverage",
+      "metadata": {
+        "Alignment method": "CLC genomics workbench",
+        "Data Provider": "Cathy Coutu",
+        "Geographic location (latitude and longitude)": "52.133560, -106.635252",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Read cleaning method": "None",
+        "Sequencing method": "illumina",
+        "Tissues/Life stage included": "larval midgut and adult head",
+        "Track legend": "This track represents an X-Y plot of RNA-Seq coverage."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "clip_marker_color": "red",
+        "height": 50,
+        "neg_color": "#005EFF",
+        "origin_color": "#888",
+        "pos_color": "#FFA600",
+        "variance_band_color": "rgba(0,0,0,0.3)"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "bigwig/BAW_454_and_Sanger.bw"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "5. Transcriptome/Coverage Plots (BigWig)",
+      "key": "Short_read_RNA_mapped_to_genome_coverage",
+      "label": "Short_read_RNA_mapped_to_genome_coverage",
+      "metadata": {
+        "Alignment method": "CLC genomics workbench Version 10",
+        "Data provider": "Cathy Coutu",
+        "Geographic location (latitude and longitude)": "52.133560, -106.635252",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Sequencing method": "illumina",
+        "Tissues/Life stage included": "larval midgut and adult head",
+        "Track legend": "This track represents an X-Y plot of RNA-Seq coverage."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "clip_marker_color": "red",
+        "height": 50,
+        "neg_color": "#005EFF",
+        "origin_color": "#888",
+        "pos_color": "#FFA600",
+        "variance_band_color": "rgba(0,0,0,0.3)"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "bigwig/merged.reduced-coverage-RGmod.bw"
+    }
+  ]
 }
diff --git a/organisms/stage/Manduca_sexta/trackList.json b/organisms/stage/Manduca_sexta/trackList.json
index 18b26f3..1aa8ae2 100644
--- a/organisms/stage/Manduca_sexta/trackList.json
+++ b/organisms/stage/Manduca_sexta/trackList.json
@@ -1,213 +1,207 @@
 {
-   "formatVersion" : 1,
-   "names" : {
-      "type" : "Hash",
-      "url" : "names/"
-   },
-   "tracks" : [
-      {
-         "category" : "Reference sequence",
-         "chunkSize" : 20000,
-         "key" : "Reference sequence",
-         "label" : "DNA",
-         "seqType" : "dna",
-         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
-         "type" : "SequenceTrack",
-         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-"
+  "formatVersion": 1,
+  "names": {
+    "type": "Hash",
+    "url": "names/"
+  },
+  "tracks": [
+    {
+      "category": "Reference sequence",
+      "chunkSize": 20000,
+      "key": "Reference sequence",
+      "label": "DNA",
+      "seqType": "dna",
+      "storeClass": "JBrowse/Store/Sequence/StaticChunked",
+      "type": "SequenceTrack",
+      "urlTemplate": "seq/{refseq_dirpath}/{refseq}-"
+    },
+    {
+      "category": "NCBI Annotation Release 102",
+      "compress": 0,
+      "key": "NCBI_Annotation_Release_102_Pseudogene",
+      "label": "NCBI_Annotation_Release_102_Pseudogene",
+      "metadata": {
+        "Data description": "ftp://ftp.ncbi.nlm.nih.gov/genomes/Manduca_sexta/README_CURRENT_RELEASE",
+        "Data provider": "NCBI",
+        "Data source": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/014/839/805/GCF_014839805.1_JHU_Msex_v1.0/GCF_014839805.1_JHU_Msex_v1.0_genomic.gff.gz",
+        "Method": "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
       },
-      {
-         "category" : "NCBI Annotation Release 102",
-         "compress" : 0,
-         "key" : "NCBI_Annotation_Release_102_Pseudogene",
-         "label" : "NCBI_Annotation_Release_102_Pseudogene",
-         "metadata" : {
-            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Manduca_sexta/README_CURRENT_RELEASE",
-            "Data provider" : "NCBI",
-            "Data source" : "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/014/839/805/GCF_014839805.1_JHU_Msex_v1.0/GCF_014839805.1_JHU_Msex_v1.0_genomic.gff.gz",
-            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
-         },
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
-         "style" : {
-            "arrowheadClass" : "trellis-arrowhead",
-            "className" : "container-16px",
-            "description" : "product, note, description",
-            "subfeatureClasses" : {
-               "CDS" : "gnomon_CDS",
-               "UTR" : "gnomon_UTR",
-               "exon" : "container-100pct",
-               "wholeCDS" : null
-            }
-         },
-         "trackType" : "HTMLFeatures",
-         "type" : "HTMLFeatures",
-         "urlTemplate" : "tracks/NCBI_Annotation_Release_102_Pseudogene/{refseq}/trackData.json"
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "description": "product, note, description",
+        "subfeatureClasses": {
+          "CDS": "gnomon_CDS",
+          "UTR": "gnomon_UTR",
+          "exon": "container-100pct",
+          "wholeCDS": null
+        }
       },
-      {
-         "autoscale" : "local",
-         "bicolor_pivot" : "zero",
-         "category" : "Reference Assembly",
-         "key" : "Gaps in assembly",
-         "label" : "Gaps in assembly",
-         "metadata" : {
-            "Track contact" : "The i5k workspace@NAL",
-            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
-            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
-         },
-         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
-         "style" : {
-            "neg_color" : "white",
-            "pos_color" : "black"
-         },
-         "type" : "JBrowse/View/Track/Wiggle/Density",
-         "urlTemplate" : "bigwig/GCF_014839805.1_JHU_Msex_v1.0_genomic.fna.gaps.bigwig"
+      "trackType": "HTMLFeatures",
+      "type": "HTMLFeatures",
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-         "urlTemplate" : "tracks/OGSv2.2_Gene/{refseq}/trackData.json"
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 }
diff --git a/organisms/stage/Mayetiola_destructor/trackList.json b/organisms/stage/Mayetiola_destructor/trackList.json
index 25ad3a7..bd5d674 100644
--- a/organisms/stage/Mayetiola_destructor/trackList.json
+++ b/organisms/stage/Mayetiola_destructor/trackList.json
@@ -1,367 +1,420 @@
 {
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+            "Analysis contact" : "Jeff Stuart, Department of Entomology, Purdue University, West Lafayette, IN",
+            "Analysis description" : "Maker version 2.22 was trained with the CEGMA gene set, M.des cufflinks output from Baylor, M. des ESTs from NCBI and protein homology from fruit fly, mosquito, honey bee and Tribolium from NCBI.  Maker output was used to train Augustus and SNAP in two interations. The resulting output was validated by blast comparison with a clade specific gene set from orthoDB.  92% of the clade specific gene set produced hits.  To produce an official gene set, the maker output was manually curated by the community using Apollo. The Official Gene Set was submitted to NCBI.",
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-            "Track legend" : "Consensus gene models from the PASA2 program",
-            "Analysis contact" : "Jeff Stuart, Department of Entomology, Purdue University, West Lafayette, IN"
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-   "alwaysOnTracks" : "DNA,Annotations",
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diff --git a/organisms/stage/Medauroidea_extradentata/trackList.json b/organisms/stage/Medauroidea_extradentata/trackList.json
index e4f3f16..af4b199 100644
--- a/organisms/stage/Medauroidea_extradentata/trackList.json
+++ b/organisms/stage/Medauroidea_extradentata/trackList.json
@@ -1,84 +1,144 @@
 {
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-         "urlTemplate" : "tracks/medext_current_models/{refseq}/trackData.json",
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-               "exon" : "container-100pct",
                "CDS" : "primary_gene_set-cds",
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-            "arrowheadClass" : "trellis-arrowhead"
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-        "category" : "Medauroidea extradentata OGS annotations v1.0/1. Gene Sets/Protein Coding",
-                "metadata" : {
-		"Publication status":"Published, please cite doi:10.1534/g3.118.200204",
-		"Data provider":"Brian Johnson, UC Davis",
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-		"Data source":"https://i5k.nal.usda.gov/annotations/739294"
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          "label" : "Gaps in assembly",
-         "type" : "JBrowse/View/Track/Wiggle/Density"
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+            "Track contact" : "The i5k workspace@NAL",
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diff --git a/organisms/stage/Megachile_rotundata/trackList.json b/organisms/stage/Megachile_rotundata/trackList.json
index 482974a..d43dd46 100644
--- a/organisms/stage/Megachile_rotundata/trackList.json
+++ b/organisms/stage/Megachile_rotundata/trackList.json
@@ -1,558 +1,611 @@
 {
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+   "css" : "./plugins/NAL_CSS/css/main.css",
+   "favicon" : "./plugins/WebApollo/img/webapollo_favicon.ico",
+   "formatVersion" : 1,
+   "names" : {
+      "type" : "Hash",
+      "url" : "names/"
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    "share_link" : 0,
-   "css" : "./plugins/NAL_CSS/css/contrib_styles.css",
    "tracks" : [
       {
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diff --git a/organisms/stage/Melipona_quadrifasciata/trackList.json b/organisms/stage/Melipona_quadrifasciata/trackList.json
index 24015ac..9e13fcc 100644
--- a/organisms/stage/Melipona_quadrifasciata/trackList.json
+++ b/organisms/stage/Melipona_quadrifasciata/trackList.json
@@ -1,157 +1,210 @@
 {
-   "css" : "./plugins/NAL_CSS/css/contrib_styles.css",
+   "alwaysOnTracks" : "DNA,Annotations",
+   "css" : "./plugins/NAL_CSS/css/main.css",
+   "favicon" : "./plugins/WebApollo/img/webapollo_favicon.ico",
+   "formatVersion" : 1,
+   "names" : {
+      "type" : "Hash",
+      "url" : "names/"
+   },
    "share_link" : 0,
-   "plugins" : [
-      {
-         "location" : "./plugins/WebApollo",
-         "name" : "WebApollo"
-      }
-   ],
    "tracks" : [
       {
-         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
+         "category" : "Reference sequence",
          "chunkSize" : 20000,
-         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-",
+         "key" : "Reference sequence",
          "label" : "DNA",
+         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
          "type" : "SequenceTrack",
-         "category" : "Reference sequence",
-         "key" : "Reference sequence"
+         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-"
       },
       {
          "autocomplete" : "none",
+         "compress" : 0,
+         "key" : "User-created Annotations",
+         "label" : "Annotations",
+         "phase" : 0,
+         "storeClass" : "WebApollo/Store/SeqFeature/ScratchPad",
          "style" : {
-            "className" : "annot",
-            "renderClassName" : "annot-render",
-            "subfeatureClasses" : {
-               "non_canonical_three_prime_splice_site" : "noncanonical-splice-site",
-               "wholeCDS" : null,
-               "exon" : "container-100pct",
-               "CDS" : "annot-CDS",
-               "non_canonical_five_prime_splice_site" : "noncanonical-splice-site",
-               "UTR" : "annot-UTR"
-            },
-            "arrowheadClass" : "annot-arrowhead",
             "alternateClasses" : {
-               "transposable_element" : {
-                  "renderClassName" : "blue-ibeam-render",
-                  "className" : "blue-ibeam"
+               "miRNA" : {
+                  "className" : "brightgreen-80pct",
+                  "renderClassName" : "gray-center-30pct"
                },
-               "pseudogene" : {
-                  "renderClassName" : "gray-center-30pct",
-                  "className" : "light-purple-80pct"
+               "ncRNA" : {
+                  "className" : "brightgreen-80pct",
+                  "renderClassName" : "gray-center-30pct"
                },
-               "snRNA" : {
-                  "renderClassName" : "gray-center-30pct",
-                  "className" : "brightgreen-80pct"
+               "pseudogene" : {
+                  "className" : "light-purple-80pct",
+                  "renderClassName" : "gray-center-30pct"
                },
                "rRNA" : {
-                  "renderClassName" : "gray-center-30pct",
-                  "className" : "brightgreen-80pct"
-               },
-               "snoRNA" : {
-                  "renderClassName" : "gray-center-30pct",
-                  "className" : "brightgreen-80pct"
+                  "className" : "brightgreen-80pct",
+                  "renderClassName" : "gray-center-30pct"
                },
                "repeat_region" : {
                   "className" : "magenta-80pct"
                },
-               "miRNA" : {
-                  "renderClassName" : "gray-center-30pct",
-                  "className" : "brightgreen-80pct"
+               "snRNA" : {
+                  "className" : "brightgreen-80pct",
+                  "renderClassName" : "gray-center-30pct"
+               },
+               "snoRNA" : {
+                  "className" : "brightgreen-80pct",
+                  "renderClassName" : "gray-center-30pct"
                },
                "tRNA" : {
-                  "renderClassName" : "gray-center-30pct",
-                  "className" : "brightgreen-80pct"
+                  "className" : "brightgreen-80pct",
+                  "renderClassName" : "gray-center-30pct"
                },
-               "ncRNA" : {
-                  "renderClassName" : "gray-center-30pct",
-                  "className" : "brightgreen-80pct"
+               "transposable_element" : {
+                  "className" : "blue-ibeam",
+                  "renderClassName" : "blue-ibeam-render"
                }
             },
-            "uniqueIdField" : "id",
+            "arrowheadClass" : "annot-arrowhead",
             "centerSubFeature" : {
-               "non_canonical_three_prime_splice_site" : false,
-               "non_canonical_five_prime_splice_site" : false
-            }
+               "non_canonical_five_prime_splice_site" : false,
+               "non_canonical_three_prime_splice_site" : false
+            },
+            "className" : "annot",
+            "renderClassName" : "annot-render",
+            "subfeatureClasses" : {
+               "CDS" : "annot-CDS",
+               "UTR" : "annot-UTR",
+               "exon" : "container-100pct",
+               "non_canonical_five_prime_splice_site" : "noncanonical-splice-site",
+               "non_canonical_three_prime_splice_site" : "noncanonical-splice-site",
+               "wholeCDS" : null
+            },
+            "uniqueIdField" : "id"
          },
-         "key" : "User-created Annotations",
-         "storeClass" : "WebApollo/Store/SeqFeature/ScratchPad",
-         "phase" : 0,
-         "compress" : 0,
-         "label" : "Annotations",
-         "type" : "WebApollo/View/Track/AnnotTrack",
-         "subfeatures" : 1
+         "subfeatures" : 1,
+         "type" : "WebApollo/View/Track/AnnotTrack"
       },
       {
+         "category" : "ASM127656v1 GLEAN gene predictions/1. Gene Sets/Protein Coding",
+         "compress" : 0,
+         "key" : "ASM127656v1 GLEAN gene predictions",
+         "label" : "melqua_current_models",
+         "metadata" : {
+            "Data provider" : "BGI and GenBank",
+            "Data source" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_001276565.1_ASM127656v1/GCA_001276565.1_ASM127656v1_genomic.gff.gz",
+            "Method" : "Integration of several gene sets via GLEAN; for full methods, see the associated publication, PMID 25977371"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "className" : "container-16px",
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "{type}",
             "subfeatureClasses" : {
-               "wholeCDS" : null,
-               "exon" : "container-100pct",
                "CDS" : "primary_gene_set-cds",
-               "UTR" : "primary_gene_set-utr"
-            },
-            "arrowheadClass" : "trellis-arrowhead"
+               "UTR" : "primary_gene_set-utr",
+               "exon" : "container-100pct",
+               "wholeCDS" : null
+            }
          },
-         "key" : "ASM127656v1 GLEAN gene predictions",
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "trackType" : null,
-         "urlTemplate" : "tracks/melqua_current_models/{refseq}/trackData.json",
-         "compress" : 0,
          "type" : "FeatureTrack",
-         "label" : "melqua_current_models",
-         "category" : "ASM127656v1 GLEAN gene predictions/1. Gene Sets/Protein Coding",
-         "metadata" : {
-            "Data source" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_001276565.1_ASM127656v1/GCA_001276565.1_ASM127656v1_genomic.gff.gz",
-            "Method" : "Integration of several gene sets via GLEAN; for full methods, see the associated publication, PMID 25977371",
-            "Data provider" : "BGI and GenBank",
-         }
+         "urlTemplate" : "tracks/melqua_current_models/{refseq}/trackData.json"
       },
       {
-         "style" : {
-            "pos_color" : "black",
-            "neg_color" : "white"
-         },
-         "bicolor_pivot" : "zero",
          "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Reference Assembly",
          "key" : "Gaps in assembly",
-         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
-         "urlTemplate" : "bigwig/GCA_001276565.1_ASM127656v1_genomic_GenBankIDs.fna.gaps.bigwig",
          "label" : "Gaps in assembly",
-         "type" : "JBrowse/View/Track/Wiggle/Density",
-         "category" : "Reference Assembly",
          "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
             "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
-            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank",
-            "Track contact" : "The i5k workspace@NAL"
-         }
+            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "white",
+            "pos_color" : "black"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/GCA_001276565.1_ASM127656v1_genomic_GenBankIDs.fna.gaps.bigwig"
       },
       {
+         "autoscale" : "local",
+         "bicolor_pivot" : "0.5",
+         "category" : "Reference Assembly",
+         "key" : "GC Content",
+         "label" : "GC Content",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+         },
+         "scoreType" : "avgScore",
          "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
-         "urlTemplate" : "bigwig/GCA_001276565.1_ASM127656v1_genomic_GenBankIDs.fna.gc.bigwig",
          "style" : {
             "neg_color" : "rgba(255,255,0,50)",
             "pos_color" : "rgba(0,0,255,50)"
          },
-         "label" : "GC Content",
          "type" : "JBrowse/View/Track/Wiggle/Density",
-         "bicolor_pivot" : "0.5",
-         "key" : "GC Content",
-         "scoreType": "avgScore",
-         "category" : "Reference Assembly",
+         "urlTemplate" : "bigwig/GCA_001276565.1_ASM127656v1_genomic_GenBankIDs.fna.gc.bigwig"
+      },
+      {
+         "category" : "RNA-Seq/Mapped Reads",
+         "key" : "Melqua_ASM127656v1_RNA-Seq-alignments_2021-06-16",
+         "label" : "Melqua_ASM127656v1_RNA-Seq-alignments_2021-06-16",
          "metadata" : {
-            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
-            "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track.",
-            "Track contact" : "The i5k workspace@NAL"
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR2001644'>SRR2001644</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11943141'>SRR11943141</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Dark red alignments: Mapped portion of read aligned to forward strand<br>Light red alignments: Spliced portion of read aligned to forward strand<br>Dark blue alignments: Mapped portion of read aligned to reverse strand<br>Light blue alignments: Spliced portion of read aligned to reverse strand<br>Red marking - deletion in the read relative to the reference<br>Green marking - insertion in the read relative to the reference<br>Yellow marking  - mismatch (hover over the mismatch to see what the snp is)"
          },
-         "autoscale" : "local"
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "unsafePopup" : true,
+         "urlTemplate" : "analyses/Melipona-quadrifasciata-RNA-Seq_2021-06-16_v1.0/Melqua_ASM127656v1_RNA-Seq-alignments_2021-06-16.bam"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "RNA-Seq/Coverage Plots",
+         "key" : "Melqua_ASM127656v1_RNA-Seq-alignments_2021-06-16_coverage",
+         "label" : "Melqua_ASM127656v1_RNA-Seq-alignments_2021-06-16_coverage",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR2001644'>SRR2001644</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11943141'>SRR11943141</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "unsafePopup" : true,
+         "urlTemplate" : "analyses/Melipona-quadrifasciata-RNA-Seq_2021-06-16_v1.0/Melqua_ASM127656v1_RNA-Seq-alignments_2021-06-16.bigwig"
+      },
+      {
+         "category" : "RNA-Seq/Splice junctions",
+         "compress" : 0,
+         "key" : "Melqua_ASM127656v1_RNA-Seq-alignments_2021-06-16_junctions",
+         "label" : "Melqua_ASM127656v1_RNA-Seq-alignments_2021-06-16_junctions",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR2001644'>SRR2001644</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11943141'>SRR11943141</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Junction reads generated by Hisat2 aligner and regtools. The number of alignments supporting the junction read is listed in blue."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "className" : "feature",
+            "description" : "score"
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "unsafePopup" : true,
+         "urlTemplate" : "tracks/Melqua_ASM127656v1_RNA-Seq-alignments_2021-06-16_junctions/{refseq}/trackData.json"
       }
-   ],
-   "names" : {
-      "url" : "names/",
-      "type" : "Hash"
-   },
-   "favicon" : "./plugins/WebApollo/img/webapollo_favicon.ico",
-   "alwaysOnTracks" : "DNA,Annotations",
-   "formatVersion" : 1
+   ]
 }
diff --git a/organisms/stage/Microplitis_demolitor/trackList.json b/organisms/stage/Microplitis_demolitor/trackList.json
index 5e1b23b..025860e 100644
--- a/organisms/stage/Microplitis_demolitor/trackList.json
+++ b/organisms/stage/Microplitis_demolitor/trackList.json
@@ -20,6 +20,18 @@
          "compress" : 0,
          "key" : "NCBI_Annotation_Release_101_Gene",
          "label" : "NCBI_Annotation_Release_101_Gene",
+         "menuTemplate" : [
+            {
+               "label" : "View details"
+            },
+            {
+               "action" : "newWindow",
+               "iconClass" : "dijitIconDatabase",
+               "label" : "function(track,feature){ return 'Find NCBI record for '+feature.get('id')}",
+               "title" : "function(track,feature){ return 'Find NCBI record for '+feature.get('id')}",
+               "url" : "function(track,feature){ return 'https://www.ncbi.nlm.nih.gov/nuccore/'+feature.get('name')}"
+            }
+         ],
          "metadata" : {
             "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Microplitis_demolitor/README_CURRENT_RELEASE",
             "Data provider" : "NCBI",
@@ -29,7 +41,7 @@
          "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
             "arrowheadClass" : "trellis-arrowhead",
-            "className" : "container-16px",
+            "className" : "{type}",
             "description" : "product, note, description",
             "subfeatureClasses" : {
                "CDS" : "gnomon_CDS",
@@ -38,8 +50,8 @@
                "wholeCDS" : null
             }
          },
-         "trackType" : "ColorByType/View/Track/ColorByTypeDraggable",
-         "type" : "ColorByType/View/Track/ColorByTypeDraggable",
+         "trackType" : "HTMLFeatures",
+         "type" : "HTMLFeatures",
          "urlTemplate" : "tracks/NCBI_Annotation_Release_101_Gene/{refseq}/trackData.json"
       },
       {
@@ -56,7 +68,7 @@
          "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
             "arrowheadClass" : "trellis-arrowhead",
-            "className" : "container-16px",
+            "className" : "{type}",
             "description" : "product, note, description",
             "subfeatureClasses" : {
                "CDS" : "gnomon_CDS",
@@ -99,6 +111,7 @@
             "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
             "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
          },
+         "scoreType" : "avgScore",
          "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
          "style" : {
             "neg_color" : "rgba(255,255,0,50)",
@@ -495,7 +508,7 @@
          "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
             "arrowheadClass" : "trellis-arrowhead",
-            "className" : "container-16px",
+            "className" : "{type}",
             "renderClassName" : "genemark"
          },
          "trackType" : null,
@@ -517,7 +530,7 @@
          "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
             "arrowheadClass" : "trellis-arrowhead",
-            "className" : "container-16px",
+            "className" : "{type}",
             "renderClassName" : "genemark"
          },
          "trackType" : null,
@@ -526,30 +539,30 @@
       },
       {
          "category" : "Official Gene Set v1.0",
-         "metadata" : {
-            "Data description" : "Microplitis demolitor OGSv1.0 is an integration of automatic gene predictions from *Microplitis demolitor* genome annotations NCBI-RefSeq's gene set NCBI Microplitis demolitor Annotation Release 101 (https://www.ncbi.nlm.nih.gov/genome/annotation_euk/Microplitis_demolitor/101/), with manual annotations by the research community, performed via the Apollo manual curation software (https://zenodo.org/record/1295754#.YDgLyJNKivg), and QC'd via the GFF3toolkit (https://github.com/NAL-i5K/gff3toolkit) and NCBI's table2asn_GFF software (https://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/table2asn_GFF/), and merged via the GFF3toolkit (https://github.com/NAL-i5K/gff3toolkit).",
-            "Data source" : "https://data.nal.usda.gov/dataset/microplitis-demolitor-official-gene-set-micdemogsv10",
-            "Publication status" : "Published dataset, please cite (dataset) Tims, Kelly; Poelchau, Monica; Burke, Gaelen. (unpublished). Microplitis demolitor Official Gene Set micdem_OGSv1.0. Ag Data Commons. https://data.nal.usda.gov/dataset/microplitis-demolitor-official-gene-set-micdemogsv10."
-         },
+         "compress" : 0,
+         "key" : "OGSv1.0 Gene",
+         "label" : "micdem_current_models",
          "menuTemplate" : [
             {
                "label" : "View details"
             },
             {
-             "label": "function(track,feature){ return 'Find gene page for '+feature.get('id')}",
-             "title": "function(track,feature){ return 'Find gene page for '+feature.get('id')}",
-             "iconClass" : "dijitIconDatabase",
-             "action": "newWindow",
-             "url" : "function(track,feature){ return 'https://i5k.nal.usda.gov/search/site/'+feature.get('id')}"
-             }
-       ],
-         "compress" : 0,
-         "key" : "OGSv1.0 Gene",
-         "label" : "micdem_current_models",
+               "action" : "newWindow",
+               "iconClass" : "dijitIconDatabase",
+               "label" : "function(track,feature){ return 'Find NCBI record for '+feature.get('id')}",
+               "title" : "function(track,feature){ return 'Find NCBI record for '+feature.get('id')}",
+               "url" : "function(track,feature){ return 'https://www.ncbi.nlm.nih.gov/protein/'+feature.get('id')}"
+            }
+         ],
+         "metadata" : {
+            "Data description" : "Microplitis demolitor OGSv1.0 is an integration of automatic gene predictions from *Microplitis demolitor* genome annotations NCBI-RefSeq's gene set NCBI Microplitis demolitor Annotation Release 101 (https://www.ncbi.nlm.nih.gov/genome/annotation_euk/Microplitis_demolitor/101/), with manual annotations by the research community, performed via the Apollo manual curation software (https://zenodo.org/record/1295754#.YDgLyJNKivg), and QC'd via the GFF3toolkit (https://github.com/NAL-i5K/gff3toolkit) and NCBI's table2asn_GFF software (https://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/table2asn_GFF/), and merged via the GFF3toolkit (https://github.com/NAL-i5K/gff3toolkit).",
+            "Data source" : "https://data.nal.usda.gov/dataset/microplitis-demolitor-official-gene-set-micdemogsv10",
+            "Publication status" : "Published dataset, please cite (dataset) Tims, Kelly; Poelchau, Monica; Burke, Gaelen. (unpublished). Microplitis demolitor Official Gene Set micdem_OGSv1.0. Ag Data Commons. https://data.nal.usda.gov/dataset/microplitis-demolitor-official-gene-set-micdemogsv10."
+         },
          "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
             "arrowheadClass" : "trellis-arrowhead",
-            "className" : "container-16px",
+            "className" : "{type}",
             "description" : "product, note, description",
             "subfeatureClasses" : {
                "CDS" : "gnomon_CDS",
@@ -564,18 +577,18 @@
       },
       {
          "category" : "Official Gene Set v1.0",
+         "compress" : 0,
+         "key" : "OGSv1.0 Pseudogene",
+         "label" : "OGSv1.0_Pseudogene",
          "metadata" : {
             "Data description" : "Microplitis demolitor OGSv1.0 is an integration of automatic gene predictions from *Microplitis demolitor* genome annotations NCBI-RefSeq's gene set NCBI Microplitis demolitor Annotation Release 101 (https://www.ncbi.nlm.nih.gov/genome/annotation_euk/Microplitis_demolitor/101/), with manual annotations by the research community, performed via the Apollo manual curation software (https://zenodo.org/record/1295754#.YDgLyJNKivg), and QC'd via the GFF3toolkit (https://github.com/NAL-i5K/gff3toolkit) and NCBI's table2asn_GFF software (https://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/table2asn_GFF/), and merged via the GFF3toolkit (https://github.com/NAL-i5K/gff3toolkit).",
             "Data source" : "https://data.nal.usda.gov/dataset/microplitis-demolitor-official-gene-set-micdemogsv10",
             "Publication status" : "Published dataset, please cite (dataset) Tims, Kelly; Poelchau, Monica; Burke, Gaelen. (unpublished). Microplitis demolitor Official Gene Set micdem_OGSv1.0. Ag Data Commons. https://data.nal.usda.gov/dataset/microplitis-demolitor-official-gene-set-micdemogsv10."
          },
-         "compress" : 0,
-         "key" : "OGSv1.0 Pseudogene",
-         "label" : "OGSv1.0_Pseudogene",
          "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
             "arrowheadClass" : "trellis-arrowhead",
-            "className" : "container-16px",
+            "className" : "{type}",
             "description" : "product, note, description",
             "subfeatureClasses" : {
                "CDS" : "gnomon_CDS",
@@ -587,6 +600,65 @@
          "trackType" : "HTMLFeatures",
          "type" : "HTMLFeatures",
          "urlTemplate" : "tracks/OGSv1.0_Pseudogene/{refseq}/trackData.json"
+      },
+      {
+         "category" : "RNA-Seq/Mapped Reads",
+         "key" : "Micdem_Mdem2_RNA-Seq-alignments_2021-06-21",
+         "label" : "Micdem_Mdem2_RNA-Seq-alignments_2021-06-21",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR955374'>SRR955374</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR955015'>SRR955015</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR955076'>SRR955076</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR955397'>SRR955397</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Dark red alignments: Mapped portion of read aligned to forward strand<br>Light red alignments: Spliced portion of read aligned to forward strand<br>Dark blue alignments: Mapped portion of read aligned to reverse strand<br>Light blue alignments: Spliced portion of read aligned to reverse strand<br>Red marking - deletion in the read relative to the reference<br>Green marking - insertion in the read relative to the reference<br>Yellow marking  - mismatch (hover over the mismatch to see what the snp is)"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "unsafePopup" : true,
+         "urlTemplate" : "analyses/Microplitis-demolitor-RNA-Seq_2021-06-21_v1.0/Micdem_Mdem2_RNA-Seq-alignments_2021-06-21.bam"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "RNA-Seq/Coverage Plots",
+         "key" : "Micdem_Mdem2_RNA-Seq-alignments_2021-06-21_coverage",
+         "label" : "Micdem_Mdem2_RNA-Seq-alignments_2021-06-21_coverage",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR955374'>SRR955374</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR955015'>SRR955015</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR955076'>SRR955076</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR955397'>SRR955397</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "unsafePopup" : true,
+         "urlTemplate" : "analyses/Microplitis-demolitor-RNA-Seq_2021-06-21_v1.0/Micdem_Mdem2_RNA-Seq-alignments_2021-06-21.bigwig"
+      },
+      {
+         "category" : "RNA-Seq/Splice junctions",
+         "compress" : 0,
+         "key" : "Micdem_Mdem2_RNA-Seq-alignments_2021-06-21_junctions",
+         "label" : "Micdem_Mdem2_RNA-Seq-alignments_2021-06-21_junctions",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR955374'>SRR955374</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR955015'>SRR955015</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR955076'>SRR955076</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR955397'>SRR955397</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Junction reads generated by Hisat2 aligner and regtools. The number of alignments supporting the junction read is listed in blue."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "className" : "feature",
+            "description" : "score"
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "unsafePopup" : true,
+         "urlTemplate" : "tracks/Micdem_Mdem2_RNA-Seq-alignments_2021-06-21_junctions/{refseq}/trackData.json"
       }
    ]
 }
diff --git a/organisms/stage/Neodiprion_fabricii/trackList.json b/organisms/stage/Neodiprion_fabricii/trackList.json
new file mode 100755
index 0000000..a1c76cf
--- /dev/null
+++ b/organisms/stage/Neodiprion_fabricii/trackList.json
@@ -0,0 +1,183 @@
+{
+   "formatVersion" : 1,
+   "names" : {
+      "type" : "Hash",
+      "url" : "names/"
+   },
+   "tracks" : [
+      {
+         "category" : "Reference sequence",
+         "chunkSize" : 20000,
+         "key" : "Reference sequence",
+         "label" : "DNA",
+         "seqType" : "dna",
+         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
+         "type" : "SequenceTrack",
+         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-"
+      },
+      {
+         "category" : "NCBI Annotation Release 100",
+         "compress" : 0,
+         "key" : "NCBI_Annotation_Release_100_Gene",
+         "label" : "neofab_current_models",
+         "menuTemplate" : [
+            {
+               "label" : "View details"
+            },
+            {
+               "action" : "newWindow",
+               "iconClass" : "dijitIconDatabase",
+               "label" : "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
+               "title" : "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
+               "url" : "function(track,feature){ return 'https://www.ncbi.nlm.nih.gov/nuccore/'+feature.get('name')}"
+            }
+         ],
+         "metadata" : {
+            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Neodiprion_fabricii/README_CURRENT_RELEASE",
+            "Data provider" : "NCBI",
+            "Data source" : "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/021/155/785/GCF_021155785.1_iyNeoFabr1.1/GCF_021155785.1_iyNeoFabr1.1_genomic.gff.gz",
+            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "container-16px",
+            "description" : "product, note, description",
+            "subfeatureClasses" : {
+               "CDS" : "gnomon_CDS",
+               "UTR" : "gnomon_UTR",
+               "exon" : "container-100pct",
+               "wholeCDS" : null
+            }
+         },
+         "trackType" : "HTMLFeatures",
+         "type" : "HTMLFeatures",
+         "urlTemplate" : "tracks/neofab_current_models/{refseq}/trackData.json"
+      },
+      {
+         "category" : "NCBI Annotation Release 100",
+         "compress" : 0,
+         "key" : "NCBI_Annotation_Release_100_Pseudogene",
+         "label" : "NCBI_Annotation_Release_100_Pseudogene",
+         "metadata" : {
+            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Neodiprion_fabricii/README_CURRENT_RELEASE",
+            "Data provider" : "NCBI",
+            "Data source" : "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/021/155/785/GCF_021155785.1_iyNeoFabr1.1/GCF_021155785.1_iyNeoFabr1.1_genomic.gff.gz",
+            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "container-16px",
+            "description" : "product, note, description",
+            "subfeatureClasses" : {
+               "CDS" : "gnomon_CDS",
+               "UTR" : "gnomon_UTR",
+               "exon" : "container-100pct",
+               "wholeCDS" : null
+            }
+         },
+         "trackType" : "HTMLFeatures",
+         "type" : "HTMLFeatures",
+         "urlTemplate" : "tracks/NCBI_Annotation_Release_100_Pseudogene/{refseq}/trackData.json"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Reference Assembly",
+         "key" : "Gaps in assembly",
+         "label" : "Gaps in assembly",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "white",
+            "pos_color" : "black"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/GCF_021155785.1_iyNeoFabr1.1_genomic.fna.gaps.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "0.5",
+         "category" : "Reference Assembly",
+         "key" : "GC Content",
+         "label" : "GC Content",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+         },
+         "scoreType" : "avgScore",
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "rgba(255,255,0,50)",
+            "pos_color" : "rgba(0,0,255,50)"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/GCF_021155785.1_iyNeoFabr1.1_genomic.fna.gc.bigwig"
+      },
+      {
+         "category" : "RNA-Seq/Mapped Reads",
+         "key" : "Neodiprion lecontei RNA-Seq alignments against iyNeoFabr1.1",
+         "label" : "Neolec_iyNeoFabr1.1_RNA-Seq-alignments_2022-03-29",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR12814109'>SRR12814109</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR12814057'>SRR12814057</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR12814099'>SRR12814099</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR12814073'>SRR12814073</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR2970130'>SRR2970130</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR12814062'>SRR12814062</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR12814078'>SRR12814078</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR12814088'>SRR12814088</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR12814047'>SRR12814047</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR12814055'>SRR12814055</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Dark red alignments: Mapped portion of read aligned to forward strand<br>Light red alignments: Spliced portion of read aligned to forward strand<br>Dark blue alignments: Mapped portion of read aligned to reverse strand<br>Light blue alignments: Spliced portion of read aligned to reverse strand<br>Red marking - deletion in the read relative to the reference<br>Green marking - insertion in the read relative to the reference<br>Yellow marking  - mismatch (hover over the mismatch to see what the snp is)"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "unsafePopup" : true,
+         "urlTemplate" : "analyses/Neodiprion-fabricii-RNA-Seq_2022-03-29_v1.0/Neolec_iyNeoFabr1.1_RNA-Seq-alignments_2022-03-29.bam"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "RNA-Seq/Coverage Plots",
+         "key" : "Neodiprion lecontei RNA-Seq alignments against iyNeoFabr1.1, coverage",
+         "label" : "Neolec_iyNeoFabr1.1_RNA-Seq-alignments_2022-03-29_coverage",
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
+         },
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR12814109'>SRR12814109</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR12814057'>SRR12814057</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR12814099'>SRR12814099</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR12814073'>SRR12814073</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR2970130'>SRR2970130</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR12814062'>SRR12814062</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR12814078'>SRR12814078</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR12814088'>SRR12814088</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR12814047'>SRR12814047</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR12814055'>SRR12814055</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage."
+         },
+         "unsafePopup" : true,
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "analyses/Neodiprion-fabricii-RNA-Seq_2022-03-29_v1.0/Neolec_iyNeoFabr1.1_RNA-Seq-alignments_2022-03-29.bigwig"
+      },
+      {
+         "category" : "RNA-Seq/Splice junctions",
+         "compress" : 0,
+         "key" : "Neodiprion lecontei RNA-Seq alignments against iyNeoFabr1.1, junctions",
+         "label" : "Neolec_iyNeoFabr1.1_RNA-Seq-alignments_2022-03-29_junctions",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR12814109'>SRR12814109</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR12814057'>SRR12814057</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR12814099'>SRR12814099</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR12814073'>SRR12814073</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR2970130'>SRR2970130</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR12814062'>SRR12814062</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR12814078'>SRR12814078</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR12814088'>SRR12814088</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR12814047'>SRR12814047</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR12814055'>SRR12814055</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Junction reads generated by Hisat2 aligner and regtools. The number of alignments supporting the junction read is listed in blue."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "className" : "feature",
+            "description" : "score"
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "unsafePopup" : true,
+         "urlTemplate" : "tracks/Neolec_iyNeoFabr1.1_RNA-Seq-alignments_2022-03-29_junctions/{refseq}/trackData.json"
+      }
+   ]
+}
diff --git a/organisms/stage/Neodiprion_lecontei/trackList.json b/organisms/stage/Neodiprion_lecontei/trackList.json
index a9eb303..ca990fd 100644
--- a/organisms/stage/Neodiprion_lecontei/trackList.json
+++ b/organisms/stage/Neodiprion_lecontei/trackList.json
@@ -1,454 +1,184 @@
 {
+   "formatVersion" : 1,
+   "names" : {
+      "type" : "Hash",
+      "url" : "names/"
+   },
    "tracks" : [
       {
-         "seqType" : "dna",
+         "category" : "Reference sequence",
+         "chunkSize" : 20000,
          "key" : "Reference sequence",
-         "useAsRefSeqStore" : 1,
-         "storeClass" : "JBrowse/Store/Sequence/IndexedFasta",
-         "urlTemplate" : "seq/GCA_001263575.2_Nlec1.1_genomic.fna",
-         "type" : "SequenceTrack",
          "label" : "DNA",
-         "category" : "Reference sequence",
-         "faiUrlTemplate" : "seq/GCA_001263575.2_Nlec1.1_genomic.fna.fai"
+         "seqType" : "dna",
+         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
+         "type" : "SequenceTrack",
+         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-"
       },
       {
+         "category" : "NCBI Annotation Release 101",
+         "compress" : 0,
+         "key" : "NCBI_Annotation_Release_101_Gene",
+         "label" : "neolec_current_models",
+         "menuTemplate" : [
+             {
+                "label" : "View details"
+             },
+             {
+              "label": "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
+              "title": "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
+              "iconClass" : "dijitIconDatabase",
+              "action": "newWindow",
+              "url" : "function(track,feature){ return 'https://www.ncbi.nlm.nih.gov/nuccore/'+feature.get('name')}"
+              }
+        ],
+         "metadata" : {
+            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Neodiprion_lecontei/README_CURRENT_RELEASE",
+            "Data provider" : "NCBI",
+            "Data source" : "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/021/901/455/GCF_021901455.1_iyNeoLeco1.1/GCF_021901455.1_iyNeoLeco1.1_genomic.gff.gz",
+            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
+            "arrowheadClass" : "trellis-arrowhead",
             "className" : "container-16px",
+            "description" : "product, note, description",
             "subfeatureClasses" : {
-               "wholeCDS" : null,
+               "CDS" : "gnomon_CDS",
+               "UTR" : "gnomon_UTR",
                "exon" : "container-100pct",
-               "CDS" : "primary_gene_set-cds",
-               "UTR" : "primary_gene_set-utr"
-            },
-            "arrowheadClass" : "trellis-arrowhead"
+               "wholeCDS" : null
+            }
          },
-         "key" : "neolec_OGSv1.1",
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
-         "trackType" : "ColorByType/View/Track/ColorByTypeDraggable",
-         "urlTemplate" : "tracks/neolec_current_models/{refseq}/trackData.json",
+         "trackType" : "HTMLFeatures",
+         "type" : "HTMLFeatures",
+         "urlTemplate" : "tracks/neolec_current_models/{refseq}/trackData.json"
+      },
+      {
+         "category" : "NCBI Annotation Release 101",
          "compress" : 0,
-         "category" : "Official Gene Set",
+         "key" : "NCBI_Annotation_Release_101_Pseudogene",
+         "label" : "NCBI_Annotation_Release_101_Pseudogene",
          "metadata" : {
-            "Data URL" : "",
-            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
-            "Method" : "Maker v2.31.8, followed by CrossMap re-mapping of coordinates to new genome assembly version",
-            "Data provider" : "Scott Geib, USDA-ARS Pacific Basin Agricultural Research Center"
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diff --git a/organisms/stage/Neodiprion_lecontei_training/trackList.json b/organisms/stage/Neodiprion_lecontei_training/trackList.json
index 52f66b2..2131ccf 100644
--- a/organisms/stage/Neodiprion_lecontei_training/trackList.json
+++ b/organisms/stage/Neodiprion_lecontei_training/trackList.json
@@ -1,688 +1,682 @@
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+          "exon": "container-100pct",
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+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/NCBI_Annotation_Release_100_Pseudogene/{refseq}/trackData.json"
+    },
+    {
+      "category": "NCBI-RefSeq Annotation Release 100/1. Gene Sets/Noncoding",
+      "compress": 0,
+      "key": "NCBI Predicted tRNAs, Annotation Release 100",
+      "label": "NCBI_Annotation_Release_100_tRNA",
+      "metadata": {
+        "Data description": "ftp://ftp.ncbi.nih.gov/genomes/Neodiprion_lecontei/README_CURRENT_RELEASE",
+        "Data provider": "NCBI",
+        "Data source": "ftp://ftp.ncbi.nih.gov/genomes/Neodiprion_lecontei/GFF/ref_Nlec1.0_top_level.gff3.gz",
+        "Method": "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
+      },
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+        "arrowheadClass": "trellis-arrowhead",
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/NCBI_Annotation_Release_100_tRNA/{refseq}/trackData.json"
+    },
+    {
+      "category": "NCBI-RefSeq Annotation Release 100/1. Gene Sets/Protein Coding",
+      "compress": 0,
+      "key": "NCBI Predicted low-quality protein coding genes, Annotation Release 100",
+      "label": "NCBI_Annotation_Release_100_Protein_Coding_low_quality",
+      "metadata": {
+        "Data description": "ftp://ftp.ncbi.nih.gov/genomes/Neodiprion_lecontei/README_CURRENT_RELEASE",
+        "Data provider": "NCBI",
+        "Data source": "ftp://ftp.ncbi.nih.gov/genomes/Neodiprion_lecontei/GFF/ref_Nlec1.0_top_level.gff3.gz",
+        "Method": "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
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+          "CDS": "gnomon_CDS",
+          "UTR": "gnomon_UTR",
+          "exon": "container-100pct",
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+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/NCBI_Annotation_Release_100_Protein_Coding_low_quality/{refseq}/trackData.json"
+    }
+  ]
 }
diff --git a/organisms/stage/Neodiprion_pinetum/trackList.json b/organisms/stage/Neodiprion_pinetum/trackList.json
new file mode 100644
index 0000000..4c0df28
--- /dev/null
+++ b/organisms/stage/Neodiprion_pinetum/trackList.json
@@ -0,0 +1,183 @@
+{
+   "formatVersion" : 1,
+   "names" : {
+      "type" : "Hash",
+      "url" : "names/"
+   },
+   "tracks" : [
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+         "chunkSize" : 20000,
+         "key" : "Reference sequence",
+         "label" : "DNA",
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+         "type" : "SequenceTrack",
+         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-"
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+      {
+         "category" : "NCBI Annotation Release 100",
+         "compress" : 0,
+         "key" : "NCBI_Annotation_Release_100_Gene",
+         "label" : "neopin_current_models",
+         "metadata" : {
+            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Neodiprion_pinetum/README_CURRENT_RELEASE",
+            "Data provider" : "NCBI",
+            "Data source" : "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/021/155/775/GCF_021155775.1_iyNeoPine1.1/GCF_021155775.1_iyNeoPine1.1_genomic.gff.gz",
+            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+  "menuTemplate" : [
+             {
+                "label" : "View details"
+             },
+             {
+              "label": "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
+              "title": "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
+              "iconClass" : "dijitIconDatabase",
+              "action": "newWindow",
+              "url" : "function(track,feature){ return 'https://www.ncbi.nlm.nih.gov/nuccore/'+feature.get('name')}"
+              }
+        ],
+         "style" : {
+            "arrowheadClass" : "trellis-arrowhead",
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+            "description" : "product, note, description",
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+               "exon" : "container-100pct",
+               "wholeCDS" : null
+            }
+         },
+         "trackType" : "HTMLFeatures",
+         "type" : "HTMLFeatures",
+         "urlTemplate" : "tracks/neopin_current_models/{refseq}/trackData.json"
+      },
+      {
+         "category" : "NCBI Annotation Release 100",
+         "compress" : 0,
+         "key" : "NCBI_Annotation_Release_100_Pseudogene",
+         "label" : "NCBI_Annotation_Release_100_Pseudogene",
+         "metadata" : {
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+            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "container-16px",
+            "description" : "product, note, description",
+            "subfeatureClasses" : {
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+               "UTR" : "gnomon_UTR",
+               "exon" : "container-100pct",
+               "wholeCDS" : null
+            }
+         },
+         "trackType" : "HTMLFeatures",
+         "type" : "HTMLFeatures",
+         "urlTemplate" : "tracks/NCBI_Annotation_Release_100_Pseudogene/{refseq}/trackData.json"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Reference Assembly",
+         "key" : "Gaps in assembly",
+         "label" : "Gaps in assembly",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "white",
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+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/GCF_021155775.1_iyNeoPine1.1_genomic.fna.gaps.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "0.5",
+         "category" : "Reference Assembly",
+         "key" : "GC Content",
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+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+         },
+         "scoreType" : "avgScore",
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "rgba(255,255,0,50)",
+            "pos_color" : "rgba(0,0,255,50)"
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+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/GCF_021155775.1_iyNeoPine1.1_genomic.fna.gc.bigwig"
+      },
+      {
+         "category" : "RNA-Seq/Mapped Reads",
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+         "label" : "Neopin_iyNeoPine1.1_RNA-Seq-alignments_2022-03-11",
+         "metadata" : {
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+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
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+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "unsafePopup" : true,
+         "urlTemplate" : "analyses/Neodiprion-pinetum-RNA-Seq_2022-03-11_v1.0/Neopin_iyNeoPine1.1_RNA-Seq-alignments_2022-03-11.bam"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
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+         "label" : "Neopin_iyNeoPine1.1_RNA-Seq-alignments_2022-03-11_coverage",
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11198135'>SRR11198135</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11198136'>SRR11198136</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11198133'>SRR11198133</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11198134'>SRR11198134</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11198129'>SRR11198129</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11198130'>SRR11198130</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11198131'>SRR11198131</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11198132'>SRR11198132</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage."
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+         "style" : {
+            "pos_color" : "#00BFFF"
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+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "unsafePopup" : true,
+         "urlTemplate" : "analyses/Neodiprion-pinetum-RNA-Seq_2022-03-11_v1.0/Neopin_iyNeoPine1.1_RNA-Seq-alignments_2022-03-11.bigwig"
+      },
+      {
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+         "compress" : 0,
+         "key" : "Neopin_iyNeoPine1.1_RNA-Seq-alignments_2022-03-11_junctions",
+         "label" : "Neopin_iyNeoPine1.1_RNA-Seq-alignments_2022-03-11_junctions",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11198135'>SRR11198135</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11198136'>SRR11198136</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11198133'>SRR11198133</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11198134'>SRR11198134</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11198129'>SRR11198129</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11198130'>SRR11198130</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11198131'>SRR11198131</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11198132'>SRR11198132</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Junction reads generated by Hisat2 aligner and regtools. The number of alignments supporting the junction read is listed in blue."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "className" : "feature",
+            "description" : "score"
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+         "type" : "FeatureTrack",
+         "unsafePopup" : true,
+         "urlTemplate" : "tracks/Neopin_iyNeoPine1.1_RNA-Seq-alignments_2022-03-11_junctions/{refseq}/trackData.json"
+      }
+   ]
+}
diff --git a/organisms/stage/Neodiprion_virginiana/trackList.json b/organisms/stage/Neodiprion_virginiana/trackList.json
new file mode 100755
index 0000000..330ee73
--- /dev/null
+++ b/organisms/stage/Neodiprion_virginiana/trackList.json
@@ -0,0 +1,183 @@
+{
+   "formatVersion" : 1,
+   "names" : {
+      "type" : "Hash",
+      "url" : "names/"
+   },
+   "tracks" : [
+      {
+         "category" : "Reference sequence",
+         "chunkSize" : 20000,
+         "key" : "Reference sequence",
+         "label" : "DNA",
+         "seqType" : "dna",
+         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
+         "type" : "SequenceTrack",
+         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-"
+      },
+      {
+         "category" : "NCBI Annotation Release 100",
+         "compress" : 0,
+         "key" : "NCBI_Annotation_Release_100_Gene",
+         "label" : "neovir_current_models",
+         "menuTemplate" : [
+            {
+               "label" : "View details"
+            },
+            {
+               "action" : "newWindow",
+               "iconClass" : "dijitIconDatabase",
+               "label" : "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
+               "title" : "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
+               "url" : "function(track,feature){ return 'https://www.ncbi.nlm.nih.gov/nuccore/'+feature.get('name')}"
+            }
+         ],
+         "metadata" : {
+            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Neodiprion_virginiana/README_CURRENT_RELEASE",
+            "Data provider" : "NCBI",
+            "Data source" : "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/021/901/495/GCF_021901495.1_iyNeoVirg1.1/GCF_021901495.1_iyNeoVirg1.1_genomic.gff.gz",
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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+            "className" : "container-16px",
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+               "UTR" : "gnomon_UTR",
+               "exon" : "container-100pct",
+               "wholeCDS" : null
+            }
+         },
+         "trackType" : "HTMLFeatures",
+         "type" : "HTMLFeatures",
+         "urlTemplate" : "tracks/neovir_current_models/{refseq}/trackData.json"
+      },
+      {
+         "category" : "NCBI Annotation Release 100",
+         "compress" : 0,
+         "key" : "NCBI_Annotation_Release_100_Pseudogene",
+         "label" : "NCBI_Annotation_Release_100_Pseudogene",
+         "metadata" : {
+            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Neodiprion_virginiana/README_CURRENT_RELEASE",
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "container-16px",
+            "description" : "product, note, description",
+            "subfeatureClasses" : {
+               "CDS" : "gnomon_CDS",
+               "UTR" : "gnomon_UTR",
+               "exon" : "container-100pct",
+               "wholeCDS" : null
+            }
+         },
+         "trackType" : "HTMLFeatures",
+         "type" : "HTMLFeatures",
+         "urlTemplate" : "tracks/NCBI_Annotation_Release_100_Pseudogene/{refseq}/trackData.json"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Reference Assembly",
+         "key" : "Gaps in assembly",
+         "label" : "Gaps in assembly",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
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+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "white",
+            "pos_color" : "black"
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+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/GCF_021901495.1_iyNeoVirg1.1_genomic.fna.gaps.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "0.5",
+         "category" : "Reference Assembly",
+         "key" : "GC Content",
+         "label" : "GC Content",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+         },
+         "scoreType" : "avgScore",
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "rgba(255,255,0,50)",
+            "pos_color" : "rgba(0,0,255,50)"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/GCF_021901495.1_iyNeoVirg1.1_genomic.fna.gc.bigwig"
+      },
+      {
+         "category" : "RNA-Seq/Mapped Reads",
+         "key" : "Neodiprion lecontei RNA-Seq aligned against Neodiprion virginiana iyNeoVirg1.1",
+         "label" : "Neolec_iyNeoVirg1.1_RNA-Seq-alignments_2022-03-29",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
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+         "unsafePopup" : true,
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "analyses/Neodiprion-virginiana-RNA-Seq_2022-03-29_v1.0/Neolec_iyNeoVirg1.1_RNA-Seq-alignments_2022-03-29.bigwig"
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+            "Track legend" : "Junction reads generated by Hisat2 aligner and regtools. The number of alignments supporting the junction read is listed in blue."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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+            "description" : "score"
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+         "type" : "FeatureTrack",
+         "unsafePopup" : true,
+         "urlTemplate" : "tracks/Neolec_iyNeoVirg1.1_RNA-Seq-alignments_2022-03-29_junctions/{refseq}/trackData.json"
+      }
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+}
diff --git a/organisms/stage/Nicrophorus_vespilloides/trackList.json b/organisms/stage/Nicrophorus_vespilloides/trackList.json
index bd58c84..d252e1c 100644
--- a/organisms/stage/Nicrophorus_vespilloides/trackList.json
+++ b/organisms/stage/Nicrophorus_vespilloides/trackList.json
@@ -1,343 +1,396 @@
 {
-   "css" : "./plugins/NAL_CSS/css/contrib_styles.css",
+   "alwaysOnTracks" : "DNA,Annotations",
+   "css" : "./plugins/NAL_CSS/css/main.css",
+   "favicon" : "./plugins/WebApollo/img/webapollo_favicon.ico",
+   "formatVersion" : 1,
    "share_link" : 0,
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          "chunkSize" : 20000,
-         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-",
+         "key" : "Reference sequence",
          "label" : "DNA",
+         "seqType" : "dna",
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          "type" : "SequenceTrack",
-         "category" : "Reference sequence"
+         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-"
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-         "urlTemplate" : "tracks/NCBI_Annotation_Release_100_lncRNA/{refseq}/trackData.json",
+         "category" : "NCBI Annotation Release 100/1. Gene Sets/Noncoding",
          "compress" : 0,
+         "key" : "NCBI Predicted lncRNA, Annotation Release 100",
          "label" : "NCBI_Annotation_Release_100_lncRNA",
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             "Data provider" : "NCBI",
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          },
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-      {
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          "style" : {
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+            "arrowheadClass" : "trellis-arrowhead",
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-         "urlTemplate" : "tracks/NCBI_Annotation_Release_100_Pseudogene/{refseq}/trackData.json",
-         "compress" : 0,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/NCBI_Annotation_Release_100_lncRNA/{refseq}/trackData.json"
+      },
+      {
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          "style" : {
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-         "compress" : 0,
          "type" : "FeatureTrack",
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+         "urlTemplate" : "tracks/NCBI_Annotation_Release_100_Pseudogene/{refseq}/trackData.json"
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-         "label" : "Annotations",
-         "type" : "WebApollo/View/Track/AnnotTrack",
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-         "bicolor_pivot" : "zero",
          "autoscale" : "local",
+         "bicolor_pivot" : "zero",
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          "metadata" : {
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             "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
-            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank",
-            "Track contact" : "The i5k workspace@NAL"
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-            "pos_color" : "rgba(0,0,255,50)"
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-         "scoreType": "avgScore",
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          "category" : "Reference Assembly",
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          "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
             "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
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-            "Track contact" : "The i5k workspace@NAL"
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+         },
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       },
       {
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+         "key" : "Official Gene Set 1.0, protein-coding genes",
+         "label" : "official-gene-set-1-0_protein",
+         "metadata" : {
+            "Data description" : "Gene set accompanying GBE publication with RefSeq Accession numbers.",
+            "Data provider" : "Chris Cunningham, Swansea University",
+            "Method" : "MAKER 2.0",
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                "CDS" : "ogs-cds",
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-            "arrowheadClass" : "trellis-arrowhead"
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-         "urlTemplate" : "tracks/official-gene-set-1-0_protein/{refseq}/trackData.json",
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/official-gene-set-1-0_protein/{refseq}/trackData.json"
+      },
+      {
+         "category" : "Official Gene Set 1.0/1. Gene Sets/Noncoding",
          "compress" : 0,
+         "key" : "Official Gene Set 1.0, non-coding RNA",
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          "metadata" : {
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-            "Publication status" : "Cunningham et al. 2015. Genome Biology and Evolution 7: 3383-3396.",
+            "Data description" : "Gene set accompanying GBE publication with RefSeq Accession numbers.",
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-            "Data description" : "Gene set accompanying GBE publication with RefSeq Accession numbers."
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-         "label" : "official-gene-set-1-0_protein"
-      },
-      {
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          "style" : {
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             "renderClassName" : "ogs-utr"
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-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
-         "urlTemplate" : "tracks/official-gene-set-1-0_RNA-motif/{refseq}/trackData.json",
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/official-gene-set-1-0_RNA-motif/{refseq}/trackData.json"
+      },
+      {
+         "category" : "Official Gene Set 1.0/2. Evidence",
          "compress" : 0,
-         "category" : "Official Gene Set 1.0/1. Gene Sets/Noncoding",
+         "key" : "Official Gene Set 1.0, repeatmasker evidence",
+         "label" : "official-gene-set-1-0_repeatmasker",
          "metadata" : {
-            "Method" : "MAKER 2.0",
-            "Publication status" : "Cunningham et al. 2015. Genome Biology and Evolution 7: 3383-3396.",
+            "Data description" : "Gene set accompanying GBE publication with RefSeq Accession numbers.",
             "Data provider" : "Chris Cunningham, Swansea University",
-            "Data description" : "Gene set accompanying GBE publication with RefSeq Accession numbers."
+            "Method" : "MAKER 2.0",
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          },
-         "label" : "official-gene-set-1-0_RNA-motif",
-         "type" : "FeatureTrack"
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
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+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/official-gene-set-1-0_repeatmasker/{refseq}/trackData.json"
       },
       {
+         "category" : "RNA-Seq/Mapped Reads",
+         "key" : "Nicves_Nicve_v1.0_RNA-Seq-alignments_2021-06-16",
+         "label" : "Nicves_Nicve_v1.0_RNA-Seq-alignments_2021-06-16",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR6348665'>SRR6348665</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR2089958'>SRR2089958</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR5307990'>SRR5307990</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR5307987'>SRR5307987</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR2086508'>SRR2086508</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR5307972'>SRR5307972</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR2086509'>SRR2086509</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR6348653'>SRR6348653</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR6348658'>SRR6348658</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR5308000'>SRR5308000</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Dark red alignments: Mapped portion of read aligned to forward strand<br>Light red alignments: Spliced portion of read aligned to forward strand<br>Dark blue alignments: Mapped portion of read aligned to reverse strand<br>Light blue alignments: Spliced portion of read aligned to reverse strand<br>Red marking - deletion in the read relative to the reference<br>Green marking - insertion in the read relative to the reference<br>Yellow marking  - mismatch (hover over the mismatch to see what the snp is)"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "unsafePopup" : true,
+         "urlTemplate" : "analyses/Nicrophorus-vespilloides-RNA-Seq_2021-06-16_v1.0/Nicves_Nicve_v1.0_RNA-Seq-alignments_2021-06-16.bam"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "RNA-Seq/Coverage Plots",
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+         "label" : "Nicves_Nicve_v1.0_RNA-Seq-alignments_2021-06-16_coverage",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR6348665'>SRR6348665</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR2089958'>SRR2089958</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR5307990'>SRR5307990</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR5307987'>SRR5307987</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR2086508'>SRR2086508</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR5307972'>SRR5307972</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR2086509'>SRR2086509</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR6348653'>SRR6348653</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR6348658'>SRR6348658</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR5308000'>SRR5308000</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
          "style" : {
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-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
-         "urlTemplate" : "tracks/official-gene-set-1-0_repeatmasker/{refseq}/trackData.json",
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+         "urlTemplate" : "analyses/Nicrophorus-vespilloides-RNA-Seq_2021-06-16_v1.0/Nicves_Nicve_v1.0_RNA-Seq-alignments_2021-06-16.bigwig"
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          "compress" : 0,
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+         "label" : "Nicves_Nicve_v1.0_RNA-Seq-alignments_2021-06-16_junctions",
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-            "Method" : "MAKER 2.0",
-            "Data provider" : "Chris Cunningham, Swansea University",
-            "Data description" : "Gene set accompanying GBE publication with RefSeq Accession numbers."
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR6348665'>SRR6348665</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR2089958'>SRR2089958</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR5307990'>SRR5307990</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR5307987'>SRR5307987</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR2086508'>SRR2086508</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR5307972'>SRR5307972</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR2086509'>SRR2086509</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR6348653'>SRR6348653</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR6348658'>SRR6348658</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR5308000'>SRR5308000</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Junction reads generated by Hisat2 aligner and regtools. The number of alignments supporting the junction read is listed in blue."
          },
-         "label" : "official-gene-set-1-0_repeatmasker",
-         "type" : "FeatureTrack"
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "className" : "feature",
+            "description" : "score"
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "unsafePopup" : true,
+         "urlTemplate" : "tracks/Nicves_Nicve_v1.0_RNA-Seq-alignments_2021-06-16_junctions/{refseq}/trackData.json"
       }
-   ],
-   "favicon" : "./plugins/WebApollo/img/webapollo_favicon.ico",
-   "alwaysOnTracks" : "DNA,Annotations",
-   "formatVersion" : 1
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 }
diff --git a/organisms/stage/Nylanderia_fulva/trackList.json b/organisms/stage/Nylanderia_fulva/trackList.json
index 8799221..4acfd30 100644
--- a/organisms/stage/Nylanderia_fulva/trackList.json
+++ b/organisms/stage/Nylanderia_fulva/trackList.json
@@ -13,6 +13,7 @@
          "seqType" : "dna",
          "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
          "type" : "SequenceTrack",
+         "unsafePopup" : true,
          "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-"
       },
       {
@@ -32,6 +33,7 @@
             "pos_color" : "black"
          },
          "type" : "JBrowse/View/Track/Wiggle/Density",
+         "unsafePopup" : true,
          "urlTemplate" : "bigwig/GCF_005281655.1_TAMU_Nfulva_1.0_genomic.fna.gaps.bigwig"
       },
       {
@@ -51,6 +53,7 @@
             "pos_color" : "rgba(0,0,255,50)"
          },
          "type" : "JBrowse/View/Track/Wiggle/Density",
+         "unsafePopup" : true,
          "urlTemplate" : "bigwig/GCF_005281655.1_TAMU_Nfulva_1.0_genomic.fna.gc.bigwig"
       },
       {
@@ -58,19 +61,25 @@
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-              "title": "function(track,feature){ return 'Find gene page for '+feature.get('id')}",
-              "iconClass" : "dijitIconDatabase",
-              "action": "newWindow",
-              "url" : "function(track,feature){ return 'https://i5k.nal.usda.gov/search/site/'+feature.get('id')}",
-              },
-        ],
+            {
+               "label" : "View details"
+            },
+            {
+               "action" : "newWindow",
+               "iconClass" : "dijitIconDatabase",
+               "label" : "function(track,feature){ return 'Find NCBI record for '+feature.get('id')}",
+               "title" : "function(track,feature){ return 'Find NCBI record for '+feature.get('id')}",
+               "url" : "function(track,feature){ return 'https://www.ncbi.nlm.nih.gov/protein/'+feature.get('id')}"
+            }
+         ],
+         "metadata" : {
+            "Data provider" : "Kranti Konganti, Texas A&M University; Ed Vargo, Texas A&M University; Aaron Tarone, Texas A&M University; Lukas Schrader, University of Muenster",
+            "Data source" : "https://data.nal.usda.gov/dataset/nylanderia-fulva-annotations-ogsv10",
+            "Materials and Methods" : "The Nylanderia fulva OGSv1.0 is the Official Gene Set of genome assembly TAMU_Nfulva_1.0 (https://www.ncbi.nlm.nih.gov/assembly/GCF_005281655.1/). It is a merge of NCBI Nylanderia fulva Annotation Release 100 (https://www.ncbi.nlm.nih.gov/genome/annotation_euk/Nylanderia_fulva/100/) and semi-automated predictions of odorant receptors.",
+            "Publication status" : "Unpublished, please refer to Fort Lauderdale/Toronto conditions of data re-use"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
             "arrowheadClass" : "trellis-arrowhead",
             "className" : "container-16px",
@@ -82,14 +91,9 @@
                "wholeCDS" : null
             }
          },
-	 "metadata" : {
-	 "Data source" : "https://data.nal.usda.gov/dataset/nylanderia-fulva-annotations-ogsv10",
-	 "Materials and Methods" : "The Nylanderia fulva OGSv1.0 is the Official Gene Set of genome assembly TAMU_Nfulva_1.0 (https://www.ncbi.nlm.nih.gov/assembly/GCF_005281655.1/). It is a merge of NCBI Nylanderia fulva Annotation Release 100 (https://www.ncbi.nlm.nih.gov/genome/annotation_euk/Nylanderia_fulva/100/) and semi-automated predictions of odorant receptors.",
-	 "Publication status" : "Unpublished, please refer to Fort Lauderdale/Toronto conditions of data re-use", 
-	 "Data provider" : "Kranti Konganti, Texas A&M University; Ed Vargo, Texas A&M University; Aaron Tarone, Texas A&M University; Lukas Schrader, University of Muenster",
-	 },	 
-         "trackType" : "ColorByType/View/Track/ColorByTypeDraggable",
-         "type" : "ColorByType/View/Track/ColorByTypeDraggable",
+         "trackType" : "HTMLFeatures",
+         "type" : "HTMLFeatures",
+         "unsafePopup" : true,
          "urlTemplate" : "tracks/nylful_current_models/{refseq}/trackData.json"
       },
       {
@@ -97,6 +101,12 @@
          "compress" : 0,
          "key" : "OGSv1.0 Pseudogene",
          "label" : "OGSv1.0_Pseudogene",
+         "metadata" : {
+            "Data provider" : "Kranti Konganti, Texas A&M University; Ed Vargo, Texas A&M University; Aaron Tarone, Texas A&M University; Lukas Schrader, University of Muenster",
+            "Data source" : "https://data.nal.usda.gov/dataset/nylanderia-fulva-annotations-ogsv10",
+            "Materials and Methods" : "The Nylanderia fulva OGSv1.0 is the Official Gene Set of genome assembly TAMU_Nfulva_1.0 (https://www.ncbi.nlm.nih.gov/assembly/GCF_005281655.1/). It is a merge of NCBI Nylanderia fulva Annotation Release 100 (https://www.ncbi.nlm.nih.gov/genome/annotation_euk/Nylanderia_fulva/100/) and semi-automated predictions of odorant receptors.",
+            "Publication status" : "Unpublished, please refer to Fort Lauderdale/Toronto conditions of data re-use"
+         },
          "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
             "arrowheadClass" : "trellis-arrowhead",
@@ -109,15 +119,69 @@
                "wholeCDS" : null
             }
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-         "Materials and Methods" : "The Nylanderia fulva OGSv1.0 is the Official Gene Set of genome assembly TAMU_Nfulva_1.0 (https://www.ncbi.nlm.nih.gov/assembly/GCF_005281655.1/). It is a merge of NCBI Nylanderia fulva Annotation Release 100 (https://www.ncbi.nlm.nih.gov/genome/annotation_euk/Nylanderia_fulva/100/) and semi-automated predictions of odorant receptors.",
-         "Publication status" : "Unpublished, please refer to Fort Lauderdale/Toronto conditions of data re-use",
-         "Data provider" : "Kranti Konganti, Texas A&M University; Ed Vargo, Texas A&M University; Aaron Tarone, Texas A&M University; Lukas Schrader, University of Muenster",
-         },
          "trackType" : "HTMLFeatures",
          "type" : "HTMLFeatures",
+         "unsafePopup" : true,
          "urlTemplate" : "tracks/OGSv1.0_Pseudogene/{refseq}/trackData.json"
+      },
+      {
+         "category" : "RNA-Seq/Mapped Reads",
+         "key" : "Nylful_TAMU_Nfulva_1.0_RNA-Seq-alignments_2021-06-16",
+         "label" : "Nylful_TAMU_Nfulva_1.0_RNA-Seq-alignments_2021-06-16",
+         "metadata" : {
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+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
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+            "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
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+         "urlTemplate" : "analyses/Nylanderia-fulva-RNA-Seq_2021-06-16_v1.0/Nylful_TAMU_Nfulva_1.0_RNA-Seq-alignments_2021-06-16.bigwig"
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+         "label" : "Nylful_TAMU_Nfulva_1.0_RNA-Seq-alignments_2021-06-16_junctions",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
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+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Junction reads generated by Hisat2 aligner and regtools. The number of alignments supporting the junction read is listed in blue."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "className" : "feature",
+            "description" : "score"
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+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "unsafePopup" : true,
+         "urlTemplate" : "tracks/Nylful_TAMU_Nfulva_1.0_RNA-Seq-alignments_2021-06-16_junctions/{refseq}/trackData.json"
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 }
diff --git a/organisms/stage/Odontomachus_brunneus/trackList.json b/organisms/stage/Odontomachus_brunneus/trackList.json
index a74f420..120d3e6 100644
--- a/organisms/stage/Odontomachus_brunneus/trackList.json
+++ b/organisms/stage/Odontomachus_brunneus/trackList.json
@@ -1,717 +1,718 @@
 {
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-         "urlTemplate" : "bigwig/GCF_010583005.1_Obru_v1_genomic.fna.gaps.bigwig",
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-         "label" : "Gaps in assembly",
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-            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
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-         "category" : "Reference Assembly",
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-         "metadata" : {
-            "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track.",
-            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
-            "Track contact" : "The i5k workspace@NAL"
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-      {
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-               "CDS" : "gnomon_CDS",
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-            "description" : "product, note, description"
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-         "label" : "NCBI_Annotation_Release_100_Pseudogene",
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+      "category": "Reference Assembly",
+      "key": "Gaps in assembly",
+      "label": "Gaps in assembly",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
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+      "category": "Reference Assembly",
+      "key": "GC Content",
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+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
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+      "label": "Odobru_Obru_v1_RNA-Seq-alignments_2020-06-02",
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+        "Analysis method": "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+        "Analysis provider": "i5k Workspace@NAL",
+        "Data source": "SRR6984027,SRR6984020,SRR6984034,SRR6984030,SRR6984019,SRR6984018,SRR6984056,SRR6984023,SRR6984021,SRR6984036",
+        "Publication status": "Analysis: NA; Source data: see individual SRA accessions",
+        "Track legend": "Dark red alignments: Mapped portion of read aligned to forward strand<br>Light red alignments: Spliced portion of read aligned to forward strand<br>Dark blue alignments: Mapped portion of read aligned to reverse strand<br>Light blue alignments: Spliced portion of read aligned to reverse strand<br>Red marking - deletion in the read relative to the reference<br>Green marking - insertion in the read relative to the reference<br>Yellow marking  - mismatch (hover over the mismatch to see what the snp is)"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "analyses/Odontomachus-brunneus-RNA-Seq_2020-06-02_v1.0/Odobru_Obru_v1_RNA-Seq-alignments_2020-06-02.bam"
+    },
+    {
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+      "category": "RNA-Seq/Coverage Plots",
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+      "label": "Odobru_Obru_v1_RNA-Seq-alignments_2020-06-02_coverage",
+      "metadata": {
+        "Analysis method": "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+        "Analysis provider": "i5k Workspace@NAL",
+        "Data source": "SRR6984027,SRR6984020,SRR6984034,SRR6984030,SRR6984019,SRR6984018,SRR6984056,SRR6984023,SRR6984021,SRR6984036",
+        "Publication status": "Analysis: NA; Source data: see individual SRA accessions",
+        "Track legend": "This track represents an X-Y plot of RNA-Seq coverage."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
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+      "urlTemplate": "analyses/Odontomachus-brunneus-RNA-Seq_2020-06-02_v1.0/Odobru_Obru_v1_RNA-Seq-alignments_2020-06-02.bigwig"
+    },
+    {
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+      "label": "Odobru_Obru_v1_RNA-Seq-alignments_2020-06-02_junctions",
+      "metadata": {
+        "Analysis method": "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+        "Analysis provider": "i5k Workspace@NAL",
+        "Data source": "SRR6984027,SRR6984020,SRR6984034,SRR6984030,SRR6984019,SRR6984018,SRR6984056,SRR6984023,SRR6984021,SRR6984036",
+        "Publication status": "Analysis: NA; Source data: see individual SRA accessions",
+        "Track legend": "Junction reads generated by Hisat2 aligner and regtools"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/Odobru_Obru_v1_RNA-Seq-alignments_2020-06-02_junctions/{refseq}/trackData.json"
+    },
+    {
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+      "key": "Male",
+      "label": "Male",
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+        "Analysis provider": "Kim Walden, University of Illinois at Urbana-Champaign",
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+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale re-use guidelines",
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+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "analyses/Odontomachus-brunneus-RNA-Seq_2020-06-09_v1.0/Odontomachus_male_2nd_passAligned.sortedByCoord.out.bam"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "RNA-Seq/Coverage Plots",
+      "key": "Male, coverage",
+      "label": "Male, coverage",
+      "metadata": {
+        "Analysis method": "Reads were trimmed with Trimmomatic (0.32) and aligned to the genome assembly by caste/life-stage using STAR (2.7.3a) in paired-end mode with the available NCBI genome gtf file. The reads were aligned to the genome in a second pass using all the available splice junction information from the first pass alignments. Bam files were indexed with SAMtools (1.10). The second pass splice junction output files were converted to bed files using the custom script available at: https://gist.github.com/fabiolib/ffb21853e3eb3780150074aeffc54901",
+        "Analysis provider": "Kim Walden, University of Illinois at Urbana-Champaign",
+        "Data source": "SRR6984018, SRR6984012, SRR6984056",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale re-use guidelines",
+        "Track legend": "This track represents an X-Y plot of RNA-Seq coverage.",
+        "development stage": "Adult Male"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "pos_color": "#00BFFF"
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+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "analyses/Odontomachus-brunneus-RNA-Seq_2020-06-09_v1.0/Odontomachus_male_2nd_passAligned.sortedByCoord.out.bigwig"
+    },
+    {
+      "category": "RNA-Seq/Mapped Reads",
+      "key": "Larva",
+      "label": "Larva",
+      "metadata": {
+        "Analysis method": "Reads were trimmed with Trimmomatic (0.32) and aligned to the genome assembly by caste/life-stage using STAR (2.7.3a) in paired-end mode with the available NCBI genome gtf file. The reads were aligned to the genome in a second pass using all the available splice junction information from the first pass alignments. Bam files were indexed with SAMtools (1.10).The second pass splice junction output files were converted to bed files using the custom script available at: https://gist.github.com/fabiolib/ffb21853e3eb3780150074aeffc54901",
+        "Analysis provider": "Kim Walden, University of Illinois at Urbana-Champaign",
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+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale re-use guidelines",
+        "Track legend": "Dark red alignments: Mapped portion of read aligned to forward strand<br>Light red alignments: Spliced portion of read aligned to forward strand<br>Dark blue alignments: Mapped portion of read aligned to reverse strand<br>Light blue alignments: Spliced portion of read aligned to reverse strand<br>Red marking - deletion in the read relative to the reference<br>Green marking - insertion in the read relative to the reference<br>Yellow marking  - mismatch (hover over the mismatch to see what the snp is)",
+        "development stage": "Larva"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "analyses/Odontomachus-brunneus-RNA-Seq_2020-06-09_v1.0/Odontomachus_larva_2nd_passAligned.sortedByCoord.out.bam"
+    },
+    {
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+      "bicolor_pivot": "zero",
+      "category": "RNA-Seq/Coverage Plots",
+      "key": "Larva, coverage",
+      "label": "Larva, coverage",
+      "metadata": {
+        "Analysis method": "Reads were trimmed with Trimmomatic (0.32) and aligned to the genome assembly by caste/life-stage using STAR (2.7.3a) in paired-end mode with the available NCBI genome gtf file. The reads were aligned to the genome in a second pass using all the available splice junction information from the first pass alignments. Bam files were indexed with SAMtools (1.10). The second pass splice junction output files were converted to bed files using the custom script available at: https://gist.github.com/fabiolib/ffb21853e3eb3780150074aeffc54901",
+        "Analysis provider": "Kim Walden, University of Illinois at Urbana-Champaign",
+        "Data source": "SRR6984019, SRR6984036, SRR6984027",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale re-use guidelines",
+        "Track legend": "This track represents an X-Y plot of RNA-Seq coverage.",
+        "development stage": "Larva"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "pos_color": "#00BFFF"
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+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "analyses/Odontomachus-brunneus-RNA-Seq_2020-06-09_v1.0/Odontomachus_larva_2nd_passAligned.sortedByCoord.out.bigwig"
+    },
+    {
+      "category": "RNA-Seq/Mapped Reads",
+      "key": "Egg",
+      "label": "Egg",
+      "metadata": {
+        "Analysis method": "Reads were trimmed with Trimmomatic (0.32) and aligned to the genome assembly by caste/life-stage using STAR (2.7.3a) in paired-end mode with the available NCBI genome gtf file. The reads were aligned to the genome in a second pass using all the available splice junction information from the first pass alignments. Bam files were indexed with SAMtools (1.10).The second pass splice junction output files were converted to bed files using the custom script available at: https://gist.github.com/fabiolib/ffb21853e3eb3780150074aeffc54901",
+        "Analysis provider": "Kim Walden, University of Illinois at Urbana-Champaign",
+        "Data source": "SRR6984010, SRR6984024, SRR6984030",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale re-use guidelines",
+        "Track legend": "Dark red alignments: Mapped portion of read aligned to forward strand<br>Light red alignments: Spliced portion of read aligned to forward strand<br>Dark blue alignments: Mapped portion of read aligned to reverse strand<br>Light blue alignments: Spliced portion of read aligned to reverse strand<br>Red marking - deletion in the read relative to the reference<br>Green marking - insertion in the read relative to the reference<br>Yellow marking  - mismatch (hover over the mismatch to see what the snp is)",
+        "development stage": "Egg"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "analyses/Odontomachus-brunneus-RNA-Seq_2020-06-09_v1.0/Odontomachus_egg_2nd_passAligned.sortedByCoord.out.bam"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "RNA-Seq/Coverage Plots",
+      "key": "Egg, coverage",
+      "label": "Egg, coverage",
+      "metadata": {
+        "Analysis method": "Reads were trimmed with Trimmomatic (0.32) and aligned to the genome assembly by caste/life-stage using STAR (2.7.3a) in paired-end mode with the available NCBI genome gtf file. The reads were aligned to the genome in a second pass using all the available splice junction information from the first pass alignments. Bam files were indexed with SAMtools (1.10). The second pass splice junction output files were converted to bed files using the custom script available at: https://gist.github.com/fabiolib/ffb21853e3eb3780150074aeffc54901",
+        "Analysis provider": "Kim Walden, University of Illinois at Urbana-Champaign",
+        "Data source": "SRR6984010, SRR6984024, SRR6984030",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale re-use guidelines",
+        "Track legend": "This track represents an X-Y plot of RNA-Seq coverage.",
+        "development stage": "Egg"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "pos_color": "#00BFFF"
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+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "analyses/Odontomachus-brunneus-RNA-Seq_2020-06-09_v1.0/Odontomachus_egg_2nd_passAligned.sortedByCoord.out.bigwig"
+    },
+    {
+      "category": "RNA-Seq/Mapped Reads",
+      "key": "Reproductive Adult Worker",
+      "label": "Reproductive Adult Worker",
+      "metadata": {
+        "Analysis method": "Reads were trimmed with Trimmomatic (0.32) and aligned to the genome assembly by caste/life-stage using STAR (2.7.3a) in paired-end mode with the available NCBI genome gtf file. The reads were aligned to the genome in a second pass using all the available splice junction information from the first pass alignments. Bam files were indexed with SAMtools (1.10).The second pass splice junction output files were converted to bed files using the custom script available at: https://gist.github.com/fabiolib/ffb21853e3eb3780150074aeffc54901",
+        "Analysis provider": "Kim Walden, University of Illinois at Urbana-Champaign",
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+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale re-use guidelines",
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+        "development stage": "Reproductive Adult Worker"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "analyses/Odontomachus-brunneus-RNA-Seq_2020-06-09_v1.0/Odontomachus_RAW_2nd_passAligned.sortedByCoord.out.bam"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "RNA-Seq/Coverage Plots",
+      "key": "Reproductive Adult Worker, coverage",
+      "label": "Reproductive Adult Worker, coverage",
+      "metadata": {
+        "Analysis method": "Reads were trimmed with Trimmomatic (0.32) and aligned to the genome assembly by caste/life-stage using STAR (2.7.3a) in paired-end mode with the available NCBI genome gtf file. The reads were aligned to the genome in a second pass using all the available splice junction information from the first pass alignments. Bam files were indexed with SAMtools (1.10). The second pass splice junction output files were converted to bed files using the custom script available at: https://gist.github.com/fabiolib/ffb21853e3eb3780150074aeffc54901",
+        "Analysis provider": "Kim Walden, University of Illinois at Urbana-Champaign",
+        "Data source": "SRR6984022, SRR6984034, SRR6984031",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale re-use guidelines",
+        "Track legend": "This track represents an X-Y plot of RNA-Seq coverage.",
+        "development stage": "Reproductive Adult Worker"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "pos_color": "#00BFFF"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "analyses/Odontomachus-brunneus-RNA-Seq_2020-06-09_v1.0/Odontomachus_RAW_2nd_passAligned.sortedByCoord.out.bigwig"
+    },
+    {
+      "category": "RNA-Seq/Mapped Reads",
+      "key": "Non-reproductive Adult Worker",
+      "label": "Non-reproductive Adult Worker",
+      "metadata": {
+        "Analysis method": "Reads were trimmed with Trimmomatic (0.32) and aligned to the genome assembly by caste/life-stage using STAR (2.7.3a) in paired-end mode with the available NCBI genome gtf file. The reads were aligned to the genome in a second pass using all the available splice junction information from the first pass alignments. Bam files were indexed with SAMtools (1.10).The second pass splice junction output files were converted to bed files using the custom script available at: https://gist.github.com/fabiolib/ffb21853e3eb3780150074aeffc54901",
+        "Analysis provider": "Kim Walden, University of Illinois at Urbana-Champaign",
+        "Data source": "SRR6984021, SRR6984013, SRR6984057",
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+          "wholeCDS": null
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+      },
+      "trackType": "HTMLFeatures",
+      "type": "HTMLFeatures",
+      "urlTemplate": "tracks/odobru_current_models/{refseq}/trackData.json"
+    },
+    {
+      "category": "NCBI Annotation Release 100",
+      "compress": 0,
+      "key": "NCBI_Annotation_Release_100_Gene - Color by CDS frame",
+      "label": "NCBI_Annotation_Release_100_Gene-CBT",
+      "menuTemplate": [
+        {
+          "label": "View details"
+        },
+        {
+          "action": "newWindow",
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+          "label": "function(track,feature){ return 'Find gene page for '+feature.get('id')}",
+          "title": "function(track,feature){ return 'Find gene page for '+feature.get('id')}",
+          "url": "function(track,feature){ return 'https://i5k.nal.usda.gov/'+feature.get('id')}"
+        }
+      ],
+      "metadata": {
+        "Data description": "ftp://ftp.ncbi.nlm.nih.gov/genomes/Odontomachus_brunneus/README_CURRENT_RELEASE",
+        "Data provider": "NCBI",
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+      "trackType": "HTMLFeatures",
+      "type": "HTMLFeatures",
+      "urlTemplate": "tracks/NCBI_Annotation_Release_100_Gene-CBT/{refseq}/trackData.json"
+    },
+    {
+      "category": "RNA-Seq/Transcriptome Assembly",
+      "key": "GIKU00000000 Trinity Assembly",
+      "label": "GIKU00000000 Trinity Assembly",
+      "metadata": {
+        "Analysis method": "The Trinity transcriptome GIKU00000000 was aligned to the genome assembly using GMAP with default parameters",
+        "Analysis provider": "Kim Walden, University of Illinois at Urbana-Champaign",
+        "Data source": "https://www.ncbi.nlm.nih.gov/nuccore/GIKU00000000.1/",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale re-use guidelines",
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+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "analyses/Odontomachus-brunneus-Transcriptome-assembly_GIKU00000000_2020-06-15/20200615_GMAP_Trinity_vs_NCBI_genome_out_sorted.bam"
+    }
+  ]
 }
diff --git a/organisms/stage/Oncopeltus_fasciatus/trackList.json b/organisms/stage/Oncopeltus_fasciatus/trackList.json
index 4953eb7..a801463 100644
--- a/organisms/stage/Oncopeltus_fasciatus/trackList.json
+++ b/organisms/stage/Oncopeltus_fasciatus/trackList.json
@@ -1,2150 +1,2132 @@
 {
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-            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
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-         "urlTemplate" : "tracks/protein2genome_Platyhelminthes/{refseq}/trackData.json"
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-         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
-         "compress" : 0,
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-            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
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-            "Track legend" : "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline."
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-            "arrowheadClass" : "webapollo-arrowhead",
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-         "compress" : 0,
-         "key" : "protein2genome_Tardigrada",
-         "label" : "protein2genome_Tardigrada",
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-            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
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-            "Track legend" : "Results from Protein2genome alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline."
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-         "compress" : 0,
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-         "label" : "protein2genome_Tunicata",
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-            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
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-         "style" : {
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-         "urlTemplate" : "tracks/protein2genome_Tunicata/{refseq}/trackData.json"
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-         "compress" : 0,
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-         "label" : "protein2genome_UNCATEGORISED",
-         "metadata" : {
-            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
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-         "urlTemplate" : "tracks/protein2genome_UNCATEGORISED/{refseq}/trackData.json"
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-         "compress" : 0,
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-         "label" : "repeatmasker",
-         "metadata" : {
-            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
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-         "key" : "repeatrunner",
-         "label" : "repeatrunner",
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-            "neg_color" : "#005EFF",
-            "pos_color" : "#FFA600"
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+        "Track legend": "Results from Protein2genome alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline."
+      },
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+        "arrowheadClass": "webapollo-arrowhead",
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Placozoa/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Platyhelminthes",
+      "label": "protein2genome_Platyhelminthes",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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+      "urlTemplate": "tracks/protein2genome_Platyhelminthes/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+      "key": "protein2genome_Priapulida",
+      "label": "protein2genome_Priapulida",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline."
+      },
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+        "arrowheadClass": "webapollo-arrowhead",
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+      "urlTemplate": "tracks/protein2genome_Priapulida/{refseq}/trackData.json"
+    },
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+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+      "key": "protein2genome_Tardigrada",
+      "label": "protein2genome_Tardigrada",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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+    },
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+      "label": "protein2genome_Tunicata",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline."
+      },
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+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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+    },
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+      "key": "protein2genome_UNCATEGORISED",
+      "label": "protein2genome_UNCATEGORISED",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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+        }
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_UNCATEGORISED/{refseq}/trackData.json"
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+      "key": "repeatmasker",
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+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from RepeatMasker as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
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+        "arrowheadClass": "webapollo-arrowhead",
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+    },
+    {
+      "category": "BCM_v0.5.3/2. Evidence/Repeats",
+      "compress": 0,
+      "key": "repeatrunner",
+      "label": "repeatrunner",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Repeatrunner as part of the MAKER automated annotation pipeline."
+      },
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+        "arrowheadClass": "webapollo-arrowhead",
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+      "type": "FeatureTrack",
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+    },
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+      "category": "BCM_v0.5.3/1. Gene Sets/Supplementary Gene Predictions",
+      "compress": 0,
+      "key": "snap_masked",
+      "label": "snap_masked",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline."
+      },
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+        "arrowheadClass": "webapollo-arrowhead",
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+      },
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/snap_masked/{refseq}/trackData.json"
+    },
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+      "category": "RNA-Seq/Mapped Reads",
+      "key": "pooled RNA-seq - cleaned reads",
+      "label": "pooled_RNA-seq_cleaned_reads",
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+        "Track legend": "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)"
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+      "autoscale": "local",
+      "bicolor_pivot": "zero",
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+      },
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+      },
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+      "urlTemplate": "bam/ivargas/cleaned_reads/accepted_hits.bigwig"
+    },
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+      "label": "pooled_RNA-seq_raw_reads",
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+        "Read cleaning method": "None",
+        "Track legend": "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)"
+      },
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+    },
+    {
+      "category": "RNA-Seq/Mapped Reads",
+      "key": "RNA-seq raw PE reads Andolfatto et al.",
+      "label": "RNA-seq_Andolfatto_raw_PE_reads",
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+        "Alignment summary": "http://de.iplantcollaborative.org/dl/d/5671A470-68E8-4FF2-AA8F-B55A8CC74AFF/align_summary.txt",
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+        "Read cleaning method": "None",
+        "Track legend": "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)"
+      },
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+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "bam/ivargas/andolfatto_raw_reads/accepted_hits.bam"
+    },
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+      "autoscale": "local",
+      "category": "RNA-Seq/Coverage Plots",
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+      "label": "RNA-seq raw PE reads Andolfatto et al, XY-plot",
+      "metadata": {
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+        "Data Source": "http://genomics-pubs.princeton.edu/insect_genomics/data/Oncopeltus_fasciatus.tar",
+        "Read cleaning method": "None",
+        "Track legend": "This track represents an X-Y plot of RNA-Seq coverage. The y-axis represents the number of mapped reads. The scale of the y-axis changes with the maximum number of reads aligned in the browser region. The y-axis has a minimum value of abs(2000); areas with higher coverage are indicated by a red clip."
+      },
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+      },
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+      "urlTemplate": "bam/ivargas/andolfatto_raw_reads/accepted_hits.bigwig",
+      "variance_band": false
+    },
+    {
+      "category": "RNA-Seq/Assembly",
+      "compress": 0,
+      "key": "Maternal and early embryonic 454 transcriptome",
+      "label": "mat_embr_454_transcriptome",
+      "metadata": {
+        "Alignment contact": "Iris Vargas-Jentzsch, University of Cologne",
+        "Alignment program and Parameters": "GMAP version 2014-05-15 called with args: Ofas_454.transcriptome_complete_short.fasta -d Ofas.scaffolds -f 2",
+        "BioProject": "PRJNA79671; Accession #s SRX022011, SRX022012, SRX022013, SRX022014",
+        "Data Source": "http://www.extavourlab.com/resources/Oncopeltus_454transcriptome_BLASTnames_01_2011.fasta<br> Here we used the complete transcriptome dataset, including singletons, obtained directly from Ben Ewen-Campen (bewencampen at oeb dot harvard dot edu).",
+        "PMCID": "PMC3040728",
+        "PMID": "21266083",
+        "Reference": "Ewen-Campen B., Shaner N., Panfilio K. A., Suzuki Y., Roth S., and Extavour C. G. (2011). The maternal and early embryonic transcriptome of the milkweed bug Oncopeltus fasciatus. BMC Genomics 12: 61."
+      },
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+        "arrowheadClass": "trellis-arrowhead",
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+          "wholeCDS": null
+        }
+      },
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/mat_embr_454_transcriptome/{refseq}/trackData.json"
+    },
+    {
+      "category": "RNA-Seq/Assembly",
+      "compress": 0,
+      "key": "Benoit Trinity transcriptome",
+      "label": "BenoitTrinity_gmapOfas",
+      "metadata": {
+        "Alignment contact": "Iris Vargas-Jentzsch, University of Cologne",
+        "Data Source": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/",
+        "Program and Parameters": "RNA-Seq: Trinity for assembly and TransDecoder to filter out ORFs.<br>Mapping to genome: GMAP version 2014-05-15 called with args: <br>Trinity.fasta.transdecoder.cds -d Ofas.scaffolds -f 2"
+      },
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+      "urlTemplate": "tracks/BenoitTrinity_gmapOfas/{refseq}/trackData.json"
+    },
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+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Reference Assembly",
+      "key": "Gaps in assembly",
+      "label": "Gaps in assembly",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "white",
+        "pos_color": "black"
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+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "bigwig/Ofas.scaffolds-GAPS.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "0.5",
+      "category": "Reference Assembly",
+      "key": "GC Content",
+      "label": "GC Content",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+      },
+      "scoreType": "avgScore",
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "rgba(255,255,0,50)",
+        "pos_color": "rgba(0,0,255,50)"
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+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "bigwig/Ofas.scaffolds_GC.bigwig"
+    },
+    {
+      "category": "Official Gene Set v1.1/1. Protein Coding Genes",
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+      "fmtDetailField_Description": "function() { return 'Note'; }",
+      "key": "OGS_v1.1",
+      "label": "OGS_v1.1_protein_coding",
+      "metadata": {
+        "Analysis description": "The Official Gene Set OGSv1.1 has been superseded by OGSv1.2. OGSv1.1 was generated from the computationally predicted gene set OFAS_v0.5.3 and manually curated models.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Official Gene Set OGS_v1.1. Note that stop codon read-through features are visualized as red bars above and below the CDS."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
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+          "three_prime_utr": "primary_gene_set-utr",
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+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/OGS_v1.1/{refseq}/trackData.json"
+    },
+    {
+      "category": "Official Gene Set v1.1/2. Noncoding Genes",
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+      "key": "OGS_v1.1_rRNA",
+      "label": "OGS_v1.1_rRNA",
+      "metadata": {
+        "Analysis description": "The Official Gene Set OGSv1.1 has been superseded by OGSv1.2. OGSv1.1 was generated from the computationally predicted gene set OFAS_v0.5.3 and manually curated models.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
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+        "arrowheadClass": "trellis-arrowhead",
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+          "CDS": "primary_gene_set-cds",
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+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/OGS_v1.1_rRNA/{refseq}/trackData.json"
+    },
+    {
+      "category": "Official Gene Set v1.1/2. Noncoding Genes",
+      "compress": 0,
+      "key": "OGS_v1.1_pseudogene",
+      "label": "OGS_v1.1_pseudogene",
+      "metadata": {
+        "Analysis description": "The Official Gene Set OGSv1.1 has been superseded by OGSv1.2. OGSv1.1 was generated from the computationally predicted gene set OFAS_v0.5.3 and manually curated models.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
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+          "CDS": "primary_gene_set-cds",
+          "UTR": "primary_gene_set-utr",
+          "pseudogenic_exon": "primary_gene_set-utr",
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+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/OGS_v1.1_pseudogene/{refseq}/trackData.json"
+    },
+    {
+      "category": "Official Gene Set v1.2/1. Gene Sets/Protein Coding",
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+      "fmtDetailValue_Id": "function(id, feature) { var name2 = id.replace(/-R./, ''); if(feature.get('type')=='mRNA') { return '<a href=\"https://i5k.nal.usda.gov/'+name2+'\" target=\"_blank\"><b>'+id+'</a> (Click for Gene page)</b>';} else {return id}}",
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+      "label": "oncfas_current_models",
+      "metadata": {
+        "Analysis description": "The Official Gene Set OGSv1.2 is an update of OGSv1.1.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Official Gene Set OGS_v1.2. Note that stop codon read-through features are visualized as red bars above and below the CDS."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
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+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/oncfas_current_models/{refseq}/trackData.json"
+    },
+    {
+      "category": "Official Gene Set v1.2/1. Gene Sets/Pseudogenes",
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+      "key": "OGSv1.2 pseudogenes",
+      "label": "OGS_v1.2_pseudogenes",
+      "metadata": {
+        "Analysis description": "The Official Gene Set OGSv1.2 is an update of OGSv1.1.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
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+        "arrowheadClass": "trellis-arrowhead",
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+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/OGS_v1.2_pseudogenes/{refseq}/trackData.json"
+    },
+    {
+      "category": "Official Gene Set v1.2/1. Gene Sets/Noncoding",
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+      "key": "OGSv1.2 rRNA",
+      "label": "OGS_v1.2_rRNA",
+      "metadata": {
+        "Analysis description": "The Official Gene Set OGSv1.2 is an update of OGSv1.1.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
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+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "CDS": "ogs-cds",
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+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/OGS_v1.2_rRNA/{refseq}/trackData.json"
+    },
+    {
+      "category": "Official Gene Set v1.2/1. Gene Sets/Other features",
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+      "key": "OGSv1.2 sequence modifications",
+      "label": "OGS_v1.2_sequence_modifications",
+      "metadata": {
+        "Analysis description": "The Official Gene Set OGSv1.2 is an update of OGSv1.1.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
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+        "arrowheadClass": null,
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+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/OGS_v1.2_sequence_modifications/{refseq}/trackData.json"
+    },
+    {
+      "category": "RNA-Seq/Mapped Reads",
+      "key": "posterior embryo, 19 hours after egg laying",
+      "label": "posterior embryo, 19 hours after egg laying",
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+        "Data description": "https://i5k.nal.usda.gov/node/933164",
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+        "Track legend": "Dark red alignments: Mapped portion of read aligned to forward strand<br>Light red alignments: Spliced portion of read aligned to forward strand<br>Dark blue alignments: Mapped portion of read aligned to reverse strand<br>Light blue alignments: Spliced portion of read aligned to reverse strand<br>Red marking - deletion in the read relative to the reference<br>Green marking - insertion in the read relative to the reference<br>Yellow marking  - mismatch (hover over the mismatch to see what the snp is)",
+        "age": "19 hours after egg laying",
+        "development stage": "embryo",
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+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
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+        "Track legend": "This track represents an X-Y plot of RNA-Seq coverage. The y-axis represents the number of mapped reads. The scale of the y-axis changes with the maximum number of reads aligned in the browser region.",
+        "age": "19 hours after egg laying",
+        "development stage": "embryo",
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+        "pos_color": "#00BFFF"
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+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "analyses/Oncopeltus-fasciatus-RNA-Seq_04-24-2020_v1.0/19P.sorted.bigwig"
+    },
+    {
+      "category": "RNA-Seq/Mapped Reads",
+      "key": "posterior embryo, 30 hours after egg laying",
+      "label": "posterior embryo, 30 hours after egg laying",
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+        "Analysis provider": "Ariel Chipman, The Hebrew University of Jerusalem; Agustin Baricalla, Universidad Nacional del Noroeste de Buenos Aires",
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+        "age": "30 hours after egg laying",
+        "development stage": "embryo",
+        "host tissue sampled": "posterior"
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+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "analyses/Oncopeltus-fasciatus-RNA-Seq_04-24-2020_v1.0/30P.sorted.bam"
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+      "category": "RNA-Seq/Coverage Plots",
+      "key": "posterior embryo, 30 hours after egg laying, coverage",
+      "label": "posterior embryo, 30 hours after egg laying, coverage",
+      "metadata": {
+        "Analysis provider": "Ariel Chipman, The Hebrew University of Jerusalem; Agustin Baricalla, Universidad Nacional del Noroeste de Buenos Aires",
+        "Data description": "https://i5k.nal.usda.gov/node/933164",
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+        "Track legend": "This track represents an X-Y plot of RNA-Seq coverage. The y-axis represents the number of mapped reads. The scale of the y-axis changes with the maximum number of reads aligned in the browser region.",
+        "age": "30 hours after egg laying",
+        "development stage": "embryo",
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+      "urlTemplate": "analyses/Oncopeltus-fasciatus-RNA-Seq_04-24-2020_v1.0/30P.sorted.bigwig"
+    },
+    {
+      "category": "RNA-Seq/Mapped Reads",
+      "key": "anterior embryo, 26 hours after egg laying",
+      "label": "anterior embryo, 26 hours after egg laying",
+      "metadata": {
+        "Analysis provider": "Ariel Chipman, The Hebrew University of Jerusalem; Agustin Baricalla, Universidad Nacional del Noroeste de Buenos Aires",
+        "Data description": "https://i5k.nal.usda.gov/node/933164",
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+        "age": "26 hours after egg laying",
+        "development stage": "embryo",
+        "host tissue sampled": "anterior"
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+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "analyses/Oncopeltus-fasciatus-RNA-Seq_04-24-2020_v1.0/26A.sorted.bam"
+    },
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+      "key": "anterior embryo, 26 hours after egg laying, coverage",
+      "label": "anterior embryo, 26 hours after egg laying, coverage",
+      "metadata": {
+        "Analysis provider": "Ariel Chipman, The Hebrew University of Jerusalem; Agustin Baricalla, Universidad Nacional del Noroeste de Buenos Aires",
+        "Data description": "https://i5k.nal.usda.gov/node/933164",
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+        "Program": "FastQC, trimomatic, MultiQC, STARaligner",
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+        "age": "26 hours after egg laying",
+        "development stage": "embryo",
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+      "urlTemplate": "analyses/Oncopeltus-fasciatus-RNA-Seq_04-24-2020_v1.0/26A.sorted.bigwig"
+    },
+    {
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+      "key": "posterior embryo, 26 hours after egg laying",
+      "label": "posterior embryo, 26 hours after egg laying",
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+        "Analysis provider": "Ariel Chipman, The Hebrew University of Jerusalem; Agustin Baricalla, Universidad Nacional del Noroeste de Buenos Aires",
+        "Data description": "https://i5k.nal.usda.gov/node/933164",
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+        "age": "26 hours after egg laying",
+        "development stage": "embryo",
+        "host tissue sampled": "posterior"
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+        "Analysis provider": "Ariel Chipman, The Hebrew University of Jerusalem; Agustin Baricalla, Universidad Nacional del Noroeste de Buenos Aires",
+        "Data description": "https://i5k.nal.usda.gov/node/933164",
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+      "urlTemplate": "analyses/Oncopeltus-fasciatus-RNA-Seq_04-24-2020_v1.0/26P.sorted.bigwig"
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+      "label": "anterior embryo, 10 hours after egg laying",
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+        "Analysis provider": "Ariel Chipman, The Hebrew University of Jerusalem; Agustin Baricalla, Universidad Nacional del Noroeste de Buenos Aires",
+        "Data description": "https://i5k.nal.usda.gov/node/933164",
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+        "age": "10 hours after egg laying",
+        "development stage": "embryo",
+        "host tissue sampled": "anterior"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "analyses/Oncopeltus-fasciatus-RNA-Seq_04-24-2020_v1.0/10A.sorted.bam"
+    },
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+        "Data description": "https://i5k.nal.usda.gov/node/933164",
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+        "age": "10 hours after egg laying",
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+      "urlTemplate": "analyses/Oncopeltus-fasciatus-RNA-Seq_04-24-2020_v1.0/10A.sorted.bigwig"
+    },
+    {
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 }
diff --git a/organisms/stage/Oncopeltus_fasciatus_training/trackList.json b/organisms/stage/Oncopeltus_fasciatus_training/trackList.json
index 4953eb7..a801463 100644
--- a/organisms/stage/Oncopeltus_fasciatus_training/trackList.json
+++ b/organisms/stage/Oncopeltus_fasciatus_training/trackList.json
@@ -1,2150 +1,2132 @@
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+      "label": "blastx_Platyhelminthes",
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+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
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+        "Track legend": "Results from Protein2genome alignments of a set of Cnidaria proteins as part of the MAKER automated annotation pipeline."
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+        "Track legend": "Results from Protein2genome alignments of a set of Crustacea proteins as part of the MAKER automated annotation pipeline."
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+      "key": "protein2genome_Nematomorpha",
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+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
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+        "Track legend": "Results from Protein2genome alignments of a set of Nematomorpha proteins as part of the MAKER automated annotation pipeline."
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+        "arrowheadClass": "webapollo-arrowhead",
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+          "match_part": "protein2genome"
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+      "urlTemplate": "tracks/protein2genome_Nematomorpha/{refseq}/trackData.json"
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+      "key": "protein2genome_Onychophora",
+      "label": "protein2genome_Onychophora",
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+      "key": "protein2genome_Parazoa",
+      "label": "protein2genome_Parazoa",
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+      "key": "protein2genome_Placozoa",
+      "label": "protein2genome_Placozoa",
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+        "Track legend": "Results from Protein2genome alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline."
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+        "arrowheadClass": "webapollo-arrowhead",
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+      "key": "protein2genome_Platyhelminthes",
+      "label": "protein2genome_Platyhelminthes",
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+    },
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+      "key": "protein2genome_Priapulida",
+      "label": "protein2genome_Priapulida",
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+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline."
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+      "key": "protein2genome_Tardigrada",
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+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline."
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+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline."
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+        "Track legend": "Results from Protein2genome alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline."
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+      "key": "repeatmasker",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
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+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from RepeatMasker as part of the MAKER automated annotation pipeline."
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+      "key": "repeatrunner",
+      "label": "repeatrunner",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Repeatrunner as part of the MAKER automated annotation pipeline."
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+      "label": "snap_masked",
+      "metadata": {
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+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "snap"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/snap_masked/{refseq}/trackData.json"
+    },
+    {
+      "category": "RNA-Seq/Mapped Reads",
+      "key": "pooled RNA-seq - cleaned reads",
+      "label": "pooled_RNA-seq_cleaned_reads",
+      "metadata": {
+        "Alignment method": "TopHat 2.0.9, option --b2-very-sensitive",
+        "Alignment summary": "http://de.iplantcollaborative.org/dl/d/C1F07955-A133-4B73-85B5-4D5E57AC764C/align_summary.txt",
+        "Data Provider": "Baylor College of Medicine",
+        "Data Source 1": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-adult-female-1-1_1pA_C1M7KACXX-7-ID03_1_sequence.txt.bz2",
+        "Data Source 2": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-adult-female-1-1_1pA_C1M7KACXX-7-ID03_2_sequence.txt.bz2",
+        "Data Source 3": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-adult-male-1-1_1pA_C22AGACXX-4-ID02_1_sequence.txt.bz2",
+        "Data Source 4": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-adult-male-1-1_1pA_C22AGACXX-4-ID02_2_sequence.txt.bz2",
+        "Data Source 5": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-juveniles-1-1_1pA_C22AGACXX-4-ID01_1_sequence.txt.bz2",
+        "Data Source 6": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-juveniles-1-1_1pA_C22AGACXX-4-ID01_2_sequence.txt.bz2",
+        "Read cleaning method": "Quality and adapter trimming with Trimmomatic3.0 (parameters ILLUMINACLIP:Trimmomatic-0.30/adapters/TruSeq3-PE.fa:2:30:10:8:true LEADING:3  TRAILING:3  SLIDINGWINDOW:4:15  MINLEN:36)",
+        "Track legend": "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "bam/ivargas/cleaned_reads/accepted_hits.bam"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "RNA-Seq/Coverage Plots",
+      "key": "pooled RNA-seq - cleaned reads, XY-plot",
+      "label": "pooled RNA-seq - cleaned reads, XY-plot",
+      "metadata": {
+        "Alignment method": "TopHat 2.0.9, option --b2-very-sensitive",
+        "Alignment summary": "http://de.iplantcollaborative.org/dl/d/C1F07955-A133-4B73-85B5-4D5E57AC764C/align_summary.txt",
+        "Data Provider": "Baylor College of Medicine",
+        "Data Source 1": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-adult-female-1-1_1pA_C1M7KACXX-7-ID03_1_sequence.txt.bz2",
+        "Data Source 2": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-adult-female-1-1_1pA_C1M7KACXX-7-ID03_2_sequence.txt.bz2",
+        "Data Source 3": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-adult-male-1-1_1pA_C22AGACXX-4-ID02_1_sequence.txt.bz2",
+        "Data Source 4": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-adult-male-1-1_1pA_C22AGACXX-4-ID02_2_sequence.txt.bz2",
+        "Data Source 5": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-juveniles-1-1_1pA_C22AGACXX-4-ID01_1_sequence.txt.bz2",
+        "Data Source 6": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-juveniles-1-1_1pA_C22AGACXX-4-ID01_2_sequence.txt.bz2",
+        "Read cleaning method": "Quality and adapter trimming with Trimmomatic3.0 (parameters ILLUMINACLIP:Trimmomatic-0.30/adapters/TruSeq3-PE.fa:2:30:10:8:true LEADING:3  TRAILING:3  SLIDINGWINDOW:4:15  MINLEN:36)",
+        "Track legend": "This track represents an X-Y plot of RNA-Seq coverage. The y-axis represents the number of mapped reads. The scale of the y-axis changes with the maximum number of reads aligned in the browser region. The y-axis has a minimum value of abs(2000); areas with higher coverage are indicated by a red clip."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "clip_marker_color": "red",
+        "height": 50,
+        "neg_color": "#005EFF",
+        "pos_color": "#FFA600"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "bam/ivargas/cleaned_reads/accepted_hits.bigwig"
+    },
+    {
+      "category": "RNA-Seq/Mapped Reads",
+      "key": "pooled RNA-seq - raw reads",
+      "label": "pooled_RNA-seq_raw_reads",
+      "metadata": {
+        "Alignment method": "TopHat 2.0.9, option --b2-very-sensitive",
+        "Alignment summary": "http://de.iplantcollaborative.org/dl/d/653A7172-438A-4688-811C-FA92A8FD22E6/align_summary.txt",
+        "Data Provider": "Baylor College of Medicine",
+        "Data Source 1": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-adult-female-1-1_1pA_C1M7KACXX-7-ID03_1_sequence.txt.bz2",
+        "Data Source 2": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-adult-female-1-1_1pA_C1M7KACXX-7-ID03_2_sequence.txt.bz2",
+        "Data Source 3": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-adult-male-1-1_1pA_C22AGACXX-4-ID02_1_sequence.txt.bz2",
+        "Data Source 4": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-adult-male-1-1_1pA_C22AGACXX-4-ID02_2_sequence.txt.bz2",
+        "Data Source 5": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-juveniles-1-1_1pA_C22AGACXX-4-ID01_1_sequence.txt.bz2",
+        "Data Source 6": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-juveniles-1-1_1pA_C22AGACXX-4-ID01_2_sequence.txt.bz2",
+        "Read cleaning method": "None",
+        "Track legend": "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "bam/ivargas/raw_reads/accepted_hits.bam"
+    },
+    {
+      "category": "RNA-Seq/Mapped Reads",
+      "key": "RNA-seq raw PE reads Andolfatto et al.",
+      "label": "RNA-seq_Andolfatto_raw_PE_reads",
+      "metadata": {
+        "Alignment method": "--align_reads together --mate-inner-dist 50 --file_query Oncopeltus_fasciatus_PE_1.fq.gz --file_query2 Oncopeltus_fasciatus_PE_2.fq.gz    --library-type  fr-unstranded --min-anchor-length  8 --splice-mismatches  0 --min-intron-length  70 --max-intron-length  50000 --min-isoform-fraction  0.15 --max-multihits  20 --min-segment-intron  50 --max-segment-intron  500000 --segment-mismatches  2 --segment-length  20 --num-threads  6 --user_database Ofas.scaffolds.fa --b2-sensitive  --tophat_version 2.0.9 --bowtie_version 2.1.0",
+        "Alignment summary": "http://de.iplantcollaborative.org/dl/d/5671A470-68E8-4FF2-AA8F-B55A8CC74AFF/align_summary.txt",
+        "Data Source": "http://genomics-pubs.princeton.edu/insect_genomics/data/Oncopeltus_fasciatus.tar",
+        "Read cleaning method": "None",
+        "Track legend": "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "bam/ivargas/andolfatto_raw_reads/accepted_hits.bam"
+    },
+    {
+      "autoscale": "local",
+      "category": "RNA-Seq/Coverage Plots",
+      "key": "RNA-seq raw PE reads Andolfatto et al, XY-plot",
+      "label": "RNA-seq raw PE reads Andolfatto et al, XY-plot",
+      "metadata": {
+        "Alignment method": "--align_reads together --mate-inner-dist 50 --file_query Oncopeltus_fasciatus_PE_1.fq.gz --file_query2 Oncopeltus_fasciatus_PE_2.fq.gz    --library-type  fr-unstranded --min-anchor-length  8 --splice-mismatches  0 --min-intron-length  70 --max-intron-length  50000 --min-isoform-fraction  0.15 --max-multihits  20 --min-segment-intron  50 --max-segment-intron  500000 --segment-mismatches  2 --segment-length  20 --num-threads  6 --user_database Ofas.scaffolds.fa --b2-sensitive  --tophat_version 2.0.9 --bowtie_version 2.1.0",
+        "Data Source": "http://genomics-pubs.princeton.edu/insect_genomics/data/Oncopeltus_fasciatus.tar",
+        "Read cleaning method": "None",
+        "Track legend": "This track represents an X-Y plot of RNA-Seq coverage. The y-axis represents the number of mapped reads. The scale of the y-axis changes with the maximum number of reads aligned in the browser region. The y-axis has a minimum value of abs(2000); areas with higher coverage are indicated by a red clip."
+      },
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+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "clip_marker_color": "red",
+        "height": 50,
+        "neg_color": "#005EFF",
+        "pos_color": "#FFA600"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "bam/ivargas/andolfatto_raw_reads/accepted_hits.bigwig",
+      "variance_band": false
+    },
+    {
+      "category": "RNA-Seq/Assembly",
+      "compress": 0,
+      "key": "Maternal and early embryonic 454 transcriptome",
+      "label": "mat_embr_454_transcriptome",
+      "metadata": {
+        "Alignment contact": "Iris Vargas-Jentzsch, University of Cologne",
+        "Alignment program and Parameters": "GMAP version 2014-05-15 called with args: Ofas_454.transcriptome_complete_short.fasta -d Ofas.scaffolds -f 2",
+        "BioProject": "PRJNA79671; Accession #s SRX022011, SRX022012, SRX022013, SRX022014",
+        "Data Source": "http://www.extavourlab.com/resources/Oncopeltus_454transcriptome_BLASTnames_01_2011.fasta<br> Here we used the complete transcriptome dataset, including singletons, obtained directly from Ben Ewen-Campen (bewencampen at oeb dot harvard dot edu).",
+        "PMCID": "PMC3040728",
+        "PMID": "21266083",
+        "Reference": "Ewen-Campen B., Shaner N., Panfilio K. A., Suzuki Y., Roth S., and Extavour C. G. (2011). The maternal and early embryonic transcriptome of the milkweed bug Oncopeltus fasciatus. BMC Genomics 12: 61."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "CDS": "transcriptome-cds",
+          "UTR": "transcriptome-utr",
+          "exon": "container-100pct",
+          "wholeCDS": null
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/mat_embr_454_transcriptome/{refseq}/trackData.json"
+    },
+    {
+      "category": "RNA-Seq/Assembly",
+      "compress": 0,
+      "key": "Benoit Trinity transcriptome",
+      "label": "BenoitTrinity_gmapOfas",
+      "metadata": {
+        "Alignment contact": "Iris Vargas-Jentzsch, University of Cologne",
+        "Data Source": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/",
+        "Program and Parameters": "RNA-Seq: Trinity for assembly and TransDecoder to filter out ORFs.<br>Mapping to genome: GMAP version 2014-05-15 called with args: <br>Trinity.fasta.transdecoder.cds -d Ofas.scaffolds -f 2"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
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+          "CDS": "transcriptome-cds",
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+          "exon": "container-100pct",
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+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/BenoitTrinity_gmapOfas/{refseq}/trackData.json"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Reference Assembly",
+      "key": "Gaps in assembly",
+      "label": "Gaps in assembly",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "white",
+        "pos_color": "black"
+      },
+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "bigwig/Ofas.scaffolds-GAPS.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "0.5",
+      "category": "Reference Assembly",
+      "key": "GC Content",
+      "label": "GC Content",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+      },
+      "scoreType": "avgScore",
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "rgba(255,255,0,50)",
+        "pos_color": "rgba(0,0,255,50)"
+      },
+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "bigwig/Ofas.scaffolds_GC.bigwig"
+    },
+    {
+      "category": "Official Gene Set v1.1/1. Protein Coding Genes",
+      "compress": 0,
+      "fmtDetailField_Description": "function() { return 'Note'; }",
+      "key": "OGS_v1.1",
+      "label": "OGS_v1.1_protein_coding",
+      "metadata": {
+        "Analysis description": "The Official Gene Set OGSv1.1 has been superseded by OGSv1.2. OGSv1.1 was generated from the computationally predicted gene set OFAS_v0.5.3 and manually curated models.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Official Gene Set OGS_v1.1. Note that stop codon read-through features are visualized as red bars above and below the CDS."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
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+          "three_prime_utr": "primary_gene_set-utr",
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+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/OGS_v1.1/{refseq}/trackData.json"
+    },
+    {
+      "category": "Official Gene Set v1.1/2. Noncoding Genes",
+      "compress": 0,
+      "key": "OGS_v1.1_rRNA",
+      "label": "OGS_v1.1_rRNA",
+      "metadata": {
+        "Analysis description": "The Official Gene Set OGSv1.1 has been superseded by OGSv1.2. OGSv1.1 was generated from the computationally predicted gene set OFAS_v0.5.3 and manually curated models.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
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+          "exon": "container-100pct",
+          "wholeCDS": null
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/OGS_v1.1_rRNA/{refseq}/trackData.json"
+    },
+    {
+      "category": "Official Gene Set v1.1/2. Noncoding Genes",
+      "compress": 0,
+      "key": "OGS_v1.1_pseudogene",
+      "label": "OGS_v1.1_pseudogene",
+      "metadata": {
+        "Analysis description": "The Official Gene Set OGSv1.1 has been superseded by OGSv1.2. OGSv1.1 was generated from the computationally predicted gene set OFAS_v0.5.3 and manually curated models.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "CDS": "primary_gene_set-cds",
+          "UTR": "primary_gene_set-utr",
+          "pseudogenic_exon": "primary_gene_set-utr",
+          "wholeCDS": null
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/OGS_v1.1_pseudogene/{refseq}/trackData.json"
+    },
+    {
+      "category": "Official Gene Set v1.2/1. Gene Sets/Protein Coding",
+      "compress": 0,
+      "fmtDetailValue_Id": "function(id, feature) { var name2 = id.replace(/-R./, ''); if(feature.get('type')=='mRNA') { return '<a href=\"https://i5k.nal.usda.gov/'+name2+'\" target=\"_blank\"><b>'+id+'</a> (Click for Gene page)</b>';} else {return id}}",
+      "key": "OGSv1.2 protein-coding genes",
+      "label": "oncfas_current_models",
+      "metadata": {
+        "Analysis description": "The Official Gene Set OGSv1.2 is an update of OGSv1.1.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Official Gene Set OGS_v1.2. Note that stop codon read-through features are visualized as red bars above and below the CDS."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "CDS": "ogs-cds",
+          "UTR": "ogs-utr",
+          "exon": "container-100pct",
+          "wholeCDS": null
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/oncfas_current_models/{refseq}/trackData.json"
+    },
+    {
+      "category": "Official Gene Set v1.2/1. Gene Sets/Pseudogenes",
+      "compress": 0,
+      "key": "OGSv1.2 pseudogenes",
+      "label": "OGS_v1.2_pseudogenes",
+      "metadata": {
+        "Analysis description": "The Official Gene Set OGSv1.2 is an update of OGSv1.1.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "CDS": "ogs-cds",
+          "UTR": "ogs-utr",
+          "exon": "container-100pct",
+          "pseudogenic_exon": "ogs-utr",
+          "wholeCDS": null
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/OGS_v1.2_pseudogenes/{refseq}/trackData.json"
+    },
+    {
+      "category": "Official Gene Set v1.2/1. Gene Sets/Noncoding",
+      "compress": 0,
+      "key": "OGSv1.2 rRNA",
+      "label": "OGS_v1.2_rRNA",
+      "metadata": {
+        "Analysis description": "The Official Gene Set OGSv1.2 is an update of OGSv1.1.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "CDS": "ogs-cds",
+          "UTR": "ogs-utr",
+          "exon": "container-100pct",
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+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/OGS_v1.2_rRNA/{refseq}/trackData.json"
+    },
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diff --git a/organisms/stage/Onthophagus_taurus/trackList.json b/organisms/stage/Onthophagus_taurus/trackList.json
index 9f9a333..fbd2ce9 100644
--- a/organisms/stage/Onthophagus_taurus/trackList.json
+++ b/organisms/stage/Onthophagus_taurus/trackList.json
@@ -1,1601 +1,1595 @@
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Arthropoda proteins as part of the MAKER automated annotation pipeline."
+      },
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+    },
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+      "key": "protein2genome_Atelocerata",
+      "label": "protein2genome_Atelocerata",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Atelocerata proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
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+        "arrowheadClass": "webapollo-arrowhead",
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+    },
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+      "key": "protein2genome_Cephalochordata",
+      "label": "protein2genome_Cephalochordata",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Cephalochordata proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
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+        "arrowheadClass": "webapollo-arrowhead",
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+          "match_part": "protein2genome"
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+    },
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+      "key": "protein2genome_Chelicerata",
+      "label": "protein2genome_Chelicerata",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Chelicerata proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
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+        "arrowheadClass": "webapollo-arrowhead",
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+          "match_part": "protein2genome"
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+    },
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+      "key": "protein2genome_Cnidaria",
+      "label": "protein2genome_Cnidaria",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Cnidaria proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
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+          "match_part": "protein2genome"
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+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Craniata",
+      "label": "protein2genome_Craniata",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Craniata proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
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+          "match_part": "protein2genome"
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Craniata/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Crustacea",
+      "label": "protein2genome_Crustacea",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Crustacea proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
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+          "match_part": "protein2genome"
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Crustacea/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Echinodermata",
+      "label": "protein2genome_Echinodermata",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Echinodermata proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
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+          "match_part": "protein2genome"
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+      },
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Echinodermata/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Mollusca",
+      "label": "protein2genome_Mollusca",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Mollusca proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Mollusca/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Nemata",
+      "label": "protein2genome_Nemata",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
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+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Nemata/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Nematomorpha",
+      "label": "protein2genome_Nematomorpha",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Nematomorpha proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Nematomorpha/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Onychophora",
+      "label": "protein2genome_Onychophora",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Onychophora proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
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+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Onychophora/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Parazoa",
+      "label": "protein2genome_Parazoa",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
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+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Parazoa/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Placozoa",
+      "label": "protein2genome_Placozoa",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
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+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Placozoa/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Platyhelminthes",
+      "label": "protein2genome_Platyhelminthes",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Platyhelminthes/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Priapulida",
+      "label": "protein2genome_Priapulida",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Priapulida/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Tardigrada",
+      "label": "protein2genome_Tardigrada",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Tardigrada/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Tunicata",
+      "label": "protein2genome_Tunicata",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Tunicata/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_UNCATEGORISED",
+      "label": "protein2genome_UNCATEGORISED",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_UNCATEGORISED/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/2. Evidence/Repeats",
+      "compress": 0,
+      "key": "repeatmasker",
+      "label": "repeatmasker",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from RepeatMasker as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "repeat"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/repeatmasker/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/2. Evidence/Repeats",
+      "compress": 0,
+      "key": "repeatrunner",
+      "label": "repeatrunner",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Repeatrunner as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "repeat"
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+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/repeatrunner/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/1. Gene Sets/Supplementary Gene Predictions",
+      "compress": 0,
+      "key": "snap_masked",
+      "label": "snap_masked",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "snap"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/snap_masked/{refseq}/trackData.json"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Reference Assembly",
+      "key": "Gaps in assembly",
+      "label": "Gaps in assembly",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "white",
+        "pos_color": "black"
+      },
+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "bigwig/Otaur.scaffolds.fa.gaps.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "0.5",
+      "category": "Reference Assembly",
+      "key": "GC Content",
+      "label": "GC Content",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+      },
+      "scoreType": "avgScore",
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "rgba(255,255,0,50)",
+        "pos_color": "rgba(0,0,255,50)"
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+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "bigwig/Otaur.scaffolds.fa.gc.bigwig"
+    },
+    {
+      "category": "Transcriptome/Mapped Reads",
+      "key": "Onthophagus taurus early male pupa brain transcripts",
+      "label": "Onthophagus taurus early male pupa brain transcripts",
+      "metadata": {
+        "Analysis method": "tophat2 v2.1.0",
+        "Date completed": "Nov-15",
+        "File provider": "Eduardo E Zattara, Indiana University Bloomington",
+        "Geographical location of specimen collection": "United States, Mapple View Farm, NC",
+        "NCBI TaxID": "166361",
+        "Other methods": "Trimmomatic 0.32",
+        "Other notes on methods": "Part of a larger project still unpublished",
+        "Other organism notes": "Large male",
+        "Publication Status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+        "Sequencing platform and version": "Illumina NextSeq 500, High Output 75 cycles ",
+        "Sex": "Male",
+        "Strain": "NC",
+        "Tissues included": "Brain"
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+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlM-BRN_S22.sorted.bam"
+    },
+    {
+      "category": "Transcriptome/Mapped Reads",
+      "key": "Onthophagus taurus early female pupa brain transcripts",
+      "label": "Onthophagus taurus early female pupa brain transcripts",
+      "metadata": {
+        "Analysis method": "tophat2 v2.1.0",
+        "Date completed": "Nov-15",
+        "File provider": "Eduardo E Zattara, Indiana University Bloomington",
+        "Geographical location of specimen collection": "United States, Mapple View Farm, NC",
+        "NCBI TaxID": "166361",
+        "Other methods": "Trimmomatic 0.32",
+        "Other notes on methods": "Part of a larger project still unpublished",
+        "Other organism notes": "Large female",
+        "Publication Status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+        "Sequencing platform and version": "Illumina NextSeq 500, High Output 75 cycles ",
+        "Sex": "Female",
+        "Strain": "NC",
+        "Tissues included": "Brain"
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+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlF-BRN_S18.sorted.bam"
+    },
+    {
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+      "category": "Transcriptome/Coverage Plots (BigWig)",
+      "key": "Onthophagus taurus early male pupa brain transcripts (Coverage Plot)",
+      "label": "Onthophagus taurus early male pupa brain transcripts (Coverage Plot)",
+      "metadata": {
+        "Analysis method": "tophat2 v2.1.0",
+        "Date completed": "Nov-15",
+        "File provider": "Eduardo E Zattara, Indiana University Bloomington",
+        "Geographical location of specimen collection": "United States, Mapple View Farm, NC",
+        "NCBI TaxID": "166361",
+        "Other methods": "Trimmomatic 0.32",
+        "Other notes on methods": "Part of a larger project still unpublished",
+        "Other organism notes": "Large male",
+        "Publication Status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+        "Sequencing platform and version": "Illumina NextSeq 500, High Output 75 cycles ",
+        "Sex": "Male",
+        "Strain": "NC",
+        "Tissues included": "Brain"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "pos_color": "#00BFFF"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlM-BRN_S22.sorted.bigwig"
+    },
+    {
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+      "category": "Transcriptome/Coverage Plots (BigWig)",
+      "key": "Onthophagus taurus early female pupa brain transcripts (Coverage Plot)",
+      "label": "Onthophagus taurus early female pupa brain transcripts (Coverage Plot)",
+      "metadata": {
+        "Analysis method": "tophat2 v2.1.0",
+        "Date completed": "Nov-15",
+        "File provider": "Eduardo E Zattara, Indiana University Bloomington",
+        "Geographical location of specimen collection": "United States, Mapple View Farm, NC",
+        "NCBI TaxID": "166361",
+        "Other methods": "Trimmomatic 0.32",
+        "Other notes on methods": "Part of a larger project still unpublished",
+        "Other organism notes": "Large female",
+        "Publication Status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+        "Sequencing platform and version": "Illumina NextSeq 500, High Output 75 cycles ",
+        "Sex": "Female",
+        "Strain": "NC",
+        "Tissues included": "Brain"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "pos_color": "#00BFFF"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlF-BRN_S18.sorted.bigwig"
+    },
+    {
+      "category": "Gene Silhouette Models/1. Gene Sets/Protein Coding",
+      "compress": 0,
+      "key": "Gene Silhouette Models v4",
+      "label": "Gene_Silhouette_Models_v4",
+      "metadata": {
+        "Analysis method": "Gene Silhouette Algorithm, alpha version, unpublished",
+        "Analysis provider": "Douglas B. Rusch, Centre for Genomics and Bioinformatics, Indiana University Bloomington",
+        "Other notes": "Novel algorithm predicts genes based on mapped RNAseq reads; based on data from early pupae, brain, dorsal head and pronotal epidermis, and posterior abdominal epidermis only"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "CDS": "gnomon_CDS",
+          "UTR": "gnomon_UTR",
+          "exon": "container-100pct",
+          "wholeCDS": null
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+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/Gene_Silhouette_Models_v4/{refseq}/trackData.json"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Transcriptome/Coverage Plots (BigWig)",
+      "key": "O. taurus M PD1 BRN+CHE+THE+GEN transcripts",
+      "label": "O. taurus M PD1 BRN+CHE+THE+GEN transcripts",
+      "metadata": {
+        "Analysis method": "tophat2 v2.1.0",
+        "Date completed": "Nov-15",
+        "File provider": "Eduardo E Zattara, Indiana University Bloomington",
+        "Geographical location of specimen collection": "United States, Mapple View Farm, NC",
+        "Other methods": "Trimmomatic 0.32",
+        "Other notes on methods": "Part of a larger project still unpublished",
+        "Other organism notes": "Large male",
+        "Publication Status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Sequencing platform and version": "Illumina NextSeq 500, High Output 75 cycles ",
+        "Sex": "Male",
+        "Strain": "NC",
+        "Tissues included": "pooled brain, dorsal head epidermis, pronotum epidermis, posterior abdominal epidermis"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "pos_color": "#00BFFF"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "user_contributed_data/ezattara/mixed_transcripts_march_2016/ctrlM-ALL.merged.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Transcriptome/Coverage Plots (BigWig)",
+      "key": "O. taurus F PD1 BRN+CHE+THE+GEN transcripts",
+      "label": "O. taurus F PD1 BRN+CHE+THE+GEN transcripts",
+      "metadata": {
+        "Analysis method": "tophat2 v2.1.0",
+        "Date completed": "Nov-15",
+        "File provider": "Eduardo E Zattara, Indiana University Bloomington",
+        "Geographical location of specimen collection": "United States, Mapple View Farm, NC",
+        "Other methods": "Trimmomatic 0.32",
+        "Other notes on methods": "Part of a larger project still unpublished",
+        "Other organism notes": "Large female",
+        "Publication Status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Sequencing platform and version": "Illumina NextSeq 500, High Output 75 cycles ",
+        "Sex": "Female",
+        "Strain": "NC",
+        "Tissues included": "pooled brain, dorsal head epidermis, pronotum epidermis, posterior abdominal epidermis"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "pos_color": "#00BFFF"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "user_contributed_data/ezattara/mixed_transcripts_march_2016/ctrlF-ALL.merged.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Transcriptome/Coverage Plots (BigWig)",
+      "key": "O. taurus M NC L3L+PP1+PD1+AD4",
+      "label": "O. taurus M NC L3L+PP1+PD1+AD4",
+      "metadata": {
+        "Analysis method": "tophat2 v2.0.14",
+        "File provider": "Eduardo E Zattara, Indiana University Bloomington",
+        "Geographical location of specimen collection": "United States, Mapple View Farm, NC",
+        "Other methods": "Trimmomatic 0.32",
+        "Other notes": "Part of a larger project still unpublished",
+        "Other organism notes": "Large male",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Sequencing platform and version": "Illumina HiSeq 100PE",
+        "Sex": "Male",
+        "Strain": "NC",
+        "Tissues included": "whole body, pooled late 3 larvae, prepupa 1, pupa day 1, adult day 4"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "pos_color": "#00BFFF"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "user_contributed_data/ezattara/NC-L3L_PP1_PD1_AD4/NC_M_merged.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Transcriptome/Coverage Plots (BigWig)",
+      "key": "O. taurus F NC L3L+PP1+PD1+AD4",
+      "label": "O. taurus F NC L3L+PP1+PD1+AD4",
+      "metadata": {
+        "Analysis method": "tophat2 v2.0.14",
+        "File provider": "Eduardo E Zattara, Indiana University Bloomington",
+        "Geographical location of specimen collection": "United States, Mapple View Farm, NC",
+        "Other methods": "Trimmomatic 0.32",
+        "Other notes": "Part of a larger project still unpublished",
+        "Other organism notes": "Large female",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Sequencing platform and version": "Illumina HiSeq 100PE",
+        "Sex": "Female",
+        "Strain": "NC",
+        "Tissues included": "whole body, pooled late 3 larvae, prepupa 1, pupa day 1, adult day 4"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
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+        "pos_color": "#00BFFF"
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+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "user_contributed_data/ezattara/NC-L3L_PP1_PD1_AD4/NC_F_merged.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Transcriptome/Coverage Plots (BigWig)",
+      "key": "O. taurus embryonic reads",
+      "label": "O. taurus embryonic",
+      "metadata": {
+        "Analysis method": "tophat2 v2.0.14",
+        "Date completed": "Nov-15",
+        "File provider": "Eduardo E Zattara, Indiana University Bloomington",
+        "Geographical location of specimen collection": "Western Australia, Busselton",
+        "NCBI TaxID": "166361",
+        "Other methods": "Trimmomatic 0.32",
+        "Other notes on methods": "Part of a larger project still unpublished",
+        "Publication Status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+        "Sequencing platform and version": "Illumina NextSeq500, 75SE",
+        "Sex": "pooled",
+        "Strain": "WA",
+        "Tissues included": "whole embryos, pooled mixed stages"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "pos_color": "#00BFFF"
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+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "user_contributed_data/ezattara/whole_embryos/Otau-embryos.bigwig"
+    },
+    {
+      "category": "Transcriptome/Mapped Reads",
+      "key": "O. taurus embryonic reads",
+      "label": "O. taurus embryonic reads",
+      "metadata": {
+        "Analysis method": "tophat2 v2.0.14",
+        "Date completed": "Nov-15",
+        "File provider": "Eduardo E Zattara, Indiana University Bloomington",
+        "Geographical location of specimen collection": "Western Australia, Busselton",
+        "NCBI TaxID": "166361",
+        "Other methods": "Trimmomatic 0.32",
+        "Other notes on methods": "Part of a larger project still unpublished",
+        "Publication Status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+        "Sequencing platform and version": "Illumina NextSeq500, 75SE",
+        "Sex": "pooled",
+        "Strain": "WA",
+        "Tissues included": "whole embryos, pooled mixed stages"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "user_contributed_data/ezattara/whole_embryos/Otau-embryos.accepted_hits.sorted.bam"
+    },
+    {
+      "category": "Transcriptome/Splice Junctions",
+      "compress": 0,
+      "key": "O. taurus embryonic junctions",
+      "label": "O. taurus embryonic junctions",
+      "metadata": {
+        "Analysis method": "tophat2 v2.0.14",
+        "Date completed": "Nov-15",
+        "File provider": "Eduardo E Zattara, Indiana University Bloomington",
+        "Geographical location of specimen collection": "Western Australia, Busselton",
+        "NCBI TaxID": "166361",
+        "Other methods": "Trimmomatic 0.32",
+        "Other notes on methods": "Part of a larger project still unpublished",
+        "Publication Status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+        "Sequencing platform and version": "Illumina NextSeq500, 75SE",
+        "Sex": "pooled",
+        "Strain": "WA",
+        "Tissues included": "whole embryos, pooled mixed stages"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
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+        "subfeatureClasses": {
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+          "UTR": "webapollo-UTR",
+          "exon": "container-100pct",
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+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/O. taurus embryonic junctions/{refseq}/trackData.json"
+    },
+    {
+      "category": "Transcriptome/Mapped Reads",
+      "key": "O. taurus whole body, mixed stage RNAseq, reduced coverage, females",
+      "label": "O. taurus whole body, mixed stage RNAseq, reduced coverage, females",
+      "metadata": {
+        "Analysis method": "tophat2 v2.1.0",
+        "Date completed": "June-16-2016",
+        "File provider": "Eduardo E Zattara, Indiana University Bloomington",
+        "Geographical location of specimen collection": "United States, Mapple View Farm, NC",
+        "NCBI TaxID": "166361",
+        "Other methods": "Trimmomatic 0.32, normalized coverage with samtools, picard and GATK",
+        "Other notes on methods": "Part of a larger project still unpublished",
+        "Other tissue notes": "Mix of late larvae, prepupae, pupae and adult RNA; pool of 12 individuals",
+        "Publication Status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+        "Sequencing platform and version": "Illumina HiSeq 2000m 100PE",
+        "Sex": "Female",
+        "Strain": "NC",
+        "Tissues included": "Whole body"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "user_contributed_data/ezattara/reduced_coverage_june_2016/NC_F_merged.reduced.bam"
+    },
+    {
+      "category": "Transcriptome/Mapped Reads",
+      "key": "O. taurus whole body, mixed stage RNAseq, reduced coverage, males",
+      "label": "O. taurus whole body, mixed stage RNAseq, reduced coverage, males",
+      "metadata": {
+        "Analysis method": "tophat2 v2.1.0",
+        "Date completed": "June-16-2016",
+        "File provider": "Eduardo E Zattara, Indiana University Bloomington",
+        "Geographical location of specimen collection": "United States, Mapple View Farm, NC",
+        "NCBI TaxID": "166361",
+        "Other methods": "Trimmomatic 0.32, normalized coverage with samtools, picard and GATK",
+        "Other notes on methods": "Part of a larger project still unpublished",
+        "Other tissue notes": "Mix of late larvae, prepupae, pupae and adult RNA; pool of 12 individuals",
+        "Publication Status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+        "Sequencing platform and version": "Illumina HiSeq 2000m 100PE",
+        "Sex": "Male",
+        "Strain": "NC",
+        "Tissues included": "Whole body"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "user_contributed_data/ezattara/reduced_coverage_june_2016/NC_M_merged.reduced.bam"
+    }
+  ]
 }
diff --git a/organisms/stage/Orussus_abietinus/trackList.json b/organisms/stage/Orussus_abietinus/trackList.json
index 6200547..29eae44 100755
--- a/organisms/stage/Orussus_abietinus/trackList.json
+++ b/organisms/stage/Orussus_abietinus/trackList.json
@@ -1,1538 +1,1532 @@
 {
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-   "share_link" : 0,
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-               "non_canonical_five_prime_splice_site" : "noncanonical-splice-site"
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-         "category" : "BCM_v0.5.3/1. Gene Sets/Primary Gene Sets: Protein Coding",
-         "metadata" : {
-            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
-            "Track legend" : "Consensus gene models from the MAKER automated annotation pipeline.",
-            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine"
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+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Placozoa/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Platyhelminthes",
+      "label": "protein2genome_Platyhelminthes",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Platyhelminthes/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Priapulida",
+      "label": "protein2genome_Priapulida",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Priapulida/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Tardigrada",
+      "label": "protein2genome_Tardigrada",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Tardigrada/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Tunicata",
+      "label": "protein2genome_Tunicata",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Tunicata/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_UNCATEGORISED",
+      "label": "protein2genome_UNCATEGORISED",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_UNCATEGORISED/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/2. Evidence/Repeats",
+      "compress": 0,
+      "key": "repeatmasker",
+      "label": "repeatmasker",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from RepeatMasker as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "repeat"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/repeatmasker/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/2. Evidence/Repeats",
+      "compress": 0,
+      "key": "repeatrunner",
+      "label": "repeatrunner",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Repeatrunner as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "repeat"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/repeatrunner/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/1. Gene Sets/Supplementary Gene Predictions",
+      "compress": 0,
+      "key": "snap_masked",
+      "label": "snap_masked",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "snap"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/snap_masked/{refseq}/trackData.json"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Reference Assembly",
+      "key": "Gaps in assembly",
+      "label": "Gaps in assembly",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "white",
+        "pos_color": "black"
+      },
+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "bigwig/Oabi11242013.GAPS.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "0.5",
+      "category": "Reference Assembly",
+      "key": "GC Content",
+      "label": "GC Content",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+      },
+      "scoreType": "avgScore",
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "rgba(255,255,0,50)",
+        "pos_color": "rgba(0,0,255,50)"
+      },
+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "bigwig/Oabi11242013.genome_GC.bigwig"
+    },
+    {
+      "category": "Transcriptome/Assembly",
+      "compress": 0,
+      "key": "O. abietinus female Trinity transcriptome",
+      "label": "Oabi-female_est2genome",
+      "metadata": {
+        "Analysis provider": "JP Oeyen (Univ. Bonn/ZFMK, ZMB), janphilipoyen@gmail.com)",
+        "Data Source 1": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Parasitic_wood_wasp/RNA_sequence/Oabi_ICD_OAi5ON.BN106-1_1pA_D2FUUACXX-1-ID01_1_sequence.txt.bz2; ftp://ftp.hgsc.bcm.edu/I5K-pilot/Parasitic_wood_wasp/RNA_sequence/Oabi_ICD_OAi5ON.BN106-1_1pA_D2FUUACXX-1-ID01_2_sequence.txt.bz2",
+        "Data description": "Raw reads cleaned with Trimmomatic v0.32, using the options ILLUMINACLIP:costumadapterlist.fa:2:30:10, SLIDINGWINDOW:4:33 and MINLEN:45. Cleaned reads were assembled using Trinity version trinityrnaseq_r20140413p1 using default settings. Assembled transcripts were mapped to the genome using Exonerate-gff3 (https://github.com/hotdogee/exonerate-gff3) with the options: --model est2genome --showtargetgff yes --gff3 yes --showalignment no --showvulgar no --geneseed 250 --bestn 2 --percent 50 --minintron 20 --maxintron 10000. Transcripts mapping to two locations were detected and marked with a note using a custom perl script (available from JP Oeyen (Univ. Bonn/ZFMK, ZMB), janphilipoyen@gmail.com)",
+        "Publication status": "unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "est_gff"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/Oabi-female_est2genome/{refseq}/trackData.json"
+    },
+    {
+      "category": "Transcriptome/Assembly",
+      "compress": 0,
+      "key": "O. abietinus male Trinity transcriptome",
+      "label": "Oabi-male_est2genome",
+      "metadata": {
+        "Analysis provider": "JP Oeyen (Univ. Bonn/ZFMK, ZMB), janphilipoyen@gmail.com)",
+        "Data Source": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Parasitic_wood_wasp/RNA_sequence/Oabi_ICD_OAi5ON.BN108-1_1pA_D2FUUACXX-1-ID02_1_sequence.txt.bz2; ftp://ftp.hgsc.bcm.edu/I5K-pilot/Parasitic_wood_wasp/RNA_sequence/Oabi_ICD_OAi5ON.BN108-1_1pA_D2FUUACXX-1-ID02_2_sequence.txt.bz2",
+        "Data description": "Raw reads cleaned with Trimmomatic v0.32, using the options ILLUMINACLIP:costumadapterlist.fa:2:30:10, SLIDINGWINDOW:4:33 and MINLEN:45. Cleaned reads were assembled using Trinity version trinityrnaseq_r20140413p1 using default settings. Assembled transcripts were mapped to the genome using Exonerate-gff3 (https://github.com/hotdogee/exonerate-gff3) with the options: --model est2genome --showtargetgff yes --gff3 yes --showalignment no --showvulgar no --geneseed 250 --bestn 2 --percent 50 --minintron 20 --maxintron 10000. Transcripts mapping to two locations were detected and marked with a note using a custom perl script (available from JP Oeyen (Univ. Bonn/ZFMK, ZMB), janphilipoyen@gmail.com)",
+        "Publication status": "unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "est_gff"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/Oabi-male_est2genome/{refseq}/trackData.json"
+    },
+    {
+      "category": "Univ. Bonn/Supplementary Gene Predictions",
+      "compress": 0,
+      "key": "O. abietinus two-pass maker",
+      "label": "Maker_Oabi11242013_iterative",
+      "metadata": {
+        "Analysis provider": "JP Oeyen (Univ. Bonn/ZFMK, ZMB), janphilipoyen@gmail.com)",
+        "Data Source": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Parasitic_wood_wasp/genome_assemblies/Oabi11242013.genome.fa",
+        "Data description": "Maker annotation with 2 consequtive runs with transcriptome and protein evidence. More details will be filled in soon!",
+        "Publication status": "unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "className": "{type}",
+        "subfeatureClasses": {
+          "CDS": "alt_gene_set-cds",
+          "UTR": "alt_gene_set-utr",
+          "exon": "container-100pct",
+          "wholeCDS": null
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/Maker_Oabi11242013_iterative/{refseq}/trackData.json"
+    },
+    {
+      "category": "Transcriptome/Mapped Reads",
+      "key": "O. abietinus female cleaned reads",
+      "label": "Oabi-female_tophat-accepted_hits",
+      "metadata": {
+        "Analysis provider": "JP Oeyen (Univ. Bonn/ZFMK, ZMB), janphilipoyen@gmail.com)",
+        "Data Source": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Parasitic_wood_wasp/RNA_sequence/Oabi_ICD_OAi5ON.BN106-1_1pA_D2FUUACXX-1-ID01_1_sequence.txt.bz2; ftp://ftp.hgsc.bcm.edu/I5K-pilot/Parasitic_wood_wasp/RNA_sequence/Oabi_ICD_OAi5ON.BN106-1_1pA_D2FUUACXX-1-ID01_2_sequence.txt.bz2",
+        "Data description": "Raw reads cleaned with Trimmomatic v0.32, using the options ILLUMINACLIP:'costumadapterlist.fa':2:30:10, SLIDINGWINDOW:4:33 and MINLEN:45. Cleaned reads mapped with TopHat v2.0.12 using default settings.",
+        "File note": "This track replaces the previous track, 'Orussus abietinus female RNAseq cleaned unassembled reads, alignments'",
+        "Publication status": "unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use",
+        "Track legend": "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "bam/janphilipoeyen/cleaned-reads-tophat/Oabi-female_tophat-accepted_hits.bam"
+    },
+    {
+      "category": "Transcriptome/Mapped Reads",
+      "key": "O. abietinus male cleaned reads",
+      "label": "Oabi-male_tophat-accepted_hits",
+      "metadata": {
+        "Analysis provider": "JP Oeyen (Univ. Bonn/ZFMK, ZMB), janphilipoyen@gmail.com)",
+        "Data Source": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Parasitic_wood_wasp/RNA_sequence/Oabi_ICD_OAi5ON.BN108-1_1pA_D2FUUACXX-1-ID02_1_sequence.txt.bz2, ftp://ftp.hgsc.bcm.edu/I5K-pilot/Parasitic_wood_wasp/RNA_sequence/Oabi_ICD_OAi5ON.BN108-1_1pA_D2FUUACXX-1-ID02_2_sequence.txt.bz2",
+        "Data description": "Raw reads cleaned with Trimmomatic v0.32, using the options ILLUMINACLIP:'costumadapterlist.fa':2:30:10, SLIDINGWINDOW:4:33 and MINLEN:45. Cleaned reads mapped with TopHat v2.0.12 using default settings.",
+        "File note": "This track replaces the previous track, 'Orussus abietinus male RNAseq cleaned unassembled reads, alignments'",
+        "Publication status": "unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use",
+        "Track legend": "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "bam/janphilipoeyen/cleaned-reads-tophat/Oabi-male_tophat-accepted_hits.bam"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Transcriptome/Coverage plots (BigWig)",
+      "key": " O. abietinus male cleaned reads, XY-plots",
+      "label": "Oabi-male_tophat-accepted_hits_bigwig",
+      "metadata": {
+        "Analysis provider": "JP Oeyen (Univ. Bonn/ZFMK, ZMB), janphilipoyen@gmail.com)",
+        "Data Source": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Parasitic_wood_wasp/RNA_sequence/Oabi_ICD_OAi5ON.BN108-1_1pA_D2FUUACXX-1-ID02_1_sequence.txt.bz2, ftp://ftp.hgsc.bcm.edu/I5K-pilot/Parasitic_wood_wasp/RNA_sequence/Oabi_ICD_OAi5ON.BN108-1_1pA_D2FUUACXX-1-ID02_2_sequence.txt.bz2",
+        "Data description": "Raw reads cleaned with Trimmomatic v0.32, using the options ILLUMINACLIP:'costumadapterlist.fa':2:30:10, SLIDINGWINDOW:4:33 and MINLEN:45. Cleaned reads mapped with TopHat v2.0.12 using default settings. Alignment files were converted by the NAL to bigwig format; reads that failed QC, secondary and supplementary alignments, and optical or PCR duplicates were ignored.",
+        "File note": "This track replaces the previous track, 'Orussus abietinus male RNAseq cleaned unassembled reads, XY-Plot'",
+        "Publication status": "unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "clip_marker_color": "red",
+        "height": 50,
+        "neg_color": "#005EFF",
+        "pos_color": "#FFA600"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "bigwig/janphilipoeyen/cleaned-reads-tophat/Oabi-male_tophat-accepted_hits.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Transcriptome/Coverage plots (BigWig)",
+      "key": " O. abietinus female cleaned reads, XY-plots",
+      "label": "Oabi-female_tophat-accepted_hits_bigwig",
+      "metadata": {
+        "Analysis provider": "JP Oeyen (Univ. Bonn/ZFMK, ZMB), janphilipoyen@gmail.com)",
+        "Data Source": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Parasitic_wood_wasp/RNA_sequence/Oabi_ICD_OAi5ON.BN106-1_1pA_D2FUUACXX-1-ID01_1_sequence.txt.bz2; ftp://ftp.hgsc.bcm.edu/I5K-pilot/Parasitic_wood_wasp/RNA_sequence/Oabi_ICD_OAi5ON.BN106-1_1pA_D2FUUACXX-1-ID01_2_sequence.txt.bz2",
+        "Data description": "Raw reads cleaned with Trimmomatic v0.32, using the options ILLUMINACLIP:'costumadapterlist.fa':2:30:10, SLIDINGWINDOW:4:33 and MINLEN:45. Cleaned reads mapped with TopHat v2.0.12 using default settings. Alignment files were converted by the NAL to bigwig format; reads that failed QC, secondary and supplementary alignments, and optical or PCR duplicates were ignored.",
+        "File note": "This track replaces the previous track, 'Orussus abietinus female RNAseq cleaned unassembled reads, XY-Plot'",
+        "Publication status": "unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "clip_marker_color": "red",
+        "height": 50,
+        "neg_color": "#005EFF",
+        "pos_color": "#FFA600"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "bigwig/janphilipoeyen/cleaned-reads-tophat/Oabi-female_tophat-accepted_hits.bigwig"
+    },
+    {
+      "category": "Orussus abietinus OGSv1.0/1. Gene Sets/Protein Coding",
+      "compress": 0,
+      "key": "Official Gene Set v1.0, protein coding",
+      "label": "oruabi_current_models",
+      "metadata": {
+        "Analysis description": "The Official Gene Set OGSv1.0 was generated from the computationally predicted gene set OABI_v0.5.3 and manually curated models.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Official Gene Set OGS_v1.0."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "CDS": "ogs-cds",
+          "UTR": "ogs-utr",
+          "exon": "container-100pct",
+          "wholeCDS": null
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/oruabi_current_models/{refseq}/trackData.json"
+    },
+    {
+      "category": "Orussus abietinus OGSv1.0/1. Gene Sets/Pseudogenes",
+      "compress": 0,
+      "key": "Official Gene Set v1.0, pseudogenes",
+      "label": "OGSv.1.0-pseudogenic_transcript",
+      "metadata": {
+        "Analysis description": "The Official Gene Set OGSv1.0 was generated from the computationally predicted gene set OABI_v0.5.3 and manually curated models.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Official Gene Set OGS_v1.0."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "CDS": "ogs-cds",
+          "UTR": "ogs-utr",
+          "exon": "container-100pct",
+          "pseudogenic_exon": "ogs-cds",
+          "wholeCDS": null
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/OGSv.1.0-pseudogenic_transcript/{refseq}/trackData.json"
+    },
+    {
+      "category": "Orussus abietinus OGSv1.0/1. Gene Sets/NonCoding",
+      "compress": 0,
+      "key": "Official Gene Set v1.0, miRNA",
+      "label": "OGSv.1.0-miRNA",
+      "metadata": {
+        "Analysis description": "The Official Gene Set OGSv1.0 was generated from the computationally predicted gene set OABI_v0.5.3 and manually curated models.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Official Gene Set OGS_v1.0."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "CDS": "gnomon_CDS",
+          "UTR": "gnomon_UTR",
+          "exon": "container-100pct",
+          "wholeCDS": null
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/OGSv.1.0-miRNA/{refseq}/trackData.json"
+    },
+    {
+      "category": "Orussus abietinus OGSv1.0/1. Gene Sets/NonCoding",
+      "compress": 0,
+      "key": "Official Gene Set v1.0, ncRNA",
+      "label": "OGSv.1.0-ncRNA",
+      "metadata": {
+        "Analysis description": "The Official Gene Set OGSv1.0 was generated from the computationally predicted gene set OABI_v0.5.3 and manually curated models.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Official Gene Set OGS_v1.0."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "CDS": "gnomon_CDS",
+          "UTR": "gnomon_UTR",
+          "exon": "container-100pct",
+          "wholeCDS": null
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/OGSv.1.0-ncRNA/{refseq}/trackData.json"
+    },
+    {
+      "category": "Orussus abietinus OGSv1.0/1. Gene Sets/NonCoding",
+      "compress": 0,
+      "key": "Official Gene Set v1.0, rRNA",
+      "label": "OGSv.1.0-rRNA",
+      "metadata": {
+        "Analysis description": "The Official Gene Set OGSv1.0 was generated from the computationally predicted gene set OABI_v0.5.3 and manually curated models.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Official Gene Set OGS_v1.0."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "CDS": "gnomon_CDS",
+          "UTR": "gnomon_UTR",
+          "exon": "container-100pct",
+          "wholeCDS": null
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/OGSv.1.0-rRNA/{refseq}/trackData.json"
+    },
+    {
+      "category": "Orussus abietinus OGSv1.0/1. Gene Sets/NonCoding",
+      "compress": 0,
+      "key": "Official Gene Set v1.0, snoRNA",
+      "label": "OGSv.1.0-snoRNA",
+      "metadata": {
+        "Analysis description": "The Official Gene Set OGSv1.0 was generated from the computationally predicted gene set OABI_v0.5.3 and manually curated models.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Official Gene Set OGS_v1.0."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "CDS": "gnomon_CDS",
+          "UTR": "gnomon_UTR",
+          "exon": "container-100pct",
+          "wholeCDS": null
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/OGSv.1.0-snoRNA/{refseq}/trackData.json"
+    },
+    {
+      "category": "Orussus abietinus OGSv1.0/1. Gene Sets/NonCoding",
+      "compress": 0,
+      "key": "Official Gene Set v1.0, tRNA",
+      "label": "OGSv.1.0-tRNA",
+      "metadata": {
+        "Analysis description": "The Official Gene Set OGSv1.0 was generated from the computationally predicted gene set OABI_v0.5.3 and manually curated models.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Official Gene Set OGS_v1.0."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "CDS": "gnomon_CDS",
+          "UTR": "gnomon_UTR",
+          "exon": "container-100pct",
+          "wholeCDS": null
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/OGSv.1.0-tRNA/{refseq}/trackData.json"
+    }
+  ]
 }
diff --git a/organisms/stage/Osmia_lignaria/trackList.json b/organisms/stage/Osmia_lignaria/trackList.json
index 762168e..db5b40f 100644
--- a/organisms/stage/Osmia_lignaria/trackList.json
+++ b/organisms/stage/Osmia_lignaria/trackList.json
@@ -26,6 +26,7 @@
             "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
             "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
          },
+         "scoreType" : "avgScore",
          "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
          "style" : {
             "neg_color" : "rgba(255,255,0,50)",
@@ -39,18 +40,18 @@
          "compress" : 0,
          "key" : "NCBI_Annotation_Release_100_Gene",
          "label" : "osmlig_current_models",
-   "menuTemplate" : [
-       {
-          "label" : "View details"
-       },
-       {
-        "label": "function(track,feature){ return 'Find gene page for '+feature.get('id')}",
-        "title": "function(track,feature){ return 'Find gene page for '+feature.get('id')}",
-        "iconClass" : "dijitIconDatabase",
-        "action": "newWindow",
-	"url" : "function(track,feature){ return 'https://i5k.nal.usda.gov/search/site/'+feature.get('id')}"
-        }
-  ],
+         "menuTemplate" : [
+            {
+               "label" : "View details"
+            },
+            {
+               "action" : "newWindow",
+               "iconClass" : "dijitIconDatabase",
+               "label" : "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
+               "title" : "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
+               "url" : "function(track,feature){ return 'https://www.ncbi.nlm.nih.gov/nuccore/'+feature.get('name')}"
+            }
+         ],
          "metadata" : {
             "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Osmia_lignaria/README_CURRENT_RELEASE",
             "Data provider" : "NCBI",
@@ -60,7 +61,7 @@
          "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
             "arrowheadClass" : "trellis-arrowhead",
-            "className" : "container-16px",
+            "className" : "{type}",
             "description" : "product, note, description",
             "subfeatureClasses" : {
                "CDS" : "gnomon_CDS",
@@ -69,8 +70,8 @@
                "wholeCDS" : null
             }
          },
-         "trackType" : "ColorByType/View/Track/ColorByTypeDraggable",
-         "type" : "ColorByType/View/Track/ColorByTypeDraggable",
+         "trackType" : "HTMLFeatures",
+         "type" : "HTMLFeatures",
          "urlTemplate" : "tracks/osmlig_current_models/{refseq}/trackData.json"
       },
       {
@@ -87,7 +88,7 @@
          "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
             "arrowheadClass" : "trellis-arrowhead",
-            "className" : "container-16px",
+            "className" : "{type}",
             "description" : "product, note, description",
             "subfeatureClasses" : {
                "CDS" : "gnomon_CDS",
@@ -99,6 +100,65 @@
          "trackType" : "HTMLFeatures",
          "type" : "HTMLFeatures",
          "urlTemplate" : "tracks/NCBI_Annotation_Release_100_Pseudogene/{refseq}/trackData.json"
+      },
+      {
+         "category" : "RNA-Seq/Mapped Reads",
+         "key" : "Osmlig_USDA_OLig_1.0_RNA-Seq-alignments_2021-06-16",
+         "label" : "Osmlig_USDA_OLig_1.0_RNA-Seq-alignments_2021-06-16",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR9670749'>SRR9670749</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR9670745'>SRR9670745</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR9676035'>SRR9676035</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR9676050'>SRR9676050</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR9676042'>SRR9676042</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR9670747'>SRR9670747</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR9676057'>SRR9676057</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR9676038'>SRR9676038</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR9676039'>SRR9676039</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR9676040'>SRR9676040</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Dark red alignments: Mapped portion of read aligned to forward strand<br>Light red alignments: Spliced portion of read aligned to forward strand<br>Dark blue alignments: Mapped portion of read aligned to reverse strand<br>Light blue alignments: Spliced portion of read aligned to reverse strand<br>Red marking - deletion in the read relative to the reference<br>Green marking - insertion in the read relative to the reference<br>Yellow marking  - mismatch (hover over the mismatch to see what the snp is)"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "unsafePopup" : true,
+         "urlTemplate" : "analyses/Osmia-lignaria-RNA-Seq_2021-06-16_v1.0/Osmlig_USDA_OLig_1.0_RNA-Seq-alignments_2021-06-16.bam"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "RNA-Seq/Coverage Plots",
+         "key" : "Osmlig_USDA_OLig_1.0_RNA-Seq-alignments_2021-06-16_coverage",
+         "label" : "Osmlig_USDA_OLig_1.0_RNA-Seq-alignments_2021-06-16_coverage",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR9670749'>SRR9670749</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR9670745'>SRR9670745</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR9676035'>SRR9676035</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR9676050'>SRR9676050</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR9676042'>SRR9676042</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR9670747'>SRR9670747</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR9676057'>SRR9676057</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR9676038'>SRR9676038</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR9676039'>SRR9676039</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR9676040'>SRR9676040</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "unsafePopup" : true,
+         "urlTemplate" : "analyses/Osmia-lignaria-RNA-Seq_2021-06-16_v1.0/Osmlig_USDA_OLig_1.0_RNA-Seq-alignments_2021-06-16.bigwig"
+      },
+      {
+         "category" : "RNA-Seq/Splice junctions",
+         "compress" : 0,
+         "key" : "Osmlig_USDA_OLig_1.0_RNA-Seq-alignments_2021-06-16_junctions",
+         "label" : "Osmlig_USDA_OLig_1.0_RNA-Seq-alignments_2021-06-16_junctions",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR9670749'>SRR9670749</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR9670745'>SRR9670745</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR9676035'>SRR9676035</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR9676050'>SRR9676050</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR9676042'>SRR9676042</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR9670747'>SRR9670747</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR9676057'>SRR9676057</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR9676038'>SRR9676038</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR9676039'>SRR9676039</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR9676040'>SRR9676040</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Junction reads generated by Hisat2 aligner and regtools. The number of alignments supporting the junction read is listed in blue."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "className" : "feature",
+            "description" : "score"
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "unsafePopup" : true,
+         "urlTemplate" : "tracks/Osmlig_USDA_OLig_1.0_RNA-Seq-alignments_2021-06-16_junctions/{refseq}/trackData.json"
       }
    ]
 }
diff --git a/organisms/stage/Pachypsylla_venusta/trackList.json b/organisms/stage/Pachypsylla_venusta/trackList.json
index 2602ce0..f324f3e 100644
--- a/organisms/stage/Pachypsylla_venusta/trackList.json
+++ b/organisms/stage/Pachypsylla_venusta/trackList.json
@@ -1,1313 +1,1209 @@
 {
-   "css" : "./plugins/NAL_CSS/css/contrib_styles.css",
-   "share_link" : 0,
-   "plugins" : [
-      {
-         "location" : "./plugins/WebApollo",
-         "name" : "WebApollo"
-      }
-   ],
-   "tracks" : [
-      {
-         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
-         "chunkSize" : 20000,
-         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-",
-         "label" : "DNA",
-         "type" : "SequenceTrack",
-         "key" : "Reference sequence"
-      },
-      {
-         "autocomplete" : "none",
-         "style" : {
-            "className" : "annot",
-            "renderClassName" : "annot-render",
-            "subfeatureClasses" : {
-               "non_canonical_three_prime_splice_site" : "noncanonical-splice-site",
-               "wholeCDS" : null,
-               "exon" : "container-100pct",
-               "CDS" : "annot-CDS",
-               "non_canonical_five_prime_splice_site" : "noncanonical-splice-site",
-               "UTR" : "annot-UTR"
-            },
-            "arrowheadClass" : "annot-arrowhead",
-            "alternateClasses" : {
-               "transposable_element" : {
-                  "renderClassName" : "blue-ibeam-render",
-                  "className" : "blue-ibeam"
-               },
-               "pseudogene" : {
-                  "renderClassName" : "gray-center-30pct",
-                  "className" : "light-purple-80pct"
-               },
-               "snRNA" : {
-                  "renderClassName" : "gray-center-30pct",
-                  "className" : "brightgreen-80pct"
-               },
-               "rRNA" : {
-                  "renderClassName" : "gray-center-30pct",
-                  "className" : "brightgreen-80pct"
-               },
-               "snoRNA" : {
-                  "renderClassName" : "gray-center-30pct",
-                  "className" : "brightgreen-80pct"
-               },
-               "repeat_region" : {
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-               },
-               "ncRNA" : {
-                  "renderClassName" : "gray-center-30pct",
-                  "className" : "brightgreen-80pct"
-               },
-               "miRNA" : {
-                  "renderClassName" : "gray-center-30pct",
-                  "className" : "brightgreen-80pct"
-               },
-               "tRNA" : {
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-                  "className" : "brightgreen-80pct"
-               }
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-            "centerSubFeature" : {
-               "non_canonical_three_prime_splice_site" : false,
-               "non_canonical_five_prime_splice_site" : false
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-         "storeClass" : "WebApollo/Store/SeqFeature/ScratchPad",
-         "phase" : 0,
-         "compress" : 0,
-         "label" : "Annotations",
-         "type" : "WebApollo/View/Track/AnnotTrack",
-         "subfeatures" : 1
-      },
-      {
-         "style" : {
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-            "subfeatureClasses" : {
-               "wholeCDS" : null,
-               "exon" : "container-100pct",
-               "CDS" : "primary_gene_set-cds",
-               "UTR" : "primary_gene_set-utr"
-            },
-            "arrowheadClass" : "trellis-arrowhead"
-         },
-	 "category" : "BCM_v0.5.3/1. Gene Sets/Primary Gene Sets: Protein Coding",
-	        "metadata" : {
-	"Track legend" : "Consensus gene models from the MAKER automated annotation pipeline.",
-	"Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-	"Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
-},
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-
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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-            "arrowheadClass" : "webapollo-arrowhead"
-         },
-	 "category" : "BCM_v0.5.3/1. Gene Sets/Supplementary Gene Predictions",
-	         "metadata" : {
-        "Track legend" : "Results from the Augustus gene prediction software as part of the MAKER automated annotation pipeline.",
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
+  "alwaysOnTracks": "DNA,Annotations",
+  "css": "./plugins/NAL_CSS/css/main.css",
+  "favicon": "./plugins/WebApollo/img/webapollo_favicon.ico",
+  "formatVersion": 1,
+  "names": {
+    "type": "Hash",
+    "url": "names/"
+  },
+  "share_link": 0,
+  "tracks": [
+    {
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+      "key": "Reference sequence",
+      "label": "DNA",
+      "storeClass": "JBrowse/Store/Sequence/StaticChunked",
+      "type": "SequenceTrack",
+      "urlTemplate": "seq/{refseq_dirpath}/{refseq}-"
     },
-         "key" : "augustus_masked",
-
-
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
-         "trackType" : null,
-         "urlTemplate" : "tracks/augustus_masked/{refseq}/trackData.json",
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+      "label": "blastx_Placozoa",
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+      "label": "blastx_Platyhelminthes",
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+        "Track legend": "Results from Blastx alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline."
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+      "label": "blastx_Priapulida",
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+        "Track legend": "Results from Blastx alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline."
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+      "label": "blastx_Tardigrada",
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+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Blastx alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline."
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+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Blastx alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline."
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diff --git a/organisms/stage/Parasteatoda_tepidariorum/trackList.json b/organisms/stage/Parasteatoda_tepidariorum/trackList.json
index 7b984ab..968bb69 100644
--- a/organisms/stage/Parasteatoda_tepidariorum/trackList.json
+++ b/organisms/stage/Parasteatoda_tepidariorum/trackList.json
@@ -1,1382 +1,1277 @@
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-        "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research"
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+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research",
+        "Track legend": "Consensus gene models from the MAKER automated annotation pipeline."
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-        "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research"
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+      "key": "augustus_masked",
+      "label": "augustus_masked",
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+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research",
+        "Track legend": "Results from the Augustus gene prediction software as part of the MAKER automated annotation pipeline."
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+      "category": "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX",
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+      "key": "blastx_Annelida",
+      "label": "blastx_Annelida",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research",
+        "Track legend": "Results from Blastx alignments of a set of Annelida proteins as part of the MAKER automated annotation pipeline."
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+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
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+        "arrowheadClass": "webapollo-arrowhead",
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+      "type": "FeatureTrack",
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     },
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-        "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research"
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+      "category": "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX",
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+      "key": "blastx_Arthropoda",
+      "label": "blastx_Arthropoda",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research",
+        "Track legend": "Results from Blastx alignments of a set of Arthropoda proteins as part of the MAKER automated annotation pipeline."
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+      "type": "FeatureTrack",
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     },
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-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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-        "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research"
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX",
+      "compress": 0,
+      "key": "blastx_Atelocerata",
+      "label": "blastx_Atelocerata",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research",
+        "Track legend": "Results from Blastx alignments of a set of Atelocerata proteins as part of the MAKER automated annotation pipeline."
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+      "type": "FeatureTrack",
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     },
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-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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-        "Track legend" : "Results from Blastx alignments of a set of Crustacea proteins as part of the MAKER automated annotation pipeline.", 
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-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research"
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+      "category": "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX",
+      "compress": 0,
+      "key": "blastx_Cephalochordata",
+      "label": "blastx_Cephalochordata",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research",
+        "Track legend": "Results from Blastx alignments of a set of Cephalochordata proteins as part of the MAKER automated annotation pipeline."
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+        "arrowheadClass": "webapollo-arrowhead",
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/blastx_Cephalochordata/{refseq}/trackData.json"
     },
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-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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-        "Track legend" : "Results from Blastx alignments of a set of Echinodermata proteins as part of the MAKER automated annotation pipeline.", 
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-        "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research"
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+      "key": "blastx_Chelicerata",
+      "label": "blastx_Chelicerata",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research",
+        "Track legend": "Results from Blastx alignments of a set of Chelicerata proteins as part of the MAKER automated annotation pipeline."
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     },
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-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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-        "Track legend" : "Results from Blastx alignments of a set of Mollusca proteins as part of the MAKER automated annotation pipeline.", 
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-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research"
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+      "label": "blastx_Cnidaria",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research",
+        "Track legend": "Results from Blastx alignments of a set of Cnidaria proteins as part of the MAKER automated annotation pipeline."
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+      "type": "FeatureTrack",
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+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research",
+        "Track legend": "Results from Blastx alignments of a set of Craniata proteins as part of the MAKER automated annotation pipeline."
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-	         "metadata" : {
-        "Track legend" : "Results from Blastx alignments of a set of Nematomorpha proteins as part of the MAKER automated annotation pipeline.", 
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-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research"
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+      "category": "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX",
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+      "key": "blastx_Crustacea",
+      "label": "blastx_Crustacea",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
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+        "Track legend": "Results from Blastx alignments of a set of Crustacea proteins as part of the MAKER automated annotation pipeline."
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     },
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-        "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research"
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+      "key": "blastx_Echinodermata",
+      "label": "blastx_Echinodermata",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research",
+        "Track legend": "Results from Blastx alignments of a set of Echinodermata proteins as part of the MAKER automated annotation pipeline."
+      },
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     },
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-        "Track legend" : "Results from Blastx alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline.", 
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-        "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research"
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX",
+      "compress": 0,
+      "key": "blastx_Mollusca",
+      "label": "blastx_Mollusca",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research",
+        "Track legend": "Results from Blastx alignments of a set of Mollusca proteins as part of the MAKER automated annotation pipeline."
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     },
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-        "Track legend" : "Results from Blastx alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline.", 
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-        "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research"
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+      "category": "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX",
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+      "key": "blastx_Nemata",
+      "label": "blastx_Nemata",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research",
+        "Track legend": "Results from Blastx alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline."
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/blastx_Nemata/{refseq}/trackData.json"
     },
-         "key" : "blastx_Placozoa",
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-
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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-               "match_part" : "blastx"
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-	         "metadata" : {
-        "Track legend" : "Results from Blastx alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline.", 
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
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-        "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research"
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX",
+      "compress": 0,
+      "key": "blastx_Nematomorpha",
+      "label": "blastx_Nematomorpha",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research",
+        "Track legend": "Results from Blastx alignments of a set of Nematomorpha proteins as part of the MAKER automated annotation pipeline."
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+        "arrowheadClass": "webapollo-arrowhead",
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+          "match_part": "blastx"
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/blastx_Nematomorpha/{refseq}/trackData.json"
     },
-         "key" : "blastx_Platyhelminthes",
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-
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
-         "trackType" : null,
-         "urlTemplate" : "tracks/blastx_Platyhelminthes/{refseq}/trackData.json",
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-         "label" : "blastx_Platyhelminthes"
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-            "subfeatureClasses" : {
-               "match_part" : "blastx"
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-         },
-	 "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX",
-	         "metadata" : {
-        "Track legend" : "Results from Blastx alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline.", 
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research"
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX",
+      "compress": 0,
+      "key": "blastx_Onychophora",
+      "label": "blastx_Onychophora",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research",
+        "Track legend": "Results from Blastx alignments of a set of Onychophora proteins as part of the MAKER automated annotation pipeline."
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+        "arrowheadClass": "webapollo-arrowhead",
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+          "match_part": "blastx"
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/blastx_Onychophora/{refseq}/trackData.json"
     },
-         "key" : "blastx_Priapulida",
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-
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
-         "trackType" : null,
-         "urlTemplate" : "tracks/blastx_Priapulida/{refseq}/trackData.json",
-         "compress" : 0,
-         "type" : "FeatureTrack",
-         "label" : "blastx_Priapulida"
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-      {
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-            "subfeatureClasses" : {
-               "match_part" : "blastx"
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-            "arrowheadClass" : "webapollo-arrowhead"
-         },
-	 "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX",
-	         "metadata" : {
-        "Track legend" : "Results from Blastx alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline.", 
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research"
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX",
+      "compress": 0,
+      "key": "blastx_Parazoa",
+      "label": "blastx_Parazoa",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research",
+        "Track legend": "Results from Blastx alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline."
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+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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+          "match_part": "blastx"
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+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/blastx_Parazoa/{refseq}/trackData.json"
     },
-         "key" : "blastx_Tardigrada",
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-
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
-         "trackType" : null,
-         "urlTemplate" : "tracks/blastx_Tardigrada/{refseq}/trackData.json",
-         "compress" : 0,
-         "type" : "FeatureTrack",
-         "label" : "blastx_Tardigrada"
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-               "match_part" : "blastx"
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-	         "metadata" : {
-        "Track legend" : "Results from Blastx alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline.", 
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research"
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX",
+      "compress": 0,
+      "key": "blastx_Placozoa",
+      "label": "blastx_Placozoa",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research",
+        "Track legend": "Results from Blastx alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline."
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+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/blastx_Placozoa/{refseq}/trackData.json"
     },
-         "key" : "blastx_Tunicata",
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-
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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-         "urlTemplate" : "tracks/blastx_Tunicata/{refseq}/trackData.json",
-         "compress" : 0,
-         "type" : "FeatureTrack",
-         "label" : "blastx_Tunicata"
-      },
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-	         "metadata" : {
-        "Track legend" : "Results from Blastx alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline.", 
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research"
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX",
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+      "key": "blastx_Platyhelminthes",
+      "label": "blastx_Platyhelminthes",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research",
+        "Track legend": "Results from Blastx alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline."
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+      "type": "FeatureTrack",
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     },
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-
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
-         "trackType" : null,
-         "urlTemplate" : "tracks/blastx_UNCATEGORISED/{refseq}/trackData.json",
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-	        "metadata" : {
-        "Track legend" : "Results from CEGMA alignments as part of the MAKER automated annotation pipeline.",
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
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-	        "metadata" : {
-        "Track legend" : "Results from EST alignments resulting from the Cufflinks software as part of the MAKER automated annotation pipeline.",
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research"
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+      "category": "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX",
+      "compress": 0,
+      "key": "blastx_Priapulida",
+      "label": "blastx_Priapulida",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research",
+        "Track legend": "Results from Blastx alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline."
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+      "type": "FeatureTrack",
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     },
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-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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-               "match_part" : "protein2genome"
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-	         "metadata" : {
-        "Track legend" : "Results from Protein2genome alignments of a set of Annelida proteins as part of the MAKER automated annotation pipeline.",
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research"
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX",
+      "compress": 0,
+      "key": "blastx_Tardigrada",
+      "label": "blastx_Tardigrada",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
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+        "Track legend": "Results from Blastx alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline."
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-        "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research"
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+      "key": "blastx_UNCATEGORISED",
+      "label": "blastx_UNCATEGORISED",
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+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
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+        "Track legend": "Results from Blastx alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline."
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-        "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research"
+    {
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+      "key": "cegma",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
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+        "Track legend": "Results from CEGMA alignments as part of the MAKER automated annotation pipeline."
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-               "match_part" : "protein2genome"
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-        "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research"
+    {
+      "category": "BCM_v0.5.3/4. Transcriptome/Assembly",
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+      "key": "est_gff:cufflinks_i5k",
+      "label": "est_gff:cufflinks_i5k",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research",
+        "Track legend": "Results from EST alignments resulting from the Cufflinks software as part of the MAKER automated annotation pipeline."
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+        "arrowheadClass": "webapollo-arrowhead",
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-        "Track legend" : "Results from Protein2genome alignments of a set of Cnidaria proteins as part of the MAKER automated annotation pipeline.",
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+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+      "key": "protein2genome_Annelida",
+      "label": "protein2genome_Annelida",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
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+        "Track legend": "Results from Protein2genome alignments of a set of Annelida proteins as part of the MAKER automated annotation pipeline."
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+      "type": "FeatureTrack",
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     },
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-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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-         "urlTemplate" : "tracks/protein2genome_Cnidaria/{refseq}/trackData.json",
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-               "match_part" : "protein2genome"
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-        "Track legend" : "Results from Protein2genome alignments of a set of Craniata proteins as part of the MAKER automated annotation pipeline.",
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-        "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research"
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Arthropoda",
+      "label": "protein2genome_Arthropoda",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research",
+        "Track legend": "Results from Protein2genome alignments of a set of Arthropoda proteins as part of the MAKER automated annotation pipeline."
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-        "Track legend" : "Results from Protein2genome alignments of a set of Crustacea proteins as part of the MAKER automated annotation pipeline.",
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-        "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research"
+    {
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+      "key": "protein2genome_Atelocerata",
+      "label": "protein2genome_Atelocerata",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
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+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+      "key": "protein2genome_Cephalochordata",
+      "label": "protein2genome_Cephalochordata",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
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+        "Track legend": "Results from Protein2genome alignments of a set of Cephalochordata proteins as part of the MAKER automated annotation pipeline."
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+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+      "key": "protein2genome_Chelicerata",
+      "label": "protein2genome_Chelicerata",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
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+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
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+      "label": "protein2genome_Craniata",
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+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
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+      "key": "protein2genome_Crustacea",
+      "label": "protein2genome_Crustacea",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research",
+        "Track legend": "Results from Protein2genome alignments of a set of Crustacea proteins as part of the MAKER automated annotation pipeline."
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+      "key": "protein2genome_Echinodermata",
+      "label": "protein2genome_Echinodermata",
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+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research",
+        "Track legend": "Results from Protein2genome alignments of a set of Echinodermata proteins as part of the MAKER automated annotation pipeline."
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+      "key": "protein2genome_Mollusca",
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+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
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+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
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+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
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+      "label": "Jpn_Pt_gene.model_oda",
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+        "Analysis method": "Mapped the RNA-seq reads to Baylor's Pt-genome (Ptep01282013genome) with BLAT, and predicted genes and transcripts with cufflinks and cuffmerge using the RNA-seq mapping data together with EST and cDNA mapping data. We removed multiple-hit (>= 3) reads and one (scaffold with larger number) of two loci of two-hit reads",
+        "Data provider": "Yasuko Akiyama-Oda and Hiroki Oda, JT Biohistory Research Hall",
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-        "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research"
+    {
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+        "Data provider": "Yasuko Akiyama-Oda and Hiroki Oda, JT Biohistory Research Hall",
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-         "bicolor_pivot" : "0.5",
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-   "alwaysOnTracks" : "DNA,Annotations"
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+      "bicolor_pivot": "0.5",
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+      "label": "GC Content",
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+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
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+  ]
 }
diff --git a/organisms/stage/Photinus_pyralis/trackList.json b/organisms/stage/Photinus_pyralis/trackList.json
index ce35688..b0a6578 100644
--- a/organisms/stage/Photinus_pyralis/trackList.json
+++ b/organisms/stage/Photinus_pyralis/trackList.json
@@ -1,337 +1,337 @@
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       },
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-         "urlTemplate" : "bigwig/GCF_008802855.1_Ppyr1.3_genomic.fna.gaps.bigwig"
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-         },
-         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
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-         "urlTemplate" : "bigwig/GCF_008802855.1_Ppyr1.3_genomic.fna.gc.bigwig"
+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "bigwig/GCF_008802855.1_Ppyr1.3_genomic.fna.gaps.bigwig"
+    },
+    {
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+      "bicolor_pivot": "0.5",
+      "category": "Reference Assembly",
+      "key": "GC Content",
+      "label": "GC Content",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
       },
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-         "category" : "RNA-Seq/Mapped Reads",
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+    {
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+      "compress": 0,
+      "key": "NCBI_Annotation_Release_100_Pseudogene",
+      "label": "NCBI_Annotation_Release_100_Pseudogene",
+      "metadata": {
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-         "trackType" : "HTMLFeatures",
-         "type" : "HTMLFeatures",
-         "urlTemplate" : "tracks/NCBI_Annotation_Release_100_Pseudogene/{refseq}/trackData.json"
+      "trackType": "HTMLFeatures",
+      "type": "HTMLFeatures",
+      "urlTemplate": "tracks/NCBI_Annotation_Release_100_Pseudogene/{refseq}/trackData.json"
+    },
+    {
+      "category": "NCBI Annotation Release 100",
+      "compress": 0,
+      "key": "NCBI_Annotation_Release_100_Gene - Color by CDS frame",
+      "label": "NCBI_Annotation_Release_100_Gene - Color by CDS frame",
+         "menuTemplate" : [
+             {
+                "label" : "View details"
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+             {
+              "label": "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
+              "title": "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
+              "iconClass" : "dijitIconDatabase",
+              "action": "newWindow",
+              "url" : "function(track,feature){ return 'https://www.ncbi.nlm.nih.gov/nuccore/'+feature.get('name')}"
+              }
+        ],
+      "metadata": {
+        "Data description": "ftp://ftp.ncbi.nlm.nih.gov/genomes/Photinus_pyralis/README_CURRENT_RELEASE",
+        "Data provider": "NCBI",
+        "Data source": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/008/802/855/GCF_008802855.1_Ppyr1.3/GCF_008802855.1_Ppyr1.3_genomic.gff.gz",
+        "Method": "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
       },
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-         "compress" : 0,
-         "key" : "NCBI_Annotation_Release_100_Gene - Color by CDS frame",
-         "label" : "NCBI_Annotation_Release_100_Gene - Color by CDS frame",
- "menuTemplate" : [
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-        "title": "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
-        "iconClass" : "dijitIconDatabase",
-        "action": "newWindow",
-        "url" : "function(track,feature){ return 'https://i5k.nal.usda.gov/search/site/'+feature.get('name')}"
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "description": "product, note, description",
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         }
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-         "metadata" : {
-            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Photinus_pyralis/README_CURRENT_RELEASE",
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-         "trackType" : "HTMLFeatures",
-         "type" : "HTMLFeatures",
-         "urlTemplate" : "tracks/phopyr_current_models/{refseq}/trackData.json"
-      }
-   ]
+      },
+      "trackType": "HTMLFeatures",
+      "type": "HTMLFeatures",
+      "urlTemplate": "tracks/phopyr_current_models/{refseq}/trackData.json"
+    }
+  ]
 }
diff --git a/organisms/stage/Rhagoletis_zephyria/trackList.json b/organisms/stage/Rhagoletis_zephyria/trackList.json
index 8dc9434..f5232d7 100644
--- a/organisms/stage/Rhagoletis_zephyria/trackList.json
+++ b/organisms/stage/Rhagoletis_zephyria/trackList.json
@@ -1,261 +1,255 @@
 {
-   "css" : "./plugins/NAL_CSS/css/contrib_styles.css",
-   "share_link" : 0,
-   "plugins" : [
-      {
-         "location" : "./plugins/WebApollo",
-         "name" : "WebApollo"
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-         "label" : "DNA",
-         "type" : "SequenceTrack",
-         "category" : "Reference sequence",
-         "key" : "Reference sequence"
+  "alwaysOnTracks": "DNA,Annotations",
+  "css": "./plugins/NAL_CSS/css/main.css",
+  "favicon": "./plugins/WebApollo/img/webapollo_favicon.ico",
+  "formatVersion": 1,
+  "names": {
+    "type": "Hash",
+    "url": "names/"
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+  "share_link": 0,
+  "tracks": [
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+      "urlTemplate": "seq/{refseq_dirpath}/{refseq}-"
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+      "autocomplete": "none",
+      "compress": 0,
+      "key": "User-created Annotations",
+      "label": "Annotations",
+      "phase": 0,
+      "storeClass": "WebApollo/Store/SeqFeature/ScratchPad",
+      "style": {
+        "alternateClasses": {
+          "miRNA": {
+            "className": "brightgreen-80pct",
+            "renderClassName": "gray-center-30pct"
+          },
+          "ncRNA": {
+            "className": "brightgreen-80pct",
+            "renderClassName": "gray-center-30pct"
+          },
+          "pseudogene": {
+            "className": "light-purple-80pct",
+            "renderClassName": "gray-center-30pct"
+          },
+          "rRNA": {
+            "className": "brightgreen-80pct",
+            "renderClassName": "gray-center-30pct"
+          },
+          "repeat_region": {
+            "className": "magenta-80pct"
+          },
+          "snRNA": {
+            "className": "brightgreen-80pct",
+            "renderClassName": "gray-center-30pct"
+          },
+          "snoRNA": {
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+            "renderClassName": "gray-center-30pct"
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+            "renderClassName": "gray-center-30pct"
+          },
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+            "renderClassName": "blue-ibeam-render"
+          }
+        },
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+          "non_canonical_three_prime_splice_site": false
+        },
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+        "renderClassName": "annot-render",
+        "subfeatureClasses": {
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+          "UTR": "annot-UTR",
+          "exon": "container-100pct",
+          "non_canonical_five_prime_splice_site": "noncanonical-splice-site",
+          "non_canonical_three_prime_splice_site": "noncanonical-splice-site",
+          "wholeCDS": null
+        },
+        "uniqueIdField": "id"
       },
-      {
-         "autocomplete" : "none",
-         "style" : {
-            "className" : "annot",
-            "renderClassName" : "annot-render",
-            "subfeatureClasses" : {
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-         "phase" : 0,
-         "compress" : 0,
-         "label" : "Annotations",
-         "type" : "WebApollo/View/Track/AnnotTrack",
-         "subfeatures" : 1
+      "subfeatures": 1,
+      "type": "WebApollo/View/Track/AnnotTrack"
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+      "bicolor_pivot": "zero",
+      "category": "Reference Assembly",
+      "key": "Gaps in assembly",
+      "label": "Gaps in assembly",
+      "metadata": {
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+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
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-            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank",
-            "Track contact" : "The i5k workspace@NAL"
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-            "Track contact" : "The i5k workspace@NAL"
-         },
-         "label" : "GC Content"
+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "bigwig/GCF_001687245.1_Rhagoletis_zephyria_1.0_genomic_RefSeqIDs.fna.gaps.bigwig"
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+      "bicolor_pivot": "0.5",
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+      "key": "GC Content",
+      "label": "GC Content",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
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-         "label" : "NCBI_Annotation_Release_100_lncRNA",
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+      "scoreType": "avgScore",
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+      "style": {
+        "neg_color": "rgba(255,255,0,50)",
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+      "urlTemplate": "tracks/NCBI_Annotation_Release_100_tRNA/{refseq}/trackData.json"
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+      "key": "cDNA match evidence from NCBI Annotation Release 100",
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+        "arrowheadClass": "webapollo-arrowhead",
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/NCBI_Annotation_Release_100_cDNA_match/{refseq}/trackData.json"
+    },
+    {
+      "category": "NCBI Annotation Release 100/1. Gene Sets/Protein Coding",
+      "compress": 0,
+      "key": "NCBI Predicted protein coding genes, Annotation Release 100",
+      "label": "rhazep_current_models",
+      "metadata": {
+        "Data description": "ftp://ftp.ncbi.nlm.nih.gov/genomes/Rhagoletis_zephyria/README_CURRENT_RELEASE",
+        "Data provider": "NCBI",
+        "Data source": "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF_001687245.1_Rhagoletis_zephyria_1.0/GCF_001687245.1_Rhagoletis_zephyria_1.0_genomic.gff.gz",
+        "Method": "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/",
+        "Note": "Some genes may have non-coding transcripts"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "description": "product,note,description",
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+          "CDS": "primary_gene_set-cds",
+          "UTR": "primary_gene_set-utr",
+          "exon": "container-100pct",
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+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/rhazep_current_models/{refseq}/trackData.json"
+    }
+  ]
 }
diff --git a/organisms/stage/Rhipicephalus_microplus/trackList.json b/organisms/stage/Rhipicephalus_microplus/trackList.json
index 2c2ad7e..79c58b3 100644
--- a/organisms/stage/Rhipicephalus_microplus/trackList.json
+++ b/organisms/stage/Rhipicephalus_microplus/trackList.json
@@ -1,128 +1,179 @@
 {
-   "css" : "./plugins/NAL_CSS/css/contrib_styles.css",
-   "share_link" : 0,
-   "plugins" : [
-      {
-         "location" : "./plugins/WebApollo",
-         "name" : "WebApollo"
-      }
-   ],
+   "formatVersion" : 1,
+   "names" : {
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    "tracks" : [
       {
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          "chunkSize" : 20000,
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+         "key" : "Reference sequence",
          "label" : "DNA",
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          "type" : "SequenceTrack",
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-         "key" : "Reference sequence"
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       },
       {
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+             {
+                "label" : "View details"
+             },
+             {
+              "label": "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
+              "title": "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
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+              "action": "newWindow",
+              "url" : "function(track,feature){ return 'https://www.ncbi.nlm.nih.gov/nuccore/'+feature.get('name')}"
+              }
+        ],
+         "metadata" : {
+            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Rhipicephalus_microplus/README_CURRENT_RELEASE",
+            "Data provider" : "NCBI",
+            "Data source" : "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/013/339/725/GCF_013339725.1_ASM1333972v1/GCF_013339725.1_ASM1333972v1_genomic.gff.gz",
+            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "className" : "annot",
-            "renderClassName" : "annot-render",
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "container-16px",
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             "subfeatureClasses" : {
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-            "centerSubFeature" : {
-               "non_canonical_three_prime_splice_site" : false,
-               "non_canonical_five_prime_splice_site" : false
+               "wholeCDS" : null
             }
          },
-         "key" : "User-created Annotations",
-         "storeClass" : "WebApollo/Store/SeqFeature/ScratchPad",
-         "phase" : 0,
-         "compress" : 0,
-         "label" : "Annotations",
-         "type" : "WebApollo/View/Track/AnnotTrack",
-         "subfeatures" : 1
+         "trackType" : "HTMLFeatures",
+         "type" : "HTMLFeatures",
+         "urlTemplate" : "tracks/rhimic_current_models/{refseq}/trackData.json"
       },
       {
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+         "label" : "NCBI_Annotation_Release_100_Pseudogene",
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+            "Data provider" : "NCBI",
+            "Data source" : "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/013/339/725/GCF_013339725.1_ASM1333972v1/GCF_013339725.1_ASM1333972v1_genomic.gff.gz",
+            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
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          "style" : {
-            "pos_color" : "black",
-            "neg_color" : "white"
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "container-16px",
+            "description" : "product, note, description",
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          },
-         "bicolor_pivot" : "zero",
+         "trackType" : "HTMLFeatures",
+         "type" : "HTMLFeatures",
+         "urlTemplate" : "tracks/NCBI_Annotation_Release_100_Pseudogene/{refseq}/trackData.json"
+      },
+      {
          "autoscale" : "local",
+         "bicolor_pivot" : "zero",
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          "key" : "Gaps in assembly",
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-         "urlTemplate" : "bigwig/GCA_002176555.1_Rmi2.0_genomic.fna.gaps.bigwig",
          "label" : "Gaps in assembly",
-         "category" : "Reference Assembly",
          "metadata" : {
-            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank",
+            "Track contact" : "The i5k workspace@NAL",
             "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
-            "Track contact" : "The i5k workspace@NAL"
+            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
          },
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+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "white",
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+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/GCF_013339725.1_ASM1333972v1_genomic.fna.gaps.bigwig"
       },
       {
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+         "bicolor_pivot" : "0.5",
+         "category" : "Reference Assembly",
+         "key" : "GC Content",
+         "label" : "GC Content",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+         },
          "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
-         "urlTemplate" : "bigwig/GCA_002176555.1_Rmi2.0_genomic.fna.gc.bigwig",
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-         "bicolor_pivot" : "0.5",
-         "key" : "GC Content",
-         "scoreType": "avgScore",
-        "category" : "Reference Assembly",
+         "urlTemplate" : "bigwig/GCF_013339725.1_ASM1333972v1_genomic.fna.gc.bigwig"
+      },
+      {
+         "category" : "RNA-Seq/Mapped Reads",
+         "key" : "Rhimic_ASM1333972v1_RNA-Seq-alignments_2021-07-25",
+         "label" : "Rhimic_ASM1333972v1_RNA-Seq-alignments_2021-07-25",
          "metadata" : {
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-            "Track contact" : "The i5k workspace@NAL"
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR7754371'>SRR7754371</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11457965'>SRR11457965</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR13614645'>SRR13614645</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR13562171'>SRR13562171</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11457967'>SRR11457967</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11457976'>SRR11457976</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR6765806'>SRR6765806</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR10740628'>SRR10740628</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11457968'>SRR11457968</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11457974'>SRR11457974</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Dark red alignments: Mapped portion of read aligned to forward strand<br>Light red alignments: Spliced portion of read aligned to forward strand<br>Dark blue alignments: Mapped portion of read aligned to reverse strand<br>Light blue alignments: Spliced portion of read aligned to reverse strand<br>Red marking - deletion in the read relative to the reference<br>Green marking - insertion in the read relative to the reference<br>Yellow marking  - mismatch (hover over the mismatch to see what the snp is)"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "analyses/Rhipicephalus-microplus-RNA-Seq_2021-07-25_v1.0/Rhimic_ASM1333972v1_RNA-Seq-alignments_2021-07-25.bam"
+      },
+      {
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+         "bicolor_pivot" : "zero",
+         "category" : "RNA-Seq/Coverage Plots",
+         "key" : "Rhimic_ASM1333972v1_RNA-Seq-alignments_2021-07-25_coverage",
+         "label" : "Rhimic_ASM1333972v1_RNA-Seq-alignments_2021-07-25_coverage",
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
+         },
+        "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR7754371'>SRR7754371</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11457965'>SRR11457965</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR13614645'>SRR13614645</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR13562171'>SRR13562171</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11457967'>SRR11457967</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11457976'>SRR11457976</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR6765806'>SRR6765806</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR10740628'>SRR10740628</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11457968'>SRR11457968</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11457974'>SRR11457974</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage."
+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "analyses/Rhipicephalus-microplus-RNA-Seq_2021-07-25_v1.0/Rhimic_ASM1333972v1_RNA-Seq-alignments_2021-07-25.bigwig"
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+      {
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+         "key" : "Rhimic_ASM1333972v1_RNA-Seq-alignments_2021-07-25_junctions",
+         "label" : "Rhimic_ASM1333972v1_RNA-Seq-alignments_2021-07-25_junctions",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR7754371'>SRR7754371</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11457965'>SRR11457965</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR13614645'>SRR13614645</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR13562171'>SRR13562171</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11457967'>SRR11457967</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11457976'>SRR11457976</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR6765806'>SRR6765806</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR10740628'>SRR10740628</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11457968'>SRR11457968</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11457974'>SRR11457974</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Junction reads generated by Hisat2 aligner and regtools. The number of alignments supporting the junction read is listed in blue."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+	    "description":"score",
+            "className" : "feature"
          },
-         "autoscale" : "local"
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+         "type" : "FeatureTrack",
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-   "alwaysOnTracks" : "DNA,Annotations",
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 }
diff --git a/organisms/stage/Rhyzopertha_dominica/trackList.json b/organisms/stage/Rhyzopertha_dominica/trackList.json
index 9b51449..39aa9b5 100644
--- a/organisms/stage/Rhyzopertha_dominica/trackList.json
+++ b/organisms/stage/Rhyzopertha_dominica/trackList.json
@@ -1,424 +1,426 @@
 {
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+          "exon": "container-100pct",
+          "wholeCDS": null
+        }
+      },
+      "trackType": "HTMLFeatures",
+      "type": "HTMLFeatures",
+      "urlTemplate": "tracks/Rhyzopertha_dominica.annotation/{refseq}/trackData.json"
+    }
+  ]
 }
diff --git a/organisms/stage/Saccharomyceseubayanus/trackList.json b/organisms/stage/Saccharomyceseubayanus/trackList.json
new file mode 100644
index 0000000..1463194
--- /dev/null
+++ b/organisms/stage/Saccharomyceseubayanus/trackList.json
@@ -0,0 +1,136 @@
+{
+   "formatVersion" : 1,
+   "names" : {
+      "type" : "Hash",
+      "url" : "names/"
+   },
+   "tracks" : [
+      {
+         "category" : "Reference sequence",
+         "chunkSize" : 20000,
+         "key" : "Reference sequence",
+         "label" : "DNA",
+         "seqType" : "dna",
+         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
+         "type" : "SequenceTrack",
+         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-"
+      },
+      {
+         "category" : "NCBI Annotation Release 100",
+         "compress" : 0,
+         "key" : "NCBI_Annotation_Release_100_Gene",
+         "label" : "saceub_current_models",
+         "metadata" : {
+            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Saccharomyces_eubayanus/README_CURRENT_RELEASE",
+            "Data provider" : "NCBI",
+            "Data source" : "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/298/625/GCF_001298625.1_SEUB3.0/GCF_001298625.1_SEUB3.0_genomic.gff.gz",
+            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "container-16px",
+            "description" : "product, note, description",
+            "subfeatureClasses" : {
+               "CDS" : "gnomon_CDS",
+               "UTR" : "gnomon_UTR",
+               "exon" : "container-100pct",
+               "wholeCDS" : null
+            }
+         },
+         "trackType" : "HTMLFeatures",
+         "type" : "HTMLFeatures",
+         "urlTemplate" : "tracks/saceub_current_models/{refseq}/trackData.json"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Reference Assembly",
+         "key" : "Gaps in assembly",
+         "label" : "Gaps in assembly",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "white",
+            "pos_color" : "black"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/GCF_001298625.1_SEUB3.0_genomic.fna.gaps.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "0.5",
+         "category" : "Reference Assembly",
+         "key" : "GC Content",
+         "label" : "GC Content",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+         },
+         "scoreType" : "avgScore",
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "rgba(255,255,0,50)",
+            "pos_color" : "rgba(0,0,255,50)"
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+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/GCF_001298625.1_SEUB3.0_genomic.fna.gc.bigwig"
+      },
+      {
+         "category" : "RNA-Seq/Mapped Reads",
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+         "label" : "Saceub_SEUB3.0_RNA-Seq-alignments_2022-01-07",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR10310353'>SRR10310353</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Dark red alignments: Mapped portion of read aligned to forward strand<br>Light red alignments: Spliced portion of read aligned to forward strand<br>Dark blue alignments: Mapped portion of read aligned to reverse strand<br>Light blue alignments: Spliced portion of read aligned to reverse strand<br>Red marking - deletion in the read relative to the reference<br>Green marking - insertion in the read relative to the reference<br>Yellow marking  - mismatch (hover over the mismatch to see what the snp is)"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "unsafePopup" : true,
+         "urlTemplate" : "analyses/Saccharomyces-eubayanus-RNA-Seq_2022-01-07_v1.0/Saceub_SEUB3.0_RNA-Seq-alignments_2022-01-07.bam"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "RNA-Seq/Coverage Plots",
+         "key" : "Saceub_SEUB3.0_RNA-Seq-alignments_2022-01-07_coverage",
+         "label" : "Saceub_SEUB3.0_RNA-Seq-alignments_2022-01-07_coverage",
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "analyses/Saccharomyces-eubayanus-RNA-Seq_2022-01-07_v1.0/Saceub_SEUB3.0_RNA-Seq-alignments_2022-01-07.bigwig"
+      },
+      {
+         "category" : "RNA-Seq/Splice junctions",
+         "compress" : 0,
+         "key" : "Saceub_SEUB3.0_RNA-Seq-alignments_2022-01-07_junctions",
+         "label" : "Saceub_SEUB3.0_RNA-Seq-alignments_2022-01-07_junctions",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR10310353'>SRR10310353</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Junction reads generated by Hisat2 aligner and regtools. The number of alignments supporting the junction read is listed in blue."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "className" : "feature",
+            "description" : "score"
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "unsafePopup" : true,
+         "urlTemplate" : "tracks/Saceub_SEUB3.0_RNA-Seq-alignments_2022-01-07_junctions/{refseq}/trackData.json"
+      }
+   ]
+}
diff --git a/organisms/stage/Schistocerca_americana/trackList.json b/organisms/stage/Schistocerca_americana/trackList.json
new file mode 100644
index 0000000..ad0a54b
--- /dev/null
+++ b/organisms/stage/Schistocerca_americana/trackList.json
@@ -0,0 +1,124 @@
+{
+   "formatVersion" : 1,
+   "tracks" : [
+      {
+         "seqType" : "dna",
+         "type" : "SequenceTrack",
+         "key" : "Reference sequence",
+         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-",
+         "chunkSize" : 20000,
+         "category" : "Reference sequence",
+         "label" : "DNA",
+         "storeClass" : "JBrowse/Store/Sequence/StaticChunked"
+      },
+      {
+         "trackType" : "HTMLFeatures",
+         "type" : "HTMLFeatures",
+         "style" : {
+            "description" : "product, note, description",
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "container-16px",
+            "subfeatureClasses" : {
+               "exon" : "container-100pct",
+               "CDS" : "gnomon_CDS",
+               "wholeCDS" : null,
+               "UTR" : "gnomon_UTR"
+            }
+         },
+         "compress" : 0,
+         "label" : "schame_current_models",
+ "menuTemplate" : [
+             {
+                "label" : "View details"
+             },
+             {
+              "label": "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
+              "title": "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
+              "iconClass" : "dijitIconDatabase",
+              "action": "newWindow",
+              "url" : "function(track,feature){ return 'https://www.ncbi.nlm.nih.gov/nuccore/'+feature.get('name')}"
+              }
+        ],
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "category" : "NCBI Annotation Release 100",
+         "urlTemplate" : "tracks/schame_current_models/{refseq}/trackData.json",
+         "key" : "NCBI_Annotation_Release_100_Gene",
+         "metadata" : {
+            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Schistocerca_americana/README_CURRENT_RELEASE",
+            "Data source" : "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/021/461/395/GCF_021461395.2_iqSchAmer2.1/GCF_021461395.2_iqSchAmer2.1_genomic.gff.gz",
+            "Data provider" : "NCBI",
+            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
+         }
+      },
+      {
+         "key" : "NCBI_Annotation_Release_100_Pseudogene",
+         "metadata" : {
+            "Data provider" : "NCBI",
+            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/",
+            "Data source" : "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/021/461/395/GCF_021461395.2_iqSchAmer2.1/GCF_021461395.2_iqSchAmer2.1_genomic.gff.gz",
+            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Schistocerca_americana/README_CURRENT_RELEASE"
+         },
+         "urlTemplate" : "tracks/NCBI_Annotation_Release_100_Pseudogene/{refseq}/trackData.json",
+         "category" : "NCBI Annotation Release 100",
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "label" : "NCBI_Annotation_Release_100_Pseudogene",
+         "style" : {
+            "description" : "product, note, description",
+            "arrowheadClass" : "trellis-arrowhead",
+            "subfeatureClasses" : {
+               "CDS" : "gnomon_CDS",
+               "exon" : "container-100pct",
+               "UTR" : "gnomon_UTR",
+               "wholeCDS" : null
+            },
+            "className" : "container-16px"
+         },
+         "compress" : 0,
+         "trackType" : "HTMLFeatures",
+         "type" : "HTMLFeatures"
+      },
+      {
+         "bicolor_pivot" : "zero",
+         "label" : "Gaps in assembly",
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "key" : "Gaps in assembly",
+         "urlTemplate" : "bigwig/GCF_021461395.2_iqSchAmer2.1_genomic.fna.gaps.bigwig",
+	"category" : "Reference Assembly",
+		"metadata" : {
+		"Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+		"Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank",
+		"Track contact" : "The i5k workspace@NAL"
+		},
+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "autoscale" : "local",
+         "style" : {
+            "neg_color" : "white",
+            "pos_color" : "black"
+         }
+      },
+      {
+         "key" : "GC Content",
+         "style" : {
+            "pos_color" : "rgba(0,0,255,50)",
+            "neg_color" : "rgba(255,255,0,50)"
+         },
+         "urlTemplate" : "bigwig/GCF_021461395.2_iqSchAmer2.1_genomic.fna.gc.bigwig",
+	"scoreType" : "avgScore",
+		"category" : "Reference Assembly",
+		"metadata" : {
+		"Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+		"Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track.",
+		"Track contact" : "The i5k workspace@NAL"
+		},
+         "bicolor_pivot" : "0.5",
+         "autoscale" : "local",
+         "label" : "GC Content",
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "type" : "JBrowse/View/Track/Wiggle/Density"
+      }
+   ],
+   "names" : {
+      "type" : "Hash",
+      "url" : "names/"
+   }
+}
diff --git a/organisms/stage/Schistocercapiceifrons/trackList.json b/organisms/stage/Schistocercapiceifrons/trackList.json
new file mode 100644
index 0000000..81f8055
--- /dev/null
+++ b/organisms/stage/Schistocercapiceifrons/trackList.json
@@ -0,0 +1,112 @@
+{
+   "formatVersion" : 1,
+   "names" : {
+      "type" : "Hash",
+      "url" : "names/"
+   },
+   "tracks" : [
+      {
+         "key" : "Reference sequence",
+         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
+         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-",
+         "chunkSize" : 20000,
+         "category" : "Reference sequence",
+         "type" : "SequenceTrack",
+         "label" : "DNA",
+         "seqType" : "dna"
+      },
+      {
+         "category" : "NCBI Annotation Release 100",
+         "type" : "HTMLFeatures",
+         "label" : "schpic_current_models",
+         "key" : "NCBI_Annotation_Release_100_Gene",
+         "trackType" : "HTMLFeatures",
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "className" : "{type}",
+            "description" : "product, note, description",
+            "subfeatureClasses" : {
+               "wholeCDS" : null,
+               "exon" : "container-100pct",
+               "CDS" : "gnomon_CDS",
+               "UTR" : "gnomon_UTR"
+            },
+            "arrowheadClass" : "trellis-arrowhead"
+         },
+         "urlTemplate" : "tracks/schpic_current_models/{refseq}/trackData.json",
+         "metadata" : {
+            "Data source" : "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/021/461/385/GCF_021461385.2_iqSchPice1.1/GCF_021461385.2_iqSchPice1.1_genomic.gff.gz",
+            "Data provider" : "NCBI",
+            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/",
+            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Schistocerca_piceifrons/README_CURRENT_RELEASE"
+         },
+         "compress" : 0
+      },
+      {
+         "category" : "NCBI Annotation Release 100",
+         "type" : "HTMLFeatures",
+         "label" : "NCBI_Annotation_Release_100_Pseudogene",
+         "trackType" : "HTMLFeatures",
+         "key" : "NCBI_Annotation_Release_100_Pseudogene",
+         "style" : {
+            "arrowheadClass" : "trellis-arrowhead",
+            "subfeatureClasses" : {
+               "CDS" : "gnomon_CDS",
+               "UTR" : "gnomon_UTR",
+               "exon" : "container-100pct",
+               "wholeCDS" : null
+            },
+            "className" : "{type}",
+            "description" : "product, note, description"
+         },
+         "urlTemplate" : "tracks/NCBI_Annotation_Release_100_Pseudogene/{refseq}/trackData.json",
+         "metadata" : {
+            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/",
+            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Schistocerca_piceifrons/README_CURRENT_RELEASE",
+            "Data provider" : "NCBI",
+            "Data source" : "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/021/461/385/GCF_021461385.2_iqSchPice1.1/GCF_021461385.2_iqSchPice1.1_genomic.gff.gz"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "compress" : 0
+      },
+      {
+         "urlTemplate" : "bigwig/GCF_021461385.2_iqSchPice1.1_genomic.fna.gaps.bigwig",
+	"category" : "Reference Assembly",
+		"metadata" : {
+		"Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+		"Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank",
+		"Track contact" : "The i5k workspace@NAL"
+		},
+         "style" : {
+            "neg_color" : "white",
+            "pos_color" : "black"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "key" : "Gaps in assembly",
+         "label" : "Gaps in assembly",
+         "bicolor_pivot" : "zero",
+         "autoscale" : "local",
+         "type" : "JBrowse/View/Track/Wiggle/Density"
+      },
+      {
+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "bicolor_pivot" : "0.5",
+         "autoscale" : "local",
+         "label" : "GC Content",
+         "key" : "GC Content",
+         "urlTemplate" : "bigwig/GCF_021461385.2_iqSchPice1.1_genomic.fna.gc.bigwig",
+	"scoreType" : "avgScore",
+		"category" : "Reference Assembly",
+		"metadata" : {
+		"Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+		"Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track.",
+		"Track contact" : "The i5k workspace@NAL"
+		},
+         "style" : {
+            "pos_color" : "rgba(0,0,255,50)",
+            "neg_color" : "rgba(255,255,0,50)"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig"
+      }
+   ]
+}
diff --git a/organisms/stage/Tigriopus_californicus/trackList.json b/organisms/stage/Tigriopus_californicus/trackList.json
index caa8f56..85693dd 100644
--- a/organisms/stage/Tigriopus_californicus/trackList.json
+++ b/organisms/stage/Tigriopus_californicus/trackList.json
@@ -1,1068 +1,1044 @@
 {
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-   "share_link" : 0,
-   "plugins" : [
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-         "autocomplete" : "none",
-         "style" : {
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-            "renderClassName" : "annot-render",
-            "subfeatureClasses" : {
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-               "CDS" : "annot-CDS",
-               "non_canonical_five_prime_splice_site" : "noncanonical-splice-site",
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-            },
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-            "alternateClasses" : {
-               "transposable_element" : {
-                  "renderClassName" : "blue-ibeam-render",
-                  "className" : "blue-ibeam"
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-               "pseudogene" : {
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-                  "className" : "light-purple-80pct"
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-         "storeClass" : "WebApollo/Store/SeqFeature/ScratchPad",
-         "phase" : 0,
-         "compress" : 0,
-         "label" : "Annotations",
-         "type" : "WebApollo/View/Track/AnnotTrack",
-         "subfeatures" : 1
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-         },
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-         "label" : "Abalone Cove population",
-         "metadata" : {
-            "Analysis method" : "BWA-0.6.2",
-            "Geographical location of specimen collection" : "USA, Abalone Cove, 33.7377°N, 118.3753°W",
-            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
-            "Sequencing platform" : "Illumina HiSeq 200bp",
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-            "Analysis contact" : "Thiago Lima, Scripps Institution of Oceanography"
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-         "metadata" : {
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-            "Geographical location of specimen collection" : "USA, Abalone Cove, 33.7377°N, 118.3753°W",
-            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
-            "Sequencing platform" : "Illumina HiSeq 200bp",
-            "Date completed" : "4/25/14",
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-"metadata" : {
-	"Geographical location of specimen collection":"USA, Catalina Island, 33°26.8’N, 118°28.6’W",
-	"Tissues included":"Pooled adult males and females",
-	"Sex":"Pooled",
-	"Sequencing platform and version":"Illumina HiSeq 200bp",
-	"Publication status":"Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
-	"File provider":"Thiago Lima, Scripps Institution of Oceanography",
-	"Analysis method":"BWA-0.6.2",
-	"Date completed":"7/24/14",
-	"Track legend":"This track displays alignments of the BWA-0.6.2 program. Aligned portions of the source data are dark blue, whereas alignment gaps are light blue. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)."
-},
-         "type" : "WebApollo/View/Track/DraggableAlignments",
-         "label" : "Catalina Island population (mapped reads)",
-         "key" : "Catalina Island population (mapped reads)"
-      },
-      {
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-         "urlTemplate" : "user_contributed_data/Tigriopus_californicus_i5k/BB_to_SD_genome4_opt_15_merged_sort.bam",
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-"category" : "DNASeq/Mapped Reads",
-"metadata" : {
-	"Geographical location of specimen collection":"USA, Bodega Bay, 38°19'4”N, 123°4'23”W",
-	"Tissues included":"Pooled adult males and females",
-	"Sex":"Pooled",
-	"Sequencing platform and version":"Illumina HiSeq 200bp",
-	"Publication status":"Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
-	"File provider":"Thiago Lima, Scripps Institution of Oceanography",
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-         "label" : "Bodega Bay population (mapped reads)",
-         "type" : "WebApollo/View/Track/DraggableAlignments",
-         "key" : "Bodega Bay population (mapped reads)"
-      },
-      {
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-"category" : "DNASeq/Mapped Reads",
-"metadata" : {
-	"Geographical location of specimen collection":"USA, Bird Rock, 32˚48’54”N, 117˚16’23”W",
-	"Tissues included":"Pooled adult males and females",
-	"Sex":"Pooled",
-	"Sequencing platform and version":"Illumina HiSeq 200bp",
-	"Publication status":"Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
-	"File provider":"Thiago Lima, Scripps Institution of Oceanography",
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-	"Date completed":"7/24/14",
-	"Track legend":"This track displays alignments of the BWA-0.6.2 program. Aligned portions of the source data are dark blue, whereas alignment gaps are light blue. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)."
-},
-         "type" : "WebApollo/View/Track/DraggableAlignments",
-         "label" : "Bird Rock population (mapped reads)",
-         "key" : "Bird Rock population (mapped reads)"
-      },
-      {
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-         "urlTemplate" : "user_contributed_data/Tigriopus_californicus_i5k/FHL_to_SD_genome4_opt_15_merged_sort.bam",
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-"category" : "DNASeq/Mapped Reads",
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-	"Geographical location of specimen collection":"USA, Friday Harbor, 48°32'47”N, 123°0'35”W",
-	"Tissues included":"Pooled adult males and females",
-	"Sex":"Pooled",
-	"Sequencing platform and version":"Illumina HiSeq 200bp",
-	"Publication status":"Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
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-      },
-      {
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-"category" : "DNASeq/Mapped Reads",
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-	"Geographical location of specimen collection":"USA, Santa Cruz, 36°56’58”N, 122°02’49”W",
-	"Tissues included":"Pooled adult males and females",
-	"Sex":"Pooled",
-	"Sequencing platform and version":"Illumina HiSeq 200bp",
-	"Publication status":"Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
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-},
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-         "label" : "Santa Cruz population (mapped reads)",
-         "key" : "Santa Cruz population (mapped reads)"
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-	"Geographical location of specimen collection":"Mexico, San Roque, 27°11'12”N, 114°23'52”W",
-	"Tissues included":"Pooled adult males and females",
-	"Sex":"Pooled",
-	"Sequencing platform and version":"Illumina HiSeq 200bp",
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-	"Sequencing platform and version":"Illumina HiSeq 200bp",
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-	"Date completed":"4/15/14",
-	"Track legend":"This track represents a coverage plot of mapped reads. See track Santa Cruz population (mapped reads) for the corresponding alignments."
-},
-         "label" : "Santa Cruz population (Coverage Plots)",
-         "type" : "JBrowse/View/Track/Wiggle/XYPlot"
-      },
-      {
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-"category" : "DNASeq/Coverage Plots (BigWig)",
-"metadata" : {
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-	"Sex":"Pooled",
-	"Sequencing platform and version":"Illumina HiSeq 200bp",
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-	"Track legend":"This track represents a coverage plot of mapped reads. See track San Roque population (mapped reads) for the corresponding alignments."
-},
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-         "type" : "JBrowse/View/Track/Wiggle/XYPlot"
-      },
-      {
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-	"Sex":"Pooled",
-	"Sequencing platform and version":"Illumina HiSeq 200bp",
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-	"Date completed":"4/25/14",
-	"Track legend":"This track represents a coverage plot of mapped reads. See track Bodega Bay population (mapped reads) for the corresponding alignments."
-},
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-      },
-      {
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-         "urlTemplate" : "user_contributed_data/Tigriopus_californicus_i5k/BR_to_SD_genome4.flt.vcf.gz",
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-"category" : "DNASeq/Variant information",
-"metadata" : {
-	"Geographical location of specimen collection":"USA, Bird Rock, 32˚48’54”N, 117˚16’23”W",
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-	"Sex":"Pooled",
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-	"Analysis method":"samtools-0.1.19",
-	"Date completed":"10/14/15",
-	"Track legend":"Variant calls from the program samtools-0.1.19. Click on each SNP for more detailed information"
-},
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-"category" : "DNASeq/Variant information",
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-	"Date completed":"10/15/17",
-	"Track legend":"Variant calls from the program samtools-1.1. Click on each SNP for more detailed information"
-},
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-         "label" : "Catalina Island population (variant calls)",
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-      {
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-"category" : "DNASeq/Variant information",
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-	"File provider":"Thiago Lima, Scripps Institution of Oceanography",
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-	"Date completed":"2/15/17",
-	"Track legend":"Variant calls from the program samtools-1.1. Click on each SNP for more detailed information"
-},
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-"category" : "DNASeq/Variant information",
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-	"Sequencing platform and version":"Illumina HiSeq 200bp",
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-	"Date completed":"10/16/15",
-	"Track legend":"Variant calls from the program samtools-1.1. Click on each SNP for more detailed information"
-},
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-"category" : "DNASeq/Variant information",
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-	"Track legend":"Variant calls from the program samtools-1.1. Click on each SNP for more detailed information"
-},
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-         "type" : "JBrowse/View/Track/HTMLVariants",
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-"category" : "DNASeq/Variant information",
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-	"Sequencing platform and version":"Illumina HiSeq 200bp",
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-},
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-         "key" : "Friday Harbor population (variant calls)"
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-   ],
-   "names" : {
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+        "Analysis contact": "Felipe Bareto, Burton lab, SIO",
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+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
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+        "File provider": "Thiago Lima, Scripps Institution of Oceanography",
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+      "urlTemplate": "user_contributed_data/Tigriopus_californicus_i5k/BB_to_SD_genome4_opt_15_merged_sort.bam"
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+      "urlTemplate": "user_contributed_data/Tigriopus_californicus_i5k/BR_to_SD_genome4_opt_15_merged_sort.bam"
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+      "urlTemplate": "user_contributed_data/Tigriopus_californicus_i5k/SC_to_SD_genome4_opt_15_merged_sort.bam"
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+      "urlTemplate": "user_contributed_data/Tigriopus_californicus_i5k/CAT_to_SD_genome4.flt.vcf.gz"
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+      "label": "Bodega Bay population (variant calls)",
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+    },
+    {
+      "category": "DNASeq/Variant information",
+      "key": "San Roque population (variant calls)",
+      "label": "San Roque population (variant calls)",
+      "metadata": {
+        "Analysis method": "samtools-1.1",
+        "Date completed": "10/26/15",
+        "File provider": "Thiago Lima, Scripps Institution of Oceanography",
+        "Geographical location of specimen collection": "Mexico, San Roque, 27°11'12”N, 114°23'52”W",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Sequencing platform and version": "Illumina HiSeq 200bp",
+        "Sex": "Pooled",
+        "Tissues included": "Pooled adult males and females",
+        "Track legend": "Variant calls from the program samtools-1.1. Click on each SNP for more detailed information"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/VCFTabix",
+      "type": "JBrowse/View/Track/HTMLVariants",
+      "urlTemplate": "user_contributed_data/Tigriopus_californicus_i5k/SRQ_to_SD_genome4.flt.vcf.gz"
+    },
+    {
+      "category": "DNASeq/Variant information",
+      "key": "Friday Harbor population (variant calls)",
+      "label": "Friday Harbor population (variant calls)",
+      "metadata": {
+        "Analysis method": "samtools-1.1",
+        "Date completed": "10/26/15",
+        "File provider": "Thiago Lima, Scripps Institution of Oceanography",
+        "Geographical location of specimen collection": "USA, Friday Harbor, 48°32'47”N, 123°0'35”W",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Sequencing platform and version": "Illumina HiSeq 200bp",
+        "Sex": "Pooled",
+        "Tissues included": "Pooled adult males and females",
+        "Track legend": "Variant calls from the program samtools-1.1. Click on each SNP for more detailed information"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/VCFTabix",
+      "type": "JBrowse/View/Track/HTMLVariants",
+      "urlTemplate": "user_contributed_data/Tigriopus_californicus_i5k/FHL_to_SD_genome4.flt.vcf.gz"
+    }
+  ]
 }
diff --git a/organisms/stage/Tribolium_castaneum/trackList.json b/organisms/stage/Tribolium_castaneum/trackList.json
index 12eb2d9..1d7087a 100644
--- a/organisms/stage/Tribolium_castaneum/trackList.json
+++ b/organisms/stage/Tribolium_castaneum/trackList.json
@@ -1,439 +1,492 @@
 {
-   "css" : "./plugins/NAL_CSS/css/contrib_styles.css",
+   "alwaysOnTracks" : "DNA,Annotations",
+   "css" : "./plugins/NAL_CSS/css/main.css",
+   "favicon" : "./plugins/WebApollo/img/webapollo_favicon.ico",
+   "formatVersion" : 1,
+   "names" : {
+      "type" : "Hash",
+      "url" : "names/"
+   },
    "share_link" : 0,
-   "plugins" : [
-      {
-         "location" : "./plugins/WebApollo",
-         "name" : "WebApollo"
-      }
-   ],
    "tracks" : [
       {
-         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
+         "category" : "Reference sequence",
          "chunkSize" : 20000,
-         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-",
+         "key" : "Reference sequence",
          "label" : "DNA",
+         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
          "type" : "SequenceTrack",
-         "category" : "Reference sequence",
-         "key" : "Reference sequence"
+         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-"
       },
       {
          "autocomplete" : "none",
+         "compress" : 0,
+         "key" : "User-created Annotations",
+         "label" : "Annotations",
+         "phase" : 0,
+         "storeClass" : "WebApollo/Store/SeqFeature/ScratchPad",
          "style" : {
-            "className" : "annot",
-            "renderClassName" : "annot-render",
-            "subfeatureClasses" : {
-               "non_canonical_three_prime_splice_site" : "noncanonical-splice-site",
-               "wholeCDS" : null,
-               "exon" : "container-100pct",
-               "CDS" : "annot-CDS",
-               "non_canonical_five_prime_splice_site" : "noncanonical-splice-site",
-               "UTR" : "annot-UTR"
-            },
-            "arrowheadClass" : "annot-arrowhead",
             "alternateClasses" : {
-               "transposable_element" : {
-                  "renderClassName" : "blue-ibeam-render",
-                  "className" : "blue-ibeam"
+               "miRNA" : {
+                  "className" : "brightgreen-80pct",
+                  "renderClassName" : "gray-center-30pct"
                },
-               "pseudogene" : {
-                  "renderClassName" : "gray-center-30pct",
-                  "className" : "light-purple-80pct"
+               "ncRNA" : {
+                  "className" : "brightgreen-80pct",
+                  "renderClassName" : "gray-center-30pct"
                },
-               "snRNA" : {
-                  "renderClassName" : "gray-center-30pct",
-                  "className" : "brightgreen-80pct"
+               "pseudogene" : {
+                  "className" : "light-purple-80pct",
+                  "renderClassName" : "gray-center-30pct"
                },
                "rRNA" : {
-                  "renderClassName" : "gray-center-30pct",
-                  "className" : "brightgreen-80pct"
-               },
-               "snoRNA" : {
-                  "renderClassName" : "gray-center-30pct",
-                  "className" : "brightgreen-80pct"
+                  "className" : "brightgreen-80pct",
+                  "renderClassName" : "gray-center-30pct"
                },
                "repeat_region" : {
                   "className" : "magenta-80pct"
                },
-               "miRNA" : {
-                  "renderClassName" : "gray-center-30pct",
-                  "className" : "brightgreen-80pct"
+               "snRNA" : {
+                  "className" : "brightgreen-80pct",
+                  "renderClassName" : "gray-center-30pct"
+               },
+               "snoRNA" : {
+                  "className" : "brightgreen-80pct",
+                  "renderClassName" : "gray-center-30pct"
                },
                "tRNA" : {
-                  "renderClassName" : "gray-center-30pct",
-                  "className" : "brightgreen-80pct"
+                  "className" : "brightgreen-80pct",
+                  "renderClassName" : "gray-center-30pct"
                },
-               "ncRNA" : {
-                  "renderClassName" : "gray-center-30pct",
-                  "className" : "brightgreen-80pct"
+               "transposable_element" : {
+                  "className" : "blue-ibeam",
+                  "renderClassName" : "blue-ibeam-render"
                }
             },
-            "uniqueIdField" : "id",
+            "arrowheadClass" : "annot-arrowhead",
             "centerSubFeature" : {
-               "non_canonical_three_prime_splice_site" : false,
-               "non_canonical_five_prime_splice_site" : false
-            }
-         },
-         "key" : "User-created Annotations",
-         "storeClass" : "WebApollo/Store/SeqFeature/ScratchPad",
-         "phase" : 0,
-         "compress" : 0,
-         "label" : "Annotations",
-         "type" : "WebApollo/View/Track/AnnotTrack",
-         "subfeatures" : 1
-      },
-      {
-         "style" : {
-            "className" : "container-16px",
+               "non_canonical_five_prime_splice_site" : false,
+               "non_canonical_three_prime_splice_site" : false
+            },
+            "className" : "annot",
+            "renderClassName" : "annot-render",
             "subfeatureClasses" : {
-               "wholeCDS" : null,
+               "CDS" : "annot-CDS",
+               "UTR" : "annot-UTR",
                "exon" : "container-100pct",
-               "CDS" : "ogs-cds",
-               "UTR" : "ogs-utr"
+               "non_canonical_five_prime_splice_site" : "noncanonical-splice-site",
+               "non_canonical_three_prime_splice_site" : "noncanonical-splice-site",
+               "wholeCDS" : null
             },
-            "arrowheadClass" : "trellis-arrowhead",
-               "label": "DBXref, name,id"
+            "uniqueIdField" : "id"
          },
-         "key" : "Tribolium castaneum OGS_v3",
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
-         "trackType" : null,
-         "urlTemplate" : "tracks/tricas_current_models/{refseq}/trackData.json",
+         "subfeatures" : 1,
+         "type" : "WebApollo/View/Track/AnnotTrack"
+      },
+      {
+         "category" : "Official Gene Set v3/1. Gene Sets/Protein Coding",
          "compress" : 0,
-         "type" : "FeatureTrack",
+         "key" : "Tribolium castaneum OGS_v3",
          "label" : "tricas_current_models",
-         "category" : "Official Gene Set v3/1. Gene Sets/Protein Coding",
          "metadata" : {
             "Analysis method" : "AUGUSTUS 3.0.2",
-            "Data source" : "ftp://ftp.ncbi.nih.gov/genomes/all/GCA_000002335.3_Tcas5.2/GCA_000002335.3_Tcas5.2_genomic.gff.gz",
             "Analysis provider" : "Lizzy Gerischer and Mario Stanke, University of Greifswald",
+            "Data source" : "ftp://ftp.ncbi.nih.gov/genomes/all/GCA_000002335.3_Tcas5.2/GCA_000002335.3_Tcas5.2_genomic.gff.gz",
             "Date completed" : "03/11/16"
-         }
-      },
-      {
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "pos_color" : "black",
-            "neg_color" : "white"
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "{type}",
+            "label" : "DBXref, name,id",
+            "subfeatureClasses" : {
+               "CDS" : "ogs-cds",
+               "UTR" : "ogs-utr",
+               "exon" : "container-100pct",
+               "wholeCDS" : null
+            }
          },
-         "bicolor_pivot" : "zero",
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/tricas_current_models/{refseq}/trackData.json"
+      },
+      {
          "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Reference Assembly",
          "key" : "Gaps in assembly",
-         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
-         "urlTemplate" : "bigwig/GCF_000002335.3_Tcas5.2_genomic_RefSeqIDs.fna.gaps.bigwig",
          "label" : "Gaps in assembly",
-         "category" : "Reference Assembly",
          "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
             "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
-            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank",
-            "Track contact" : "The i5k workspace@NAL"
+            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
          },
-         "type" : "JBrowse/View/Track/Wiggle/Density"
-      },
-      {
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
          "style" : {
-            "neg_color" : "rgba(255,255,0,50)",
-            "pos_color" : "rgba(0,0,255,50)"
+            "neg_color" : "white",
+            "pos_color" : "black"
          },
-         "bicolor_pivot" : "0.5",
-         "key" : "GC Content",
-         "scoreType": "avgScore",
-         "autoscale" : "local",
-         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
-         "urlTemplate" : "bigwig/GCF_000002335.3_Tcas5.2_genomic_RefSeqIDs.fna.gc.bigwig",
          "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/GCF_000002335.3_Tcas5.2_genomic_RefSeqIDs.fna.gaps.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "0.5",
          "category" : "Reference Assembly",
+         "key" : "GC Content",
          "label" : "GC Content",
          "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
             "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
-            "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track.",
-            "Track contact" : "The i5k workspace@NAL"
-         }
-      },
-      {
+            "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+         },
+         "scoreType" : "avgScore",
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
          "style" : {
-            "className" : "container-16px",
-            "subfeatureClasses" : {
-               "wholeCDS" : null,
-               "exon" : "container-100pct",
-               "CDS" : "gnomon_CDS",
-               "UTR" : "gnomon_UTR"
-            },
-            "arrowheadClass" : "trellis-arrowhead"
+            "neg_color" : "rgba(255,255,0,50)",
+            "pos_color" : "rgba(0,0,255,50)"
          },
-         "key" : "NCBI Predicted protein coding genes, Annotation Release 103",
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
-         "trackType" : null,
-         "urlTemplate" : "tracks/NCBI_Annotation_Release_103_Protein_Coding_high_quality/{refseq}/trackData.json",
+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/GCF_000002335.3_Tcas5.2_genomic_RefSeqIDs.fna.gc.bigwig"
+      },
+      {
+         "category" : "NCBI Annotation Release 103/1. Gene Sets/Protein Coding",
          "compress" : 0,
+         "key" : "NCBI Predicted protein coding genes, Annotation Release 103",
+         "label" : "NCBI_Annotation_Release_103_Protein_Coding_high_quality",
          "metadata" : {
-            "Data source" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF_000002335.3_Tcas5.2/GCF_000002335.3_Tcas5.2_genomic.gff.gz",
-            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/",
+            "Data description" : "ftp://ftp.ncbi.nih.gov/genomes/all/GCF_000002335.3_Tcas5.2/README.txt",
             "Data provider" : "NCBI",
-            "Data description" : "ftp://ftp.ncbi.nih.gov/genomes/all/GCF_000002335.3_Tcas5.2/README.txt"
+            "Data source" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF_000002335.3_Tcas5.2/GCF_000002335.3_Tcas5.2_genomic.gff.gz",
+            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
          },
-         "type" : "FeatureTrack",
-         "category" : "NCBI Annotation Release 103/1. Gene Sets/Protein Coding",
-         "label" : "NCBI_Annotation_Release_103_Protein_Coding_high_quality"
-      },
-      {
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "className" : "container-16px",
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "{type}",
             "subfeatureClasses" : {
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-               "exon" : "container-100pct",
                "CDS" : "gnomon_CDS",
-               "UTR" : "gnomon_UTR"
-            },
-            "arrowheadClass" : "trellis-arrowhead"
+               "UTR" : "gnomon_UTR",
+               "exon" : "container-100pct",
+               "wholeCDS" : null
+            }
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-         "key" : "NCBI Predicted low-quality protein coding genes, Annotation Release 103",
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "trackType" : null,
-         "urlTemplate" : "tracks/NCBI_Annotation_Release_103_Protein_Coding_low_quality/{refseq}/trackData.json",
-         "compress" : 0,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/NCBI_Annotation_Release_103_Protein_Coding_high_quality/{refseq}/trackData.json"
+      },
+      {
          "category" : "NCBI Annotation Release 103/1. Gene Sets/Protein Coding",
+         "compress" : 0,
+         "key" : "NCBI Predicted low-quality protein coding genes, Annotation Release 103",
          "label" : "NCBI_Annotation_Release_103_Protein_Coding_low_quality",
-         "type" : "FeatureTrack",
          "metadata" : {
-            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/",
-            "Data source" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF_000002335.3_Tcas5.2/GCF_000002335.3_Tcas5.2_genomic.gff.gz",
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+            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "className" : "container-16px",
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "{type}",
             "subfeatureClasses" : {
-               "wholeCDS" : null,
-               "exon" : "container-100pct",
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-               "UTR" : "gnomon_UTR"
-            },
-            "arrowheadClass" : "trellis-arrowhead"
+               "UTR" : "gnomon_UTR",
+               "exon" : "container-100pct",
+               "wholeCDS" : null
+            }
          },
-         "key" : "NCBI Predicted protein coding genes, mtDNA, Annotation Release 103",
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          "trackType" : null,
-         "urlTemplate" : "tracks/NCBI_Annotation_Release_103_Protein_Coding_mtDNA/{refseq}/trackData.json",
-         "compress" : 0,
          "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/NCBI_Annotation_Release_103_Protein_Coding_low_quality/{refseq}/trackData.json"
+      },
+      {
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+         "compress" : 0,
+         "key" : "NCBI Predicted protein coding genes, mtDNA, Annotation Release 103",
+         "label" : "NCBI_Annotation_Release_103_Protein_Coding_mtDNA",
          "metadata" : {
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-            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/",
+            "Data description" : "ftp://ftp.ncbi.nih.gov/genomes/all/GCF_000002335.3_Tcas5.2/README.txt",
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+            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
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-         "category" : "NCBI Annotation Release 103/1. Gene Sets/Protein Coding"
-      },
-      {
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
-            "className" : "container-16px",
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "{type}",
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                "CDS" : "gnomon_CDS",
-               "UTR" : "gnomon_UTR"
-            },
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+               "UTR" : "gnomon_UTR",
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+            }
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-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "trackType" : null,
-         "urlTemplate" : "tracks/NCBI_Annotation_Release_103_lncRNA/{refseq}/trackData.json",
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/NCBI_Annotation_Release_103_Protein_Coding_mtDNA/{refseq}/trackData.json"
+      },
+      {
+         "category" : "NCBI Annotation Release 103/1. Gene Sets/Noncoding",
          "compress" : 0,
+         "key" : "NCBI Predicted lncRNA, Annotation Release 103",
          "label" : "NCBI_Annotation_Release_103_lncRNA",
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          "metadata" : {
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-            "Data source" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF_000002335.3_Tcas5.2/GCF_000002335.3_Tcas5.2_genomic.gff.gz",
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+            "Data source" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF_000002335.3_Tcas5.2/GCF_000002335.3_Tcas5.2_genomic.gff.gz",
+            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
          },
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-      },
-      {
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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-            "className" : "container-16px",
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "{type}",
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                "CDS" : "gnomon_CDS",
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+               "UTR" : "gnomon_UTR",
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+               "wholeCDS" : null
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-         "key" : "NCBI Predicted miscRNA, Annotation Release 103",
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "trackType" : null,
-         "urlTemplate" : "tracks/NCBI_Annotation_Release_103_miscRNA/{refseq}/trackData.json",
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/NCBI_Annotation_Release_103_lncRNA/{refseq}/trackData.json"
+      },
+      {
+         "category" : "NCBI Annotation Release 103/1. Gene Sets/Noncoding",
          "compress" : 0,
+         "key" : "NCBI Predicted miscRNA, Annotation Release 103",
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diff --git a/organisms/stage/Tribolium_madens/trackList.json b/organisms/stage/Tribolium_madens/trackList.json
new file mode 100644
index 0000000..48bba9f
--- /dev/null
+++ b/organisms/stage/Tribolium_madens/trackList.json
@@ -0,0 +1,568 @@
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+            "Data source" : "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/002/335/GCA_000002335.3_Tcas5.2/GCA_000002335.3_Tcas5.2_rna_from_genomic.fna.gz",
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diff --git a/organisms/stage/Trichogramma_pretiosum/trackList.json b/organisms/stage/Trichogramma_pretiosum/trackList.json
index 0a52768..40a6cc8 100644
--- a/organisms/stage/Trichogramma_pretiosum/trackList.json
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+        "Track legend": "Results from Blastx alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline."
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+      "label": "protein2genome_Crustacea",
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+        "Track legend": "Results from Protein2genome alignments of a set of Crustacea proteins as part of the MAKER automated annotation pipeline."
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+      "key": "protein2genome_Echinodermata",
+      "label": "protein2genome_Echinodermata",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline."
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-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
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+      "key": "protein2genome_Placozoa",
+      "label": "protein2genome_Placozoa",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline."
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+        "arrowheadClass": "webapollo-arrowhead",
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-        "Track legend" : "Results from Protein2genome alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline.",
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-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
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+      "key": "protein2genome_Platyhelminthes",
+      "label": "protein2genome_Platyhelminthes",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline."
+      },
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-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
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+      "key": "protein2genome_Priapulida",
+      "label": "protein2genome_Priapulida",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline."
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+        "arrowheadClass": "webapollo-arrowhead",
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-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
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+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Tardigrada",
+      "label": "protein2genome_Tardigrada",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
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+        "arrowheadClass": "webapollo-arrowhead",
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-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
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+      "key": "protein2genome_Tunicata",
+      "label": "protein2genome_Tunicata",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline."
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+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
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+        "arrowheadClass": "webapollo-arrowhead",
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-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
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+      "key": "protein2genome_UNCATEGORISED",
+      "label": "protein2genome_UNCATEGORISED",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
+    {
+      "category": "BCM_v0.5.3/2. Evidence/Repeats",
+      "compress": 0,
+      "key": "repeatmasker",
+      "label": "repeatmasker",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from RepeatMasker as part of the MAKER automated annotation pipeline."
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+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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+      "type": "FeatureTrack",
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-	 "category" : "BCM_v0.5.3/2. Evidence/Repeats",
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-        "Track legend" : "Results from RepeatMasker as part of the MAKER automated annotation pipeline.",
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
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-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
+    {
+      "category": "BCM_v0.5.3/2. Evidence/Repeats",
+      "compress": 0,
+      "key": "repeatrunner",
+      "label": "repeatrunner",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Repeatrunner as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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+      "type": "FeatureTrack",
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-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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-            "arrowheadClass" : "webapollo-arrowhead"
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-	 "category" : "BCM_v0.5.3/2. Evidence/Repeats",
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-        "Track legend" : "Results from Repeatrunner as part of the MAKER automated annotation pipeline.",
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
+    {
+      "category": "BCM_v0.5.3/1. Gene Sets/Supplementary Gene Predictions",
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+      "key": "snap_masked",
+      "label": "snap_masked",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
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-
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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-	 "category" : "BCM_v0.5.3/1. Gene Sets/Supplementary Gene Predictions",
-	        "metadata" : {
-        "Track legend" : "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline.",
-        "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
-        "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
-        "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Reference Assembly",
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+      "label": "Gaps in assembly",
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+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
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+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "white",
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+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "bigwig/Tpre_FINAL.GAPS.bigwig"
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-         "label" : "snap_masked"
-      },
-      {
-         "style" : {
-            "pos_color" : "black",
-            "neg_color" : "white"
-         },
-         "bicolor_pivot" : "zero",
-         "autoscale" : "local",
-	 "category" : "Reference Assembly",
-	        "metadata" : {
-        "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank",
-        "Track contact" : "The i5k workspace@NAL",
-        "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
-},
-         "key" : "Gaps in assembly",
-
-
-         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
-         "urlTemplate" : "bigwig/Tpre_FINAL.GAPS.bigwig",
-         "label" : "Gaps in assembly",
-         "type" : "JBrowse/View/Track/Wiggle/Density"
-      },
-      {
-         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
-         "urlTemplate" : "bigwig/Tpre_FINAL.scaffolds_GC.bigwig",
-         "style" : {
-            "neg_color" : "rgba(255,255,0,50)",
-            "pos_color" : "rgba(0,0,255,50)"
-         },
-         "label" : "GC Content",
-         "type" : "JBrowse/View/Track/Wiggle/Density",
-         "bicolor_pivot" : "0.5",
-	 "category" : "Reference Assembly",
-           "metadata" : {
-        "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track.",
-        "Track contact" : "The i5k workspace@NAL",
-        "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
-},
-         "key" : "GC Content",
-         "scoreType": "avgScore",
-
-
-         "autoscale" : "local"
-      }
-   ],
-   "names" : {
-      "url" : "names/",
-      "type" : "Hash"
-   },
-   "favicon" : "./plugins/WebApollo/img/webapollo_favicon.ico",
-   "alwaysOnTracks" : "DNA,Annotations",
-   "formatVersion" : 1
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "0.5",
+      "category": "Reference Assembly",
+      "key": "GC Content",
+      "label": "GC Content",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+      },
+      "scoreType": "avgScore",
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "rgba(255,255,0,50)",
+        "pos_color": "rgba(0,0,255,50)"
+      },
+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "bigwig/Tpre_FINAL.scaffolds_GC.bigwig"
+    }
+  ]
 }
diff --git a/organisms/stage/Varroa_destructor/trackList.json b/organisms/stage/Varroa_destructor/trackList.json
index ad1013a..758cd0f 100644
--- a/organisms/stage/Varroa_destructor/trackList.json
+++ b/organisms/stage/Varroa_destructor/trackList.json
@@ -46,6 +46,7 @@
             "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
             "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
          },
+         "scoreType" : "avgScore",
          "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
          "style" : {
             "neg_color" : "rgba(255,255,0,50)",
@@ -68,7 +69,7 @@
          "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
             "arrowheadClass" : "trellis-arrowhead",
-            "className" : "container-16px",
+            "className" : "{type}",
             "description" : "product, note, description",
             "subfeatureClasses" : {
                "CDS" : "gnomon_CDS",
@@ -95,7 +96,7 @@
          "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
             "arrowheadClass" : "trellis-arrowhead",
-            "className" : "container-16px",
+            "className" : "{type}",
             "description" : "product, note, description",
             "subfeatureClasses" : {
                "CDS" : "gnomon_CDS",
@@ -104,9 +105,68 @@
                "wholeCDS" : null
             }
          },
-         "trackType" : "ColorByType/View/Track/ColorByTypeDraggable",
-         "type" : "ColorByType/View/Track/ColorByTypeDraggable",
+         "trackType" : "HTMLFeatures",
+         "type" : "HTMLFeatures",
          "urlTemplate" : "tracks/NCBI_Annotation_Release_100_Gene/{refseq}/trackData.json"
+      },
+      {
+         "category" : "RNA-Seq/Mapped Reads",
+         "key" : "Vardes_Vdes_3.0_RNA-Seq-alignments_2021-07-03",
+         "label" : "Vardes_Vdes_3.0_RNA-Seq-alignments_2021-07-03",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR5760837'>SRR5760837</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR5377264'>SRR5377264</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11624168'>SRR11624168</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR6824277'>SRR6824277</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR12215902'>SRR12215902</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR12108023'>SRR12108023</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR12215913'>SRR12215913</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR5377266'>SRR5377266</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR12108022'>SRR12108022</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR5377269'>SRR5377269</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Dark red alignments: Mapped portion of read aligned to forward strand<br>Light red alignments: Spliced portion of read aligned to forward strand<br>Dark blue alignments: Mapped portion of read aligned to reverse strand<br>Light blue alignments: Spliced portion of read aligned to reverse strand<br>Red marking - deletion in the read relative to the reference<br>Green marking - insertion in the read relative to the reference<br>Yellow marking  - mismatch (hover over the mismatch to see what the snp is)"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "unsafePopup" : true,
+         "urlTemplate" : "analyses/Varroa-destructor-RNA-Seq_2021-07-03_v1.0/Vardes_Vdes_3.0_RNA-Seq-alignments_2021-07-03.bam"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "RNA-Seq/Coverage Plots",
+         "key" : "Vardes_Vdes_3.0_RNA-Seq-alignments_2021-07-03_coverage",
+         "label" : "Vardes_Vdes_3.0_RNA-Seq-alignments_2021-07-03_coverage",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR5760837'>SRR5760837</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR5377264'>SRR5377264</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11624168'>SRR11624168</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR6824277'>SRR6824277</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR12215902'>SRR12215902</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR12108023'>SRR12108023</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR12215913'>SRR12215913</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR5377266'>SRR5377266</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR12108022'>SRR12108022</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR5377269'>SRR5377269</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "unsafePopup" : true,
+         "urlTemplate" : "analyses/Varroa-destructor-RNA-Seq_2021-07-03_v1.0/Vardes_Vdes_3.0_RNA-Seq-alignments_2021-07-03.bigwig"
+      },
+      {
+         "category" : "RNA-Seq/Splice junctions",
+         "compress" : 0,
+         "key" : "Vardes_Vdes_3.0_RNA-Seq-alignments_2021-07-03_junctions",
+         "label" : "Vardes_Vdes_3.0_RNA-Seq-alignments_2021-07-03_junctions",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR5760837'>SRR5760837</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR5377264'>SRR5377264</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11624168'>SRR11624168</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR6824277'>SRR6824277</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR12215902'>SRR12215902</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR12108023'>SRR12108023</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR12215913'>SRR12215913</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR5377266'>SRR5377266</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR12108022'>SRR12108022</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR5377269'>SRR5377269</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Junction reads generated by Hisat2 aligner and regtools. The number of alignments supporting the junction read is listed in blue."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "className" : "feature",
+            "description" : "score"
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "unsafePopup" : true,
+         "urlTemplate" : "tracks/Vardes_Vdes_3.0_RNA-Seq-alignments_2021-07-03_junctions/{refseq}/trackData.json"
       }
    ]
 }
diff --git a/organisms/stage/Varroa_jacobsoni/trackList.json b/organisms/stage/Varroa_jacobsoni/trackList.json
index d10b760..bc56f73 100644
--- a/organisms/stage/Varroa_jacobsoni/trackList.json
+++ b/organisms/stage/Varroa_jacobsoni/trackList.json
@@ -60,28 +60,28 @@
          "key" : "NCBI_Annotation_Release_100_Gene",
          "label" : "varjac_current_models",
          "menuTemplate" : [
-             {
-                "label" : "View details",
-             },
-             {
-              "label": "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
-              "title": "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
-              "iconClass" : "dijitIconDatabase",
-              "action": "newWindow",
-              "url" : "function(track,feature){ return 'https://i5k.nal.usda.gov/search/site/'+feature.get('name')}",
-              },
-        ],
+            {
+               "label" : "View details"
+            },
+            {
+               "action" : "newWindow",
+               "iconClass" : "dijitIconDatabase",
+               "label" : "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
+               "title" : "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
+               "url" : "function(track,feature){ return 'https://www.ncbi.nlm.nih.gov/nuccore/'+feature.get('name')}"
+            }
+         ],
          "metadata" : {
-            "Publication status" : "Unpublished, please refer to Fort Lauderdale/Toronto conditions of data re-use",
             "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Varroa_jacobsoni/README_CURRENT_RELEASE",
             "Data provider" : "NCBI",
             "Data source" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/532/875/GCF_002532875.1_vjacob_1.0/GCF_002532875.1_vjacob_1.0_genomic.gff.gz",
-            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
+            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/",
+            "Publication status" : "Unpublished, please refer to Fort Lauderdale/Toronto conditions of data re-use"
          },
          "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
             "arrowheadClass" : "trellis-arrowhead",
-            "className" : "container-16px",
+            "className" : "{type}",
             "description" : "product, note, description",
             "subfeatureClasses" : {
                "CDS" : "gnomon_CDS",
@@ -90,8 +90,8 @@
                "wholeCDS" : null
             }
          },
-         "trackType" : "ColorByType/View/Track/ColorByTypeDraggable",
-         "type" : "ColorByType/View/Track/ColorByTypeDraggable",
+         "trackType" : "HTMLFeatures",
+         "type" : "HTMLFeatures",
          "urlTemplate" : "tracks/varjac_current_models/{refseq}/trackData.json"
       },
       {
@@ -100,16 +100,16 @@
          "key" : "NCBI_Annotation_Release_100_Pseudogene",
          "label" : "NCBI_Annotation_Release_100_Pseudogene",
          "metadata" : {
-            "Publication status" : "Unpublished, please refer to Fort Lauderdale/Toronto conditions of data re-use",
             "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Varroa_jacobsoni/README_CURRENT_RELEASE",
             "Data provider" : "NCBI",
             "Data source" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/532/875/GCF_002532875.1_vjacob_1.0/GCF_002532875.1_vjacob_1.0_genomic.gff.gz",
-            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
+            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/",
+            "Publication status" : "Unpublished, please refer to Fort Lauderdale/Toronto conditions of data re-use"
          },
          "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
             "arrowheadClass" : "trellis-arrowhead",
-            "className" : "container-16px",
+            "className" : "{type}",
             "description" : "product, note, description",
             "subfeatureClasses" : {
                "CDS" : "gnomon_CDS",
@@ -121,6 +121,65 @@
          "trackType" : "HTMLFeatures",
          "type" : "HTMLFeatures",
          "urlTemplate" : "tracks/NCBI_Annotation_Release_100_Pseudogene/{refseq}/trackData.json"
+      },
+      {
+         "category" : "RNA-Seq/Mapped Reads",
+         "key" : "Varjac_vjacob_1.0_RNA-Seq-alignments_2021-06-19",
+         "label" : "Varjac_vjacob_1.0_RNA-Seq-alignments_2021-06-19",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR3634929'>SRR3634929</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR3634700'>SRR3634700</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR3632582'>SRR3632582</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR3634772'>SRR3634772</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR3633003'>SRR3633003</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR3635001'>SRR3635001</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11879881'>SRR11879881</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11879882'>SRR11879882</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR3635050'>SRR3635050</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR3635105'>SRR3635105</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Dark red alignments: Mapped portion of read aligned to forward strand<br>Light red alignments: Spliced portion of read aligned to forward strand<br>Dark blue alignments: Mapped portion of read aligned to reverse strand<br>Light blue alignments: Spliced portion of read aligned to reverse strand<br>Red marking - deletion in the read relative to the reference<br>Green marking - insertion in the read relative to the reference<br>Yellow marking  - mismatch (hover over the mismatch to see what the snp is)"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "unsafePopup" : true,
+         "urlTemplate" : "analyses/Varroa-jacobsoni-RNA-Seq_2021-06-19_v1.0/Varjac_vjacob_1.0_RNA-Seq-alignments_2021-06-19.bam"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "RNA-Seq/Coverage Plots",
+         "key" : "Varjac_vjacob_1.0_RNA-Seq-alignments_2021-06-19_coverage",
+         "label" : "Varjac_vjacob_1.0_RNA-Seq-alignments_2021-06-19_coverage",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR3634929'>SRR3634929</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR3634700'>SRR3634700</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR3632582'>SRR3632582</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR3634772'>SRR3634772</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR3633003'>SRR3633003</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR3635001'>SRR3635001</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11879881'>SRR11879881</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11879882'>SRR11879882</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR3635050'>SRR3635050</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR3635105'>SRR3635105</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "unsafePopup" : true,
+         "urlTemplate" : "analyses/Varroa-jacobsoni-RNA-Seq_2021-06-19_v1.0/Varjac_vjacob_1.0_RNA-Seq-alignments_2021-06-19.bigwig"
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+         "compress" : 0,
+         "key" : "Varjac_vjacob_1.0_RNA-Seq-alignments_2021-06-19_junctions",
+         "label" : "Varjac_vjacob_1.0_RNA-Seq-alignments_2021-06-19_junctions",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR3634929'>SRR3634929</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR3634700'>SRR3634700</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR3632582'>SRR3632582</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR3634772'>SRR3634772</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR3633003'>SRR3633003</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR3635001'>SRR3635001</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11879881'>SRR11879881</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11879882'>SRR11879882</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR3635050'>SRR3635050</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR3635105'>SRR3635105</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Junction reads generated by Hisat2 aligner and regtools. The number of alignments supporting the junction read is listed in blue."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "className" : "feature",
+            "description" : "score"
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "unsafePopup" : true,
+         "urlTemplate" : "tracks/Varjac_vjacob_1.0_RNA-Seq-alignments_2021-06-19_junctions/{refseq}/trackData.json"
       }
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 }
diff --git a/organisms/stage/Venturia_canescens/trackList.json b/organisms/stage/Venturia_canescens/trackList.json
new file mode 100644
index 0000000..b684238
--- /dev/null
+++ b/organisms/stage/Venturia_canescens/trackList.json
@@ -0,0 +1,219 @@
+{
+   "formatVersion" : 1,
+   "names" : {
+      "type" : "Hash",
+      "url" : "names/"
+   },
+   "tracks" : [
+      {
+         "category" : "Reference sequence",
+         "chunkSize" : 20000,
+         "key" : "Reference sequence",
+         "label" : "DNA",
+         "seqType" : "dna",
+         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
+         "type" : "SequenceTrack",
+         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-"
+      },
+      {
+         "category" : "NCBI Annotation Release 100",
+         "compress" : 0,
+         "key" : "NCBI_Annotation_Release_100_Gene",
+         "label" : "vencan_current_models",
+         "menuTemplate" : [
+            {
+               "label" : "View details"
+            },
+            {
+               "action" : "newWindow",
+               "iconClass" : "dijitIconDatabase",
+               "label" : "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
+               "title" : "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
+               "url" : "function(track,feature){ return 'https://www.ncbi.nlm.nih.gov/nuccore/'+feature.get('name')}"
+            }
+         ],
+         "metadata" : {
+            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Venturia_canescens/README_CURRENT_RELEASE",
+            "Data provider" : "NCBI",
+            "Data source" : "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/019/457/755/GCF_019457755.1_ASM1945775v1/GCF_019457755.1_ASM1945775v1_genomic.gff.gz",
+            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "container-16px",
+            "description" : "product, note, description",
+            "subfeatureClasses" : {
+               "CDS" : "gnomon_CDS",
+               "UTR" : "gnomon_UTR",
+               "exon" : "container-100pct",
+               "wholeCDS" : null
+            }
+         },
+         "trackType" : "HTMLFeatures",
+         "type" : "HTMLFeatures",
+         "urlTemplate" : "tracks/vencan_current_models/{refseq}/trackData.json"
+      },
+      {
+         "category" : "NCBI Annotation Release 100",
+         "compress" : 0,
+         "key" : "NCBI_Annotation_Release_100_Pseudogene",
+         "label" : "NCBI_Annotation_Release_100_Pseudogene",
+         "metadata" : {
+            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Venturia_canescens/README_CURRENT_RELEASE",
+            "Data provider" : "NCBI",
+            "Data source" : "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/019/457/755/GCF_019457755.1_ASM1945775v1/GCF_019457755.1_ASM1945775v1_genomic.gff.gz",
+            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "container-16px",
+            "description" : "product, note, description",
+            "subfeatureClasses" : {
+               "CDS" : "gnomon_CDS",
+               "UTR" : "gnomon_UTR",
+               "exon" : "container-100pct",
+               "wholeCDS" : null
+            }
+         },
+         "trackType" : "HTMLFeatures",
+         "type" : "HTMLFeatures",
+         "urlTemplate" : "tracks/NCBI_Annotation_Release_100_Pseudogene/{refseq}/trackData.json"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Reference Assembly",
+         "key" : "Gaps in assembly",
+         "label" : "Gaps in assembly",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "white",
+            "pos_color" : "black"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/GCF_019457755.1_ASM1945775v1_genomic.fna.gaps.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "0.5",
+         "category" : "Reference Assembly",
+         "key" : "GC Content",
+         "label" : "GC Content",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+         },
+         "scoreType" : "avgScore",
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "rgba(255,255,0,50)",
+            "pos_color" : "rgba(0,0,255,50)"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/GCF_019457755.1_ASM1945775v1_genomic.fna.gc.bigwig"
+      },
+      {
+         "category" : "RNA-Seq/Mapped Reads",
+         "key" : "Vencan_ASM1945775v1_RNA-Seq-alignments_2021-09-27",
+         "label" : "Vencan_ASM1945775v1_RNA-Seq-alignments_2021-09-27",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR8354707'>SRR8354707</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR8354715'>SRR8354715</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR8354705'>SRR8354705</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR14772628'>SRR14772628</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR8354708'>SRR8354708</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR8354711'>SRR8354711</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR14772631'>SRR14772631</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=ERR791800'>ERR791800</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR8354702'>SRR8354702</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR8354698'>SRR8354698</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Dark red alignments: Mapped portion of read aligned to forward strand<br>Light red alignments: Spliced portion of read aligned to forward strand<br>Dark blue alignments: Mapped portion of read aligned to reverse strand<br>Light blue alignments: Spliced portion of read aligned to reverse strand<br>Red marking - deletion in the read relative to the reference<br>Green marking - insertion in the read relative to the reference<br>Yellow marking  - mismatch (hover over the mismatch to see what the snp is)"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "analyses/Venturia-canescens-RNA-Seq_2021-09-27_v1.0/Vencan_ASM1945775v1_RNA-Seq-alignments_2021-09-27.bam"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "RNA-Seq/Coverage Plots",
+         "key" : "Vencan_ASM1945775v1_RNA-Seq-alignments_2021-09-27_coverage",
+         "label" : "Vencan_ASM1945775v1_RNA-Seq-alignments_2021-09-27_coverage",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR8354707'>SRR8354707</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR8354715'>SRR8354715</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR8354705'>SRR8354705</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR14772628'>SRR14772628</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR8354708'>SRR8354708</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR8354711'>SRR8354711</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR14772631'>SRR14772631</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=ERR791800'>ERR791800</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR8354702'>SRR8354702</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR8354698'>SRR8354698</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "analyses/Venturia-canescens-RNA-Seq_2021-09-27_v1.0/Vencan_ASM1945775v1_RNA-Seq-alignments_2021-09-27.bigwig"
+      },
+      {
+         "category" : "RNA-Seq/Splice junctions",
+         "compress" : 0,
+         "key" : "Vencan_ASM1945775v1_RNA-Seq-alignments_2021-09-27_junctions",
+         "label" : "Vencan_ASM1945775v1_RNA-Seq-alignments_2021-09-27_junctions",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR8354707'>SRR8354707</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR8354715'>SRR8354715</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR8354705'>SRR8354705</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR14772628'>SRR14772628</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR8354708'>SRR8354708</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR8354711'>SRR8354711</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR14772631'>SRR14772631</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=ERR791800'>ERR791800</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR8354702'>SRR8354702</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR8354698'>SRR8354698</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Junction reads generated by Hisat2 aligner and regtools. The number of alignments supporting the junction read is listed in blue."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "className" : "feature",
+            "description" : "score",
+            "subfeatureClasses" : {
+               "CDS" : "junction-cds",
+               "UTR" : "webapollo-UTR",
+               "exon" : "container-100pct",
+               "intron" : null,
+               "match_part" : "darkblue-80pct",
+               "start_codon" : null,
+               "stop_codon" : null,
+               "wholeCDS" : null
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/Vencan_ASM1945775v1_RNA-Seq-alignments_2021-09-27_junctions/{refseq}/trackData.json"
+      },
+      {
+         "category" : "Community annotations",
+         "compress" : 0,
+         "key" : "Venturia_canescens_community_annotations-JAHMHP000000000",
+         "label" : "Venturia_canescens_community_annotations-JAHMHP000000000",
+         "metadata" : {
+            "Analysis method" : "manual curation",
+            "Analysis provider" : "Gaelen Burke and Meng Mao, University of Georgia",
+            "Data source" : "<a href=https://www.ncbi.nlm.nih.gov/protein?LinkName=nuccore_protein_wgs&from_uid=2076936269>https://www.ncbi.nlm.nih.gov/protein?LinkName=nuccore_protein_wgs&from_uid=2076936269</a>",
+            "Publication status" : "unpublished",
+            "Track legend" : "This track represents manual curation of NCBI Venturia canescens Annotation Release 100, released under NCBI WGS accession number JAHMHP000000000"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "container-16px",
+            "description" : "product,description,curator_note",
+            "subfeatureClasses" : {
+               "CDS" : "gnomon_CDS",
+               "UTR" : "gnomon_UTR",
+               "exon" : "container-100pct",
+               "wholeCDS" : null
+            }
+         },
+         "trackType" : "HTMLFeatures",
+         "type" : "HTMLFeatures",
+         "unsafePopup" : true,
+         "urlTemplate" : "tracks/Venturia_canescens_community_annotations-JAHMHP000000000/{refseq}/trackData.json"
+      }
+   ]
+}
diff --git a/organisms/stage/make_dir_and_cp_files_08_2022.sh b/organisms/stage/make_dir_and_cp_files_08_2022.sh
new file mode 100644
index 0000000..560f853
--- /dev/null
+++ b/organisms/stage/make_dir_and_cp_files_08_2022.sh
@@ -0,0 +1,142 @@
+mkdir 10_-_Onthophagus_taurus_training; cd 10_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 11_-_Onthophagus_taurus_training; cd 11_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 12_-_Onthophagus_taurus_training; cd 12_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 13_-_Onthophagus_taurus_training; cd 13_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 14_-_Onthophagus_taurus_training; cd 14_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 15_-_Onthophagus_taurus_training; cd 15_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 16_-_Onthophagus_taurus_training; cd 16_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 17_-_Onthophagus_taurus_training; cd 17_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 18_-_Onthophagus_taurus_training; cd 18_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 19_-_Onthophagus_taurus_training; cd 19_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 1_-_Onthophagus_taurus_training; cd 1_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 20_-_Onthophagus_taurus_training; cd 20_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 21_-_Onthophagus_taurus_training; cd 21_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 22_-_Onthophagus_taurus_training; cd 22_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 23_-_Onthophagus_taurus_training; cd 23_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 24_-_Onthophagus_taurus_training; cd 24_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 25_-_Onthophagus_taurus_training; cd 25_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 26_-_Onthophagus_taurus_training; cd 26_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 27_-_Onthophagus_taurus_training; cd 27_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 28_-_Onthophagus_taurus_training; cd 28_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 29_-_Onthophagus_taurus_training; cd 29_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 2_-_Onthophagus_taurus_training; cd 2_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 30_-_Onthophagus_taurus_training; cd 30_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 31_-_Onthophagus_taurus_training; cd 31_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 32_-_Onthophagus_taurus_training; cd 32_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 33_-_Onthophagus_taurus_training; cd 33_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 34_-_Onthophagus_taurus_training; cd 34_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 35_-_Onthophagus_taurus_training; cd 35_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 36_-_Onthophagus_taurus_training; cd 36_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 37_-_Onthophagus_taurus_training; cd 37_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 38_-_Onthophagus_taurus_training; cd 38_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 39_-_Onthophagus_taurus_training; cd 39_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 3_-_Onthophagus_taurus_training; cd 3_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 40_-_Onthophagus_taurus_training; cd 40_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 4_-_Onthophagus_taurus_training; cd 4_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 5_-_Onthophagus_taurus_training; cd 5_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 6_-_Onthophagus_taurus_training; cd 6_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 7_-_Onthophagus_taurus_training; cd 7_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 8_-_Onthophagus_taurus_training; cd 8_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 9_-_Onthophagus_taurus_training; cd 9_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir Aethina_tumida; cd Aethina_tumida; cp /app/data/other_species/aettum/jbrowse/data/trackList.json .; cd .. 
+mkdir Agrilus_planipennis; cd Agrilus_planipennis; cp /app/data/BCM_i5k_pilot/agrpla/jbrowse/data/trackList.json .; cd .. 
+mkdir Amyelois_transitella; cd Amyelois_transitella; cp /app/data/other_species/amytra/jbrowse/data/trackList.json .; cd .. 
+mkdir Anoplophora_glabripennis; cd Anoplophora_glabripennis; cp /app/data/BCM_i5k_pilot/anogla/BCM/jbrowse/data/trackList.json .; cd .. 
+mkdir Apis_mellifera; cd Apis_mellifera; cp /app/data/other_species/apimel/Amel_4.5/jbrowse/data//trackList.json .; cd .. 
+mkdir Athalia_rosae; cd Athalia_rosae; cp /app/data/BCM_i5k_pilot/athros/BCM/jbrowse/data/trackList.json .; cd .. 
+mkdir Bactrocera_cucurbitae; cd Bactrocera_cucurbitae; cp /app/data/other_species/baccuc/jbrowse/data/trackList.json .; cd .. 
+mkdir Bactrocera_dorsalis; cd Bactrocera_dorsalis; cp /app/data/other_species/bacdor/jbrowse/data/trackList.json .; cd .. 
+mkdir Bactrocera_oleae; cd Bactrocera_oleae; cp /app/data/other_species/bacole/jbrowse/data/trackList.json .; cd .. 
+mkdir Bemisia_tabaci; cd Bemisia_tabaci; cp /app/data/other_species/bemtab/jbrowse/data/trackList.json .; cd .. 
+mkdir Blattella_germanica; cd Blattella_germanica; cp /app/data/BCM_i5k_pilot/blager/BCM/jbrowse/data/trackList.json .; cd .. 
+mkdir Bombus_impatiens; cd Bombus_impatiens; cp /app/data/other_species/bomimp/BIMP_2.1/jbrowse/data/trackList.json .; cd .. 
+mkdir Bombus_terrestris; cd Bombus_terrestris; cp /app/data/other_species/bomter/Bter_1.0/jbrowse/data/trackList.json .; cd .. 
+mkdir Bradysia_coprophila; cd Bradysia_coprophila; cp /app/data/other_species/bracop/BU_Bcop_v1/jbrowse/data/trackList.json .; cd .. 
+mkdir Catajapyx_aquilonaris; cd Catajapyx_aquilonaris; cp /app/data/BCM_i5k_pilot/cataqu/jbrowse/data/trackList.json .; cd .. 
+mkdir Centruroides_sculpturatus; cd Centruroides_sculpturatus; cp /app/data/BCM_i5k_pilot/censcu/jbrowse/data/trackList.json .; cd .. 
+mkdir Cephus_cinctus; cd Cephus_cinctus; cp /app/data/other_species/cepcin/Ccin1/jbrowse/data//trackList.json .; cd .. 
+mkdir Ceratitis_capitata; cd Ceratitis_capitata; cp /app/data/BCM_i5k_pilot/cercap/jbrowse/data/trackList.json .; cd .. 
+mkdir Chelonus_insularis; cd Chelonus_insularis; cp /app/data/other_species/cheins/ASM1335770v1/jbrowse/data/trackList.json .; cd .. 
+mkdir Cimex_lectularius; cd Cimex_lectularius; cp /app/data/BCM_i5k_pilot/cimlec/BCM/jbrowse/data/trackList.json .; cd .. 
+mkdir Clitarchus_hookeri; cd Clitarchus_hookeri; cp /app/data/other_species/clihoo/jbrowse/data/trackList.json .; cd .. 
+mkdir Contarinia_nasturtii; cd Contarinia_nasturtii; cp /app/data/other_species/connas/AAFC_CNas_1.1/jbrowse/data/trackList.json .; cd .. 
+mkdir Copidosoma_floridanum; cd Copidosoma_floridanum; cp /app/data/BCM_i5k_pilot/copflo/jbrowse/data/trackList.json .; cd .. 
+mkdir Culex_quinquefasciatus; cd Culex_quinquefasciatus; cp /app/data/other_species/culqui/VPISU_Cqui_1.0_pri_paternal/jbrowse/data/trackList.json .; cd .. 
+mkdir Diabrotica_virgifera_training; cd Diabrotica_virgifera_training; cp /app/data/other_species/diavir/Dvir_v2.0_RefSeq/jbrowse/data/trackList.json .; cd .. 
+mkdir Diachasma_alloeum; cd Diachasma_alloeum; cp /app/data/other_species/diaall/Dall2.0/jbrowse/data/trackList.json .; cd .. 
+mkdir Diaphorina_citri; cd Diaphorina_citri; cp /app/data/other_species/diacit/jbrowse/data/trackList.json .; cd .. 
+mkdir Diaphorina_citri_legacy; cd Diaphorina_citri_legacy; cp /app/data/other_species/diacit_legacy/jbrowse/data/trackList.json .; cd .. 
+mkdir Diprion_similis; cd Diprion_similis; cp /app/data//other_species/dipsim/iyDipSimi1.1/jbrowse/data/trackList.json .; cd .. 
+mkdir Drosophila_biarmipes; cd Drosophila_biarmipes; cp /app/data/modencode/drobia/Dbia_2.0/jbrowse/data/trackList.json .; cd .. 
+mkdir Drosophila_bipectinata; cd Drosophila_bipectinata; cp /app/data/other_species/drobip/ASM1815384v1/jbrowse/data/trackList.json .; cd .. 
+mkdir Drosophila_elegans; cd Drosophila_elegans; cp /app/data/other_species/droele/ASM1815250v1/jbrowse/data/trackList.json .; cd .. 
+mkdir Drosophila_eugracilis; cd Drosophila_eugracilis; cp /app/data/other_species/droeug/ASM1815383v1/jbrowse/data/trackList.json .; cd .. 
+mkdir Drosophila_ficusphila; cd Drosophila_ficusphila; cp /app/data/other_species/drofic/ASM1815226v1/jbrowse/data/trackList.json .; cd .. 
+mkdir Drosophila_kikkawai; cd Drosophila_kikkawai; cp /app/data/other_species/drokik/ASM1815253v1/jbrowse/data/trackList.json .; cd .. 
+mkdir Drosophila_rhopaloa; cd Drosophila_rhopaloa; cp /app/data/other_species/drorho/ASM1815211v1/jbrowse/data/trackList.json .; cd .. 
+mkdir Drosophila_takahashii; cd Drosophila_takahashii; cp /app/data/other_species/drotak/ASM1815269v1/jbrowse/data/trackList.json .; cd .. 
+mkdir Dufourea_novaeangliae; cd Dufourea_novaeangliae; cp /app/data/other_species/dufnov/jbrowse/data/trackList.json .; cd .. 
+mkdir Ephemera_danica; cd Ephemera_danica; cp /app/data/BCM_i5k_pilot/ephdan/Edan_2.0/jbrowse/data//trackList.json .; cd .. 
+mkdir Eufriesea_mexicana; cd Eufriesea_mexicana; cp /app/data/other_species/eufmex/ASM148370v1/jbrowse/data/trackList.json .; cd .. 
+mkdir Euglossa_dilemma; cd Euglossa_dilemma; cp /app/data/other_species/eugdil/jbrowse/data/trackList.json .; cd .. 
+mkdir Eurytemora_affinis; cd Eurytemora_affinis; cp /app/data/BCM_i5k_pilot/euraff/jbrowse/data/trackList.json .; cd .. 
+mkdir Eurytemora_affinis_-_training; cd Eurytemora_affinis_-_training; cp /app/data/BCM_i5k_pilot/euraff/jbrowse/data/trackList.json .; cd .. 
+mkdir Fopius_arisanus; cd Fopius_arisanus; cp /app/data/other_species/fopari/jbrowse/data/trackList.json .; cd .. 
+mkdir Frankliniella_occidentalis; cd Frankliniella_occidentalis; cp /app/data/BCM_i5k_pilot/fraocc/Focc_3.0/jbrowse/data/trackList.json .; cd .. 
+mkdir Galleria_mellonella; cd Galleria_mellonella; cp /app/data/other_species/galmel/ASM364042v2/jbrowse/data/trackList.json .; cd .. 
+mkdir Gerris_buenoi; cd Gerris_buenoi; cp /app/data/BCM_i5k_pilot/gerbue/jbrowse/data//trackList.json .; cd .. 
+mkdir Habropoda_laboriosa; cd Habropoda_laboriosa; cp /app/data/other_species/hablab/jbrowse/data/trackList.json .; cd .. 
+mkdir Halyomorpha_halys; cd Halyomorpha_halys; cp /app/data/BCM_i5k_pilot/halhal/Hhal_1.1/jbrowse/data/trackList.json .; cd .. 
+mkdir Helicoverpa_zea; cd Helicoverpa_zea; cp /app/data/other_species/helzea/ilHelZeax1.1/jbrowse/data/trackList.json .; cd .. 
+mkdir Heliothis_virescens; cd Heliothis_virescens; cp /app/data/other_species/helvir/jbrowse/data//trackList.json .; cd .. 
+mkdir Holacanthella_duospinosa; cd Holacanthella_duospinosa; cp /app/data/other_species/holduo/ASM273828v1/jbrowse/data/trackList.json .; cd .. 
+mkdir Homalodisca_vitripennis; cd Homalodisca_vitripennis; cp /app/data/BCM_i5k_pilot/homvit/jbrowse/data/trackList.json .; cd .. 
+mkdir Hyalella_azteca; cd Hyalella_azteca; cp /app/data/BCM_i5k_pilot/hyaazt/Hazt_2.0.1/jbrowse/data/trackList.json .; cd .. 
+mkdir Ladona_fulva; cd Ladona_fulva; cp /app/data/other_species/ladful/Lful_2.0/jbrowse/data/trackList.json .; cd .. 
+mkdir Laodelphax_striatellus; cd Laodelphax_striatellus; cp /app/data/other_species/laostr/ASM333518v2/jbrowse/data/trackList.json .; cd .. 
+mkdir Lasioglossum_albipes; cd Lasioglossum_albipes; cp /app/data/other_species/lasalb/jbrowse/data/trackList.json .; cd .. 
+mkdir Latrodectus_hesperus; cd Latrodectus_hesperus; cp /app/data/BCM_i5k_pilot/lathes/GCA_000697925.1/jbrowse/data/trackList.json .; cd .. 
+mkdir Leptinotarsa_decemlineata; cd Leptinotarsa_decemlineata; cp /app/data/BCM_i5k_pilot/lepdec/Ldec_2.0/jbrowse/data/trackList.json .; cd .. 
+mkdir Leptinotarsa_decemlineata_training; cd Leptinotarsa_decemlineata_training; cp /app/data/BCM_i5k_pilot/lepdec/jbrowse/data/trackList.json .; cd .. 
+mkdir Limnephilus_lunatus; cd Limnephilus_lunatus; cp /app/data/BCM_i5k_pilot/limlun/jbrowse/data/trackList.json .; cd .. 
+mkdir Locusta_migratoria; cd Locusta_migratoria; cp /app/data/other_species/locmig/jbrowse/data//trackList.json .; cd .. 
+mkdir Loxosceles_reclusa; cd Loxosceles_reclusa; cp /app/data/BCM_i5k_pilot/loxrec/GCA_001188405.1/jbrowse/data/trackList.json .; cd .. 
+mkdir Lucilia_sericata; cd Lucilia_sericata; cp /app/data/other_species/lucser/ASM1558622v1/jbrowse/data/trackList.json .; cd .. 
+mkdir Mamestra_configurata; cd Mamestra_configurata; cp /app/data/other_species/mamcon/GCA_002192655.1/jbrowse/data/trackList.json .; cd .. 
+mkdir Manduca_sexta; cd Manduca_sexta; cp /app/data/other_species/mansex/JHU_Msex_v1.0/jbrowse/data/trackList.json .; cd .. 
+mkdir Mayetiola_destructor; cd Mayetiola_destructor; cp /app/data/other_species/maydes/jbrowse/data/trackList.json .; cd .. 
+mkdir Medauroidea_extradentata; cd Medauroidea_extradentata; cp /app/data/other_species/medext/GCA_003012365.1/jbrowse/data/trackList.json .; cd .. 
+mkdir Megachile_rotundata; cd Megachile_rotundata; cp /app/data/other_species/megrot/jbrowse/data/trackList.json .; cd .. 
+mkdir Melipona_quadrifasciata; cd Melipona_quadrifasciata; cp /app/data/other_species/melqua/jbrowse/data/trackList.json .; cd .. 
+mkdir Microplitis_demolitor; cd Microplitis_demolitor; cp /app/data/other_species/micdem/jbrowse/data/trackList.json .; cd .. 
+mkdir Neodiprion_fabricii; cd Neodiprion_fabricii; cp /app/data/other_species/neofab/iyNeoFabr1.1/jbrowse/data/trackList.json .; cd .. 
+mkdir Neodiprion_lecontei; cd Neodiprion_lecontei; cp /app/data/other_species/neolec/iyNeoLeco1.1/jbrowse/data/trackList.json .; cd .. 
+mkdir Neodiprion_lecontei_training; cd Neodiprion_lecontei_training; cp /app/data/other_species/neolec/jbrowse/data/trackList.json .; cd .. 
+mkdir Neodiprion_pinetum; cd Neodiprion_pinetum; cp /app/data/other_species/neopin/iyNeoPine1.1/jbrowse/data/trackList.json .; cd .. 
+mkdir Neodiprion_virginiana; cd Neodiprion_virginiana; cp /app/data/other_species/neovir/iyNeoVirg1.1/jbrowse/data/trackList.json .; cd .. 
+mkdir Nicrophorus_vespilloides; cd Nicrophorus_vespilloides; cp /app/data/other_species/nicves/jbrowse/data/trackList.json .; cd .. 
+mkdir Nylanderia_fulva; cd Nylanderia_fulva; cp /app/data/other_species/nylful/TAMU_Nfulva_1.0/jbrowse/data/trackList.json .; cd .. 
+mkdir Odontomachus_brunneus; cd Odontomachus_brunneus; cp /app/data/other_species/odobru/Obru_v1/jbrowse/data/trackList.json .; cd .. 
+mkdir Oncopeltus_fasciatus; cd Oncopeltus_fasciatus; cp /app/data/BCM_i5k_pilot/oncfas/jbrowse/data/trackList.json .; cd .. 
+mkdir Oncopeltus_fasciatus_training; cd Oncopeltus_fasciatus_training; cp /app/data/BCM_i5k_pilot/oncfas/jbrowse/data/trackList.json .; cd .. 
+mkdir Onthophagus_taurus; cd Onthophagus_taurus; cp /app/data/BCM_i5k_pilot/onttau/jbrowse/data/trackList.json .; cd .. 
+mkdir Orussus_abietinus; cd Orussus_abietinus; cp /app/data/BCM_i5k_pilot/oruabi/BCM/jbrowse/data/trackList.json .; cd .. 
+mkdir Osmia_lignaria; cd Osmia_lignaria; cp /app/data/other_species/osmlig/USDA_OLig_1.0/jbrowse/data/trackList.json .; cd .. 
+mkdir Pachypsylla_venusta; cd Pachypsylla_venusta; cp /app/data/BCM_i5k_pilot/pacven/jbrowse/data/trackList.json .; cd .. 
+mkdir Parasteatoda_tepidariorum; cd Parasteatoda_tepidariorum; cp /app/data/BCM_i5k_pilot/partep/jbrowse/data/trackList.json .; cd .. 
+mkdir Photinus_pyralis; cd Photinus_pyralis; cp /app/data/other_species/phopyr/Ppyr1.3/jbrowse/data/trackList.json .; cd .. 
+mkdir Rhagoletis_zephyria; cd Rhagoletis_zephyria; cp /app/data/other_species/rhazep/jbrowse/data/trackList.json .; cd .. 
+mkdir Rhipicephalus_microplus; cd Rhipicephalus_microplus; cp /app/data/other_species/rhimic/ASM1333972v1/jbrowse/data/trackList.json .; cd .. 
+mkdir Rhyzopertha_dominica; cd Rhyzopertha_dominica; cp /app/data/other_species/rhydom/RdoDt3_tmp/jbrowse/data/trackList.json .; cd .. 
+mkdir Saccharomyceseubayanus; cd Saccharomyceseubayanus; cp /app/data/other_species/saceub/SEUB3.0/jbrowse/data/trackList.json .; cd .. 
+mkdir Schistocerca_americana; cd Schistocerca_americana; cp /app/data/other_species/schame/iqSchAmer2.1/jbrowse/data/trackList.json .; cd .. 
+mkdir Schistocercapiceifrons; cd Schistocercapiceifrons; cp /app/data/other_species/schpic/iqSchPice1.1/jbrowse/data//trackList.json .; cd .. 
+mkdir Tigriopus_californicus; cd Tigriopus_californicus; cp /app/data/other_species/tigcal/jbrowse/data/trackList.json .; cd .. 
+mkdir Tribolium_castaneum; cd Tribolium_castaneum; cp /app/data/other_species/tricas/jbrowse/data/trackList.json .; cd .. 
+mkdir Tribolium_madens; cd Tribolium_madens; cp /app/data/other_species/trimad/Tmad_KSU_1.1/jbrowse/data/trackList.json .; cd .. 
+mkdir Trichogramma_pretiosum; cd Trichogramma_pretiosum; cp /app/data/BCM_i5k_pilot/tripre/jbrowse/data/trackList.json .; cd .. 
+mkdir Varroa_destructor; cd Varroa_destructor; cp /app/data/other_species/vardes/Vdes_3.0/jbrowse/data/trackList.json .; cd .. 
+mkdir Varroa_jacobsoni; cd Varroa_jacobsoni; cp /app/data/other_species/varjac/vjacob_1.0/jbrowse/data/trackList.json .; cd .. 
+mkdir Venturia_canescens; cd Venturia_canescens; cp /app/data/other_species/vencan/ASM1945775v1/jbrowse/data/trackList.json .; cd .. 
+mkdir Venturia_canescens; cd Venturia_canescens; cp /app/data/other_species/vencan/ASM1945775v1/jbrowse/data/trackList.json .; cd .. 
+mkdir Venturia_canescens; cd Venturia_canescens; cp /app/data/other_species/vencan/ASM1945775v1/jbrowse/data/trackList.json .; cd .. 
diff --git a/organisms/stage/manifest.md5 b/organisms/stage/manifest.md5
new file mode 100644
index 0000000..0fc97f0
--- /dev/null
+++ b/organisms/stage/manifest.md5
@@ -0,0 +1,127 @@
+9875a5e7cf043a27f48495fab6f8c486  ./10_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./11_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./12_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./13_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./14_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./15_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./16_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./17_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./18_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./19_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./1_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./20_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./21_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./22_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./23_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./24_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./25_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./26_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./27_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./28_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./29_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./2_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./30_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./31_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./32_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./33_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./34_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./35_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./36_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./37_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./38_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./39_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./3_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./40_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./4_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./5_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./6_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./7_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./8_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./9_-_Onthophagus_taurus_training/trackList.json
+73646df96da1166cd30a38bebf80195a  ./Aethina_tumida/trackList.json
+2a1972b947f6841c9a9aed9e5679476d  ./Agrilus_planipennis/trackList.json
+74ba054dd52792a38a486216d3e470cb  ./Amyelois_transitella/trackList.json
+d1b3d94011effc800e8398702809d959  ./Anoplophora_glabripennis/trackList.json
+bc6b5a0451bca2cb1441e2d2bbe04910  ./Apis_mellifera/trackList.json
+2dc6f71365969d06c76008146329cd46  ./Athalia_rosae/trackList.json
+6df1714763887e190e1140bd70c6306a  ./Bactrocera_cucurbitae/trackList.json
+827fac31d06e3d6d9d2aa507015af66d  ./Bactrocera_dorsalis/trackList.json
+981ba92d98c51e350171a303174cea72  ./Bactrocera_oleae/trackList.json
+459a489feb018e0e59735cf3ae0cb19e  ./Bemisia_tabaci/trackList.json
+de9fd3c3240021ed7f08e2990953ef12  ./Blattella_germanica/trackList.json
+0cfc7188f49a855d833d9f7edc5c4c43  ./Bombus_impatiens/trackList.json
+d319d967516ec006c420db1ce685092d  ./Bombus_terrestris/trackList.json
+a77f58cf4f09a63ab315107beeb550f1  ./Bradysia_coprophila/trackList.json
+63d967caecb7b8b718fb96af5668cf4a  ./Catajapyx_aquilonaris/trackList.json
+6e0964cd65cab811ae6d66d6c7186175  ./Centruroides_sculpturatus/trackList.json
+be0acc687c254929835a118242c8b80d  ./Cephus_cinctus/trackList.json
+b78fbb636f2dc1bdfea5408d5c9034dc  ./Ceratitis_capitata/trackList.json
+5cb5a771c75b9795440f1c68b8dbebbe  ./Chelonus_insularis/trackList.json
+258e614e2f20e1051be0ac4c046ae7d5  ./Cimex_lectularius/trackList.json
+9b4647705c606f8cd3a5d826c18e407c  ./Clitarchus_hookeri/trackList.json
+b319c4301e820bd0c444f7275480615c  ./Contarinia_nasturtii/trackList.json
+4dde816d5c51b79a20b751f9af1295b5  ./Copidosoma_floridanum/trackList.json
+49f02a414ec131186d8bfe16aafba07f  ./Diabrotica_virgifera_training/trackList.json
+44192d73bd17b07c4d96ebb5cf6ce87e  ./Diachasma_alloeum/trackList.json
+b77db88c5344a3b5ed0886c87ecde93f  ./Diaphorina_citri_legacy/trackList.json
+ff0d272b2b55ed87b948e4316a61e6b8  ./Diaphorina_citri/trackList.json
+9a4ad20f8d07b47bd4ac616732af8f2f  ./Drosophila_biarmipes/trackList.json
+6e24f24d7dbf6663971b785851762241  ./Drosophila_bipectinata/trackList.json
+f2a43993463d5371b924ad02820eda17  ./Drosophila_elegans/trackList.json
+9d8b5ace901eb50baf5c5f4d5e8de290  ./Drosophila_eugracilis/trackList.json
+0d57c7f0c604348da80f52784ef5302f  ./Drosophila_ficusphila/trackList.json
+5797c8a7a4336a569d9bbc44aafd9069  ./Drosophila_kikkawai/trackList.json
+6f35b7b4701d4deccf60e81d8e8af9f6  ./Drosophila_rhopaloa/trackList.json
+9f26a329f6b15adcc0bf081de7430a37  ./Drosophila_takahashii/trackList.json
+f8f06ac07efa32fc80cd1c8c762323c6  ./Dufourea_novaeangliae/trackList.json
+20859b8e2a368fee17ab67308ba2b7dc  ./Ephemera_danica/trackList.json
+074a645adae3937b35c8aa350bbc17c9  ./Eufriesea_mexicana/trackList.json
+02590ee8edb81a40567c0b86178cb7b9  ./Euglossa_dilemma/trackList.json
+1d6fd304321335a046145aa077acc38a  ./Eurytemora_affinis/trackList.json
+1d6fd304321335a046145aa077acc38a  ./Eurytemora_affinis_-_training/trackList.json
+9a6963cad06a6cd07d27cf7c428d5c65  ./Fopius_arisanus/trackList.json
+c6dca7739768478dbdd6df20daba2fbd  ./Frankliniella_occidentalis/trackList.json
+c235409a662dd7d4e5983d5c55f21f42  ./Galleria_mellonella/trackList.json
+f50f8110ff572b3b901f99c181299641  ./Gerris_buenoi/trackList.json
+255444ae665abc7679b87dddba3de9b4  ./Habropoda_laboriosa/trackList.json
+cea33bcb2db50270eaceb05076b5ce4f  ./Halyomorpha_halys/trackList.json
+14db59e7b6d54dc08664e6c54f1d39bb  ./Heliothis_virescens/trackList.json
+e2f52b4118009cf89ea6bfdc501089eb  ./Holacanthella_duospinosa/trackList.json
+e9bc561ec56b301252f1ffb0c540efef  ./Homalodisca_vitripennis/trackList.json
+fd3b60db8381052776abf8116fd0180c  ./Hyalella_azteca/trackList.json
+854cdac934afc5b82f7ff37cd849170e  ./Laodelphax_striatellus/trackList.json
+685a1e08f0f029e6545011c582804775  ./Lasioglossum_albipes/trackList.json
+2a28cb284299243eb56ee11d714ffa7a  ./Latrodectus_hesperus/trackList.json
+e84a20706602a27116d3e7f003be96ba  ./Leptinotarsa_decemlineata/trackList.json
+69a5a4f0e26fec12aaef1eb27488b72f  ./Leptinotarsa_decemlineata_training/trackList.json
+1a7809c807541f40a6d0de2f1c6b4e7d  ./Limnephilus_lunatus/trackList.json
+81601f35a3616b5cd0132ec1b3098110  ./Locusta_migratoria/trackList.json
+6bee3f4c5af461a730cdcc90da4ffeb7  ./Loxosceles_reclusa/trackList.json
+b472bc7087756090613a9a369fd435fb  ./Mamestra_configurata/trackList.json
+8ff5b2b9c657429aea0280fc6f5fc76c  ./Manduca_sexta/trackList.json
+67a592e3a7c6b702b0dcc9b9e6771515  ./Mayetiola_destructor/trackList.json
+38b7867ca690867f5739962d433c0828  ./Medauroidea_extradentata/trackList.json
+9fa0226e20b1e5578a15726c6bc4a238  ./Megachile_rotundata/trackList.json
+79cab08b89326d6727dc68e91cb085d6  ./Melipona_quadrifasciata/trackList.json
+bdb5bafc32a74022dea3f90d07f03f61  ./Microplitis_demolitor/trackList.json
+965665c71fb3f9b549c0af88b012c03b  ./Neodiprion_lecontei/trackList.json
+d1341c414d452723f630eaf7ae66a2aa  ./Neodiprion_lecontei_training/trackList.json
+d73b899e0fdfc0b20a1f6c368dc7aac6  ./Nicrophorus_vespilloides/trackList.json
+d640ee444d670cf6dcc7455e15b6c89f  ./Nylanderia_fulva/trackList.json
+0bb2f28b9870d041d0effa2e36ed6214  ./Odontomachus_brunneus/trackList.json
+2686590197f1bdc037a38fd60e665ee1  ./Oncopeltus_fasciatus/trackList.json
+2686590197f1bdc037a38fd60e665ee1  ./Oncopeltus_fasciatus_training/trackList.json
+957907b8a69c08037d5ed3db39816f98  ./Onthophagus_taurus/trackList.json
+33d35d86dbfc312c8cdba1a5a561a879  ./Orussus_abietinus/trackList.json
+35f9a1a800f0572ec5ce46fc6b12790b  ./Osmia_lignaria/trackList.json
+f81b350db3ea1a82a6d1253d7a0db8fb  ./Pachypsylla_venusta/trackList.json
+7c458ee03cbe372d5bd8ece05e65fefa  ./Parasteatoda_tepidariorum/trackList.json
+f4bb8abebb9f78d70bee481d19eb0d8d  ./Photinus_pyralis/trackList.json
+e71a903e88a05f21faccc3b02f7f67a3  ./Rhagoletis_zephyria/trackList.json
+01f29c90f3798a7ceda00cfd97fabeae  ./Rhipicephalus_microplus/trackList.json
+a85c77319c20539a8a4dd52c9c1e2fcb  ./Rhyzopertha_dominica/trackList.json
+83b29e7dd751971c1f1b824e262b3952  ./Tigriopus_californicus/trackList.json
+bcf2ba9ed203eae9c0195c0695b0bee6  ./Tribolium_castaneum/trackList.json
+6348ef622fab9ebe74cae8dac5cdbe07  ./Trichogramma_pretiosum/trackList.json
+d695fd7a00f16e59ada39da2bc5b5a7c  ./Varroa_destructor/trackList.json
+98e6622539f46fa2c1770d329cace3d7  ./Varroa_jacobsoni/trackList.json
diff --git a/organisms/stage/organism_list.txt2 b/organisms/stage/organism_list.txt2
index 54691ba..c83a107 100644
--- a/organisms/stage/organism_list.txt2
+++ b/organisms/stage/organism_list.txt2
@@ -61,18 +61,20 @@ Cimex_lectularius|/app/data/BCM_i5k_pilot/cimlec/BCM/jbrowse/data
 Clitarchus_hookeri|/app/data/other_species/clihoo/jbrowse/data
 Contarinia_nasturtii|/app/data/other_species/connas/AAFC_CNas_1.1/jbrowse/data
 Copidosoma_floridanum|/app/data/BCM_i5k_pilot/copflo/jbrowse/data
+Culex_quinquefasciatus|/app/data/other_species/culqui/VPISU_Cqui_1.0_pri_paternal/jbrowse/data
 Diabrotica_virgifera_training|/app/data/other_species/diavir/Dvir_v2.0_RefSeq/jbrowse/data
 Diachasma_alloeum|/app/data/other_species/diaall/Dall2.0/jbrowse/data
 Diaphorina_citri|/app/data/other_species/diacit/jbrowse/data
 Diaphorina_citri_legacy|/app/data/other_species/diacit_legacy/jbrowse/data
+Diprion_similis|/app/data//other_species/dipsim/iyDipSimi1.1/jbrowse/data
 Drosophila_biarmipes|/app/data/modencode/drobia/Dbia_2.0/jbrowse/data
-Drosophila_bipectinata|/app/data/modencode/drobip/Dbip_2.0/jbrowse/data
-Drosophila_elegans|/app/data/modencode/droele/Dele_2.0/jbrowse/data
-Drosophila_eugracilis|/app/data/modencode/droeug/Deug_2.0/jbrowse/data
-Drosophila_ficusphila|/app/data/modencode/drofic/Dfic_2.0/jbrowse/data
-Drosophila_kikkawai|/app/data/modencode/drokik/Dkik_2.0/jbrowse/data
-Drosophila_rhopaloa|/app/data/modencode/drorho/Drho_2.0/jbrowse/data
-Drosophila_takahashii|/app/data/modencode/drotak/Dtak_2.0/jbrowse/data
+Drosophila_bipectinata|/app/data/other_species/drobip/ASM1815384v1/jbrowse/data
+Drosophila_elegans|/app/data/other_species/droele/ASM1815250v1/jbrowse/data
+Drosophila_eugracilis|/app/data/other_species/droeug/ASM1815383v1/jbrowse/data
+Drosophila_ficusphila|/app/data/other_species/drofic/ASM1815226v1/jbrowse/data
+Drosophila_kikkawai|/app/data/other_species/drokik/ASM1815253v1/jbrowse/data
+Drosophila_rhopaloa|/app/data/other_species/drorho/ASM1815211v1/jbrowse/data
+Drosophila_takahashii|/app/data/other_species/drotak/ASM1815269v1/jbrowse/data
 Dufourea_novaeangliae|/app/data/other_species/dufnov/jbrowse/data
 Ephemera_danica|/app/data/BCM_i5k_pilot/ephdan/Edan_2.0/jbrowse/data/
 Eufriesea_mexicana|/app/data/other_species/eufmex/ASM148370v1/jbrowse/data
@@ -85,10 +87,12 @@ Galleria_mellonella|/app/data/other_species/galmel/ASM364042v2/jbrowse/data
 Gerris_buenoi|/app/data/BCM_i5k_pilot/gerbue/jbrowse/data/
 Habropoda_laboriosa|/app/data/other_species/hablab/jbrowse/data
 Halyomorpha_halys|/app/data/BCM_i5k_pilot/halhal/Hhal_1.1/jbrowse/data
+Helicoverpa_zea|/app/data/other_species/helzea/ilHelZeax1.1/jbrowse/data
 Heliothis_virescens|/app/data/other_species/helvir/jbrowse/data/
 Holacanthella_duospinosa|/app/data/other_species/holduo/ASM273828v1/jbrowse/data
 Homalodisca_vitripennis|/app/data/BCM_i5k_pilot/homvit/jbrowse/data
 Hyalella_azteca|/app/data/BCM_i5k_pilot/hyaazt/Hazt_2.0.1/jbrowse/data
+Ladona_fulva|/app/data/other_species/ladful/Lful_2.0/jbrowse/data
 Laodelphax_striatellus|/app/data/other_species/laostr/ASM333518v2/jbrowse/data
 Lasioglossum_albipes|/app/data/other_species/lasalb/jbrowse/data
 Latrodectus_hesperus|/app/data/BCM_i5k_pilot/lathes/GCA_000697925.1/jbrowse/data
@@ -97,6 +101,7 @@ Leptinotarsa_decemlineata_training|/app/data/BCM_i5k_pilot/lepdec/jbrowse/data
 Limnephilus_lunatus|/app/data/BCM_i5k_pilot/limlun/jbrowse/data
 Locusta_migratoria|/app/data/other_species/locmig/jbrowse/data/
 Loxosceles_reclusa|/app/data/BCM_i5k_pilot/loxrec/GCA_001188405.1/jbrowse/data
+Lucilia_sericata|/app/data/other_species/lucser/ASM1558622v1/jbrowse/data
 Mamestra_configurata|/app/data/other_species/mamcon/GCA_002192655.1/jbrowse/data
 Manduca_sexta|/app/data/other_species/mansex/JHU_Msex_v1.0/jbrowse/data
 Mayetiola_destructor|/app/data/other_species/maydes/jbrowse/data
@@ -104,8 +109,11 @@ Medauroidea_extradentata|/app/data/other_species/medext/GCA_003012365.1/jbrowse/
 Megachile_rotundata|/app/data/other_species/megrot/jbrowse/data
 Melipona_quadrifasciata|/app/data/other_species/melqua/jbrowse/data
 Microplitis_demolitor|/app/data/other_species/micdem/jbrowse/data
-Neodiprion_lecontei|/app/data/other_species/neolec/Nlec1.1/jbrowse/data
+Neodiprion_fabricii|/app/data/other_species/neofab/iyNeoFabr1.1/jbrowse/data
+Neodiprion_lecontei|/app/data/other_species/neolec/iyNeoLeco1.1/jbrowse/data
 Neodiprion_lecontei_training|/app/data/other_species/neolec/jbrowse/data
+Neodiprion_pinetum|/app/data/other_species/neopin/iyNeoPine1.1/jbrowse/data
+Neodiprion_virginiana|/app/data/other_species/neovir/iyNeoVirg1.1/jbrowse/data
 Nicrophorus_vespilloides|/app/data/other_species/nicves/jbrowse/data
 Nylanderia_fulva|/app/data/other_species/nylful/TAMU_Nfulva_1.0/jbrowse/data
 Odontomachus_brunneus|/app/data/other_species/odobru/Obru_v1/jbrowse/data
@@ -118,11 +126,17 @@ Pachypsylla_venusta|/app/data/BCM_i5k_pilot/pacven/jbrowse/data
 Parasteatoda_tepidariorum|/app/data/BCM_i5k_pilot/partep/jbrowse/data
 Photinus_pyralis|/app/data/other_species/phopyr/Ppyr1.3/jbrowse/data
 Rhagoletis_zephyria|/app/data/other_species/rhazep/jbrowse/data
-Rhipicephalus_microplus|/app/data/other_species/rhimic/jbrowse/data
+Rhipicephalus_microplus|/app/data/other_species/rhimic/ASM1333972v1/jbrowse/data
 Rhyzopertha_dominica|/app/data/other_species/rhydom/RdoDt3_tmp/jbrowse/data
 Saccharomyceseubayanus|/app/data/other_species/saceub/SEUB3.0/jbrowse/data
+Schistocerca_americana|/app/data/other_species/schame/iqSchAmer2.1/jbrowse/data
+Schistocercapiceifrons|/app/data/other_species/schpic/iqSchPice1.1/jbrowse/data/
 Tigriopus_californicus|/app/data/other_species/tigcal/jbrowse/data
 Tribolium_castaneum|/app/data/other_species/tricas/jbrowse/data
+Tribolium_madens|/app/data/other_species/trimad/Tmad_KSU_1.1/jbrowse/data
 Trichogramma_pretiosum|/app/data/BCM_i5k_pilot/tripre/jbrowse/data
 Varroa_destructor|/app/data/other_species/vardes/Vdes_3.0/jbrowse/data
 Varroa_jacobsoni|/app/data/other_species/varjac/vjacob_1.0/jbrowse/data
+Venturia_canescens|/app/data/other_species/vencan/ASM1945775v1/jbrowse/data
+(140rows)
+
diff --git a/organisms/stage/stage-v2/10_-_Onthophagus_taurus_training/trackList.json b/organisms/stage/stage-v2/10_-_Onthophagus_taurus_training/trackList.json
new file mode 100644
index 0000000..3d98296
--- /dev/null
+++ b/organisms/stage/stage-v2/10_-_Onthophagus_taurus_training/trackList.json
@@ -0,0 +1,1603 @@
+{
+   "alwaysOnTracks" : "DNA,Annotations",
+   "css" : "data/contrib_styles.css",
+   "favicon" : "./plugins/WebApollo/img/webapollo_favicon.ico",
+   "formatVersion" : 1,
+   "names" : {
+      "type" : "Hash",
+      "url" : "names/"
+   },
+   "plugins" : [
+      {
+         "location" : "./plugins/WebApollo",
+         "name" : "WebApollo"
+      }
+   ],
+   "share_link" : 0,
+   "tracks" : [
+      {
+         "category" : "Reference sequence",
+         "chunkSize" : 20000,
+         "faiUrlTemplate" : "seq/onttau_genome.fa.fai",
+         "key" : "Reference sequence",
+         "label" : "DNA",
+         "seqType" : "dna",
+         "storeClass" : "JBrowse/Store/Sequence/IndexedFasta",
+         "type" : "SequenceTrack",
+         "urlTemplate" : "seq/onttau_genome.fa",
+         "useAsRefSeqStore" : 1
+      },
+      {
+         "autocomplete" : "none",
+         "compress" : 0,
+         "key" : "User-created Annotations",
+         "label" : "Annotations",
+         "phase" : 0,
+         "storeClass" : "WebApollo/Store/SeqFeature/ScratchPad",
+         "style" : {
+            "alternateClasses" : {
+               "miRNA" : {
+                  "className" : "brightgreen-80pct",
+                  "renderClassName" : "gray-center-30pct"
+               },
+               "ncRNA" : {
+                  "className" : "brightgreen-80pct",
+                  "renderClassName" : "gray-center-30pct"
+               },
+               "pseudogene" : {
+                  "className" : "light-purple-80pct",
+                  "renderClassName" : "gray-center-30pct"
+               },
+               "rRNA" : {
+                  "className" : "brightgreen-80pct",
+                  "renderClassName" : "gray-center-30pct"
+               },
+               "repeat_region" : {
+                  "className" : "magenta-80pct"
+               },
+               "snRNA" : {
+                  "className" : "brightgreen-80pct",
+                  "renderClassName" : "gray-center-30pct"
+               },
+               "snoRNA" : {
+                  "className" : "brightgreen-80pct",
+                  "renderClassName" : "gray-center-30pct"
+               },
+               "tRNA" : {
+                  "className" : "brightgreen-80pct",
+                  "renderClassName" : "gray-center-30pct"
+               },
+               "transposable_element" : {
+                  "className" : "blue-ibeam",
+                  "renderClassName" : "blue-ibeam-render"
+               }
+            },
+            "arrowheadClass" : "annot-arrowhead",
+            "centerSubFeature" : {
+               "non_canonical_five_prime_splice_site" : false,
+               "non_canonical_three_prime_splice_site" : false
+            },
+            "className" : "annot",
+            "renderClassName" : "annot-render",
+            "subfeatureClasses" : {
+               "CDS" : "annot-CDS",
+               "UTR" : "annot-UTR",
+               "exon" : "container-100pct",
+               "non_canonical_five_prime_splice_site" : "noncanonical-splice-site",
+               "non_canonical_three_prime_splice_site" : "noncanonical-splice-site",
+               "wholeCDS" : null
+            },
+            "uniqueIdField" : "id"
+         },
+         "subfeatures" : 1,
+         "type" : "WebApollo/View/Track/AnnotTrack"
+      },
+      {
+         "category" : "BCM_v0.5.3/1. Gene Sets/Primary Gene Sets: Protein Coding",
+         "compress" : 0,
+         "key" : "OTAU_v0.5.3-Models",
+         "label" : "onttau_current_models",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Consensus gene models from the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "container-16px",
+            "subfeatureClasses" : {
+               "CDS" : "primary_gene_set-cds",
+               "UTR" : "primary_gene_set-utr",
+               "exon" : "container-100pct",
+               "wholeCDS" : null
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/onttau_current_models/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/1. Gene Sets/Supplementary Gene Predictions",
+         "compress" : 0,
+         "key" : "augustus_masked",
+         "label" : "augustus_masked",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from the Augustus gene prediction software as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "augustus"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/augustus_masked/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX",
+         "compress" : 0,
+         "key" : "blastx_Annelida",
+         "label" : "blastx_Annelida",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Blastx alignments of a set of Annelida proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "blastx"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/blastx_Annelida/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX",
+         "compress" : 0,
+         "key" : "blastx_Arthropoda",
+         "label" : "blastx_Arthropoda",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Blastx alignments of a set of Arthropoda proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "blastx"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/blastx_Arthropoda/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX",
+         "compress" : 0,
+         "key" : "blastx_Atelocerata",
+         "label" : "blastx_Atelocerata",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Blastx alignments of a set of Atelocerata proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "blastx"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/blastx_Atelocerata/{refseq}/trackData.json"
+      },
+      {
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+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
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+            "Track legend" : "Results from Protein2genome alignments of a set of Arthropoda proteins as part of the MAKER automated annotation pipeline."
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+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
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+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
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+            "Track legend" : "Results from Protein2genome alignments of a set of Cephalochordata proteins as part of the MAKER automated annotation pipeline."
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+            "Track legend" : "Results from Protein2genome alignments of a set of Chelicerata proteins as part of the MAKER automated annotation pipeline."
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+      },
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+         "key" : "protein2genome_Echinodermata",
+         "label" : "protein2genome_Echinodermata",
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+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
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+            "Track legend" : "Results from Protein2genome alignments of a set of Echinodermata proteins as part of the MAKER automated annotation pipeline."
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+         "urlTemplate" : "tracks/protein2genome_Echinodermata/{refseq}/trackData.json"
+      },
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+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+         "key" : "protein2genome_Mollusca",
+         "label" : "protein2genome_Mollusca",
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+      },
+      {
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+         "key" : "protein2genome_Nemata",
+         "label" : "protein2genome_Nemata",
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+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline."
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+         "urlTemplate" : "tracks/protein2genome_Nemata/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+         "key" : "protein2genome_Nematomorpha",
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+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Nematomorpha proteins as part of the MAKER automated annotation pipeline."
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+         "urlTemplate" : "tracks/protein2genome_Nematomorpha/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+         "key" : "protein2genome_Onychophora",
+         "label" : "protein2genome_Onychophora",
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+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
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+            "Track legend" : "Results from Protein2genome alignments of a set of Onychophora proteins as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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+            "arrowheadClass" : "webapollo-arrowhead",
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+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Onychophora/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Parazoa",
+         "label" : "protein2genome_Parazoa",
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+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
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+            "Track legend" : "Results from Protein2genome alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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+            "arrowheadClass" : "webapollo-arrowhead",
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+      },
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+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline."
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+            "arrowheadClass" : "webapollo-arrowhead",
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+         "urlTemplate" : "tracks/protein2genome_Placozoa/{refseq}/trackData.json"
+      },
+      {
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+         "key" : "protein2genome_Platyhelminthes",
+         "label" : "protein2genome_Platyhelminthes",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
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+            "Track legend" : "Results from Protein2genome alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline."
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+         "urlTemplate" : "tracks/protein2genome_Platyhelminthes/{refseq}/trackData.json"
+      },
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+         "key" : "protein2genome_Priapulida",
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+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
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+            "Track legend" : "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline."
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+            "arrowheadClass" : "webapollo-arrowhead",
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+         "urlTemplate" : "tracks/protein2genome_Priapulida/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+         "key" : "protein2genome_Tardigrada",
+         "label" : "protein2genome_Tardigrada",
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+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
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+            "Track legend" : "Results from Protein2genome alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline."
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+         "urlTemplate" : "tracks/protein2genome_Tardigrada/{refseq}/trackData.json"
+      },
+      {
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+         "key" : "protein2genome_Tunicata",
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+            "Track legend" : "Results from Protein2genome alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline."
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+         "urlTemplate" : "tracks/protein2genome_Tunicata/{refseq}/trackData.json"
+      },
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+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+         "key" : "protein2genome_UNCATEGORISED",
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+         "metadata" : {
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+            "Track legend" : "Results from Protein2genome alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline."
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+         "urlTemplate" : "tracks/protein2genome_UNCATEGORISED/{refseq}/trackData.json"
+      },
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+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
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+            "Track legend" : "Results from RepeatMasker as part of the MAKER automated annotation pipeline."
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+         "urlTemplate" : "tracks/repeatmasker/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/2. Evidence/Repeats",
+         "compress" : 0,
+         "key" : "repeatrunner",
+         "label" : "repeatrunner",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
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+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Repeatrunner as part of the MAKER automated annotation pipeline."
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+      },
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+         "category" : "BCM_v0.5.3/1. Gene Sets/Supplementary Gene Predictions",
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+         "key" : "snap_masked",
+         "label" : "snap_masked",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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+            "arrowheadClass" : "webapollo-arrowhead",
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+               "match_part" : "snap"
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+         },
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+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/snap_masked/{refseq}/trackData.json"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Reference Assembly",
+         "key" : "Gaps in assembly",
+         "label" : "Gaps in assembly",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "white",
+            "pos_color" : "black"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/onttau_genome.fa.gaps.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "0.5",
+         "category" : "Reference Assembly",
+         "key" : "GC Content",
+         "label" : "GC Content",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+         },
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+            "neg_color" : "rgba(255,255,0,50)",
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+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "Onthophagus taurus early male pupa brain transcripts",
+         "label" : "Onthophagus taurus early male pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
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+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlM-BRN_S22.sorted.subset.bam"
+      },
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+         "key" : "Onthophagus taurus early female pupa brain transcripts",
+         "label" : "Onthophagus taurus early female pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
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+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
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+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
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+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
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+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
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+      },
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+         "key" : "Onthophagus taurus early female pupa brain transcripts (Coverage Plot)",
+         "label" : "Onthophagus taurus early female pupa brain transcripts (Coverage Plot)",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
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+      },
+      {
+         "category" : "Gene Silhouette Models/1. Gene Sets/Protein Coding",
+         "compress" : 0,
+         "key" : "Gene Silhouette Models v4",
+         "label" : "Gene_Silhouette_Models_v4",
+         "metadata" : {
+            "Analysis method" : "Gene Silhouette Algorithm, alpha version, unpublished",
+            "Analysis provider" : "Douglas B. Rusch, Centre for Genomics and Bioinformatics, Indiana University Bloomington",
+            "Other notes" : "Novel algorithm predicts genes based on mapped RNAseq reads; based on data from early pupae, brain, dorsal head and pronotal epidermis, and posterior abdominal epidermis only"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "container-16px",
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+               "CDS" : "gnomon_CDS",
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+         },
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+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus M PD1 BRN+CHE+THE+GEN transcripts",
+         "label" : "O. taurus M PD1 BRN+CHE+THE+GEN transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
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+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
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+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
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+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/mixed_transcripts_march_2016/ctrlM-ALL.merged.subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus F PD1 BRN+CHE+THE+GEN transcripts",
+         "label" : "O. taurus F PD1 BRN+CHE+THE+GEN transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Female",
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+            "Tissues included" : "pooled brain, dorsal head epidermis, pronotum epidermis, posterior abdominal epidermis"
+         },
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+         "style" : {
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+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/mixed_transcripts_march_2016/ctrlF-ALL.merged_subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus M NC L3L+PP1+PD1+AD4",
+         "label" : "O. taurus M NC L3L+PP1+PD1+AD4",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version" : "Illumina HiSeq 100PE",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "whole body, pooled late 3 larvae, prepupa 1, pupa day 1, adult day 4"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
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+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/NC-L3L_PP1_PD1_AD4/NC_M_merged.subset.bigwig"
+      },
+      {
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+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus F NC L3L+PP1+PD1+AD4",
+         "label" : "O. taurus F NC L3L+PP1+PD1+AD4",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version" : "Illumina HiSeq 100PE",
+            "Sex" : "Female",
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+            "Tissues included" : "whole body, pooled late 3 larvae, prepupa 1, pupa day 1, adult day 4"
+         },
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+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus embryonic reads",
+         "label" : "O. taurus embryonic",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "Western Australia, Busselton",
+            "NCBI TaxID" : "166361",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq500, 75SE",
+            "Sex" : "pooled",
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+         "category" : "Transcriptome/Mapped Reads",
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+         "label" : "O. taurus embryonic reads",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "Western Australia, Busselton",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
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+            "Sequencing platform and version" : "Illumina NextSeq500, 75SE",
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+      {
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+         "compress" : 0,
+         "key" : "O. taurus embryonic junctions",
+         "label" : "O. taurus embryonic junctions",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
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+            "NCBI TaxID" : "166361",
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+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
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+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/O. taurus embryonic junctions/{refseq}/trackData.json"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "O. taurus whole body, mixed stage RNAseq, reduced coverage, females",
+         "label" : "O. taurus whole body, mixed stage RNAseq, reduced coverage, females",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "June-16-2016",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32, normalized coverage with samtools, picard and GATK",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other tissue notes" : "Mix of late larvae, prepupae, pupae and adult RNA; pool of 12 individuals",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina HiSeq 2000m 100PE",
+            "Sex" : "Female",
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+         "urlTemplate" : "user_contributed_data/ezattara/reduced_coverage_june_2016/NC_F_merged.reduced.subset.bam"
+      },
+      {
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+         "key" : "O. taurus whole body, mixed stage RNAseq, reduced coverage, males",
+         "label" : "O. taurus whole body, mixed stage RNAseq, reduced coverage, males",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "June-16-2016",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32, normalized coverage with samtools, picard and GATK",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other tissue notes" : "Mix of late larvae, prepupae, pupae and adult RNA; pool of 12 individuals",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina HiSeq 2000m 100PE",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "Whole body"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "user_contributed_data/ezattara/reduced_coverage_june_2016/NC_M_merged.reduced.subset.bam"
+      }
+   ]
+}
diff --git a/organisms/stage/stage-v2/11_-_Onthophagus_taurus_training/trackList.json b/organisms/stage/stage-v2/11_-_Onthophagus_taurus_training/trackList.json
new file mode 100644
index 0000000..3d98296
--- /dev/null
+++ b/organisms/stage/stage-v2/11_-_Onthophagus_taurus_training/trackList.json
@@ -0,0 +1,1603 @@
+{
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+   "names" : {
+      "type" : "Hash",
+      "url" : "names/"
+   },
+   "plugins" : [
+      {
+         "location" : "./plugins/WebApollo",
+         "name" : "WebApollo"
+      }
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+   "tracks" : [
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+         "urlTemplate" : "seq/onttau_genome.fa",
+         "useAsRefSeqStore" : 1
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+      {
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+         "key" : "User-created Annotations",
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+                  "renderClassName" : "gray-center-30pct"
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+               "ncRNA" : {
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+               "pseudogene" : {
+                  "className" : "light-purple-80pct",
+                  "renderClassName" : "gray-center-30pct"
+               },
+               "rRNA" : {
+                  "className" : "brightgreen-80pct",
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+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Platyhelminthes/{refseq}/trackData.json"
+      },
+      {
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+         "compress" : 0,
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+         "label" : "protein2genome_Priapulida",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
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+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
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+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Priapulida/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Tardigrada",
+         "label" : "protein2genome_Tardigrada",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
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+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Tardigrada/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Tunicata",
+         "label" : "protein2genome_Tunicata",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
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+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Tunicata/{refseq}/trackData.json"
+      },
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+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_UNCATEGORISED",
+         "label" : "protein2genome_UNCATEGORISED",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline."
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+         "style" : {
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+            "className" : "container-10px",
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+               "match_part" : "protein2genome"
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+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_UNCATEGORISED/{refseq}/trackData.json"
+      },
+      {
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+         "compress" : 0,
+         "key" : "repeatmasker",
+         "label" : "repeatmasker",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from RepeatMasker as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
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+         "urlTemplate" : "tracks/repeatmasker/{refseq}/trackData.json"
+      },
+      {
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+         "compress" : 0,
+         "key" : "repeatrunner",
+         "label" : "repeatrunner",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Repeatrunner as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
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+            "subfeatureClasses" : {
+               "match_part" : "repeat"
+            }
+         },
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+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/repeatrunner/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/1. Gene Sets/Supplementary Gene Predictions",
+         "compress" : 0,
+         "key" : "snap_masked",
+         "label" : "snap_masked",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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+            "arrowheadClass" : "webapollo-arrowhead",
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+               "match_part" : "snap"
+            }
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+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/snap_masked/{refseq}/trackData.json"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Reference Assembly",
+         "key" : "Gaps in assembly",
+         "label" : "Gaps in assembly",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "white",
+            "pos_color" : "black"
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+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/onttau_genome.fa.gaps.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "0.5",
+         "category" : "Reference Assembly",
+         "key" : "GC Content",
+         "label" : "GC Content",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "rgba(255,255,0,50)",
+            "pos_color" : "rgba(0,0,255,50)"
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+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/onttau_genome.fa.gc.bigwig"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "Onthophagus taurus early male pupa brain transcripts",
+         "label" : "Onthophagus taurus early male pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlM-BRN_S22.sorted.subset.bam"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "Onthophagus taurus early female pupa brain transcripts",
+         "label" : "Onthophagus taurus early female pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Female",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlF-BRN_S18.sorted.subset.bam"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "Onthophagus taurus early male pupa brain transcripts (Coverage Plot)",
+         "label" : "Onthophagus taurus early male pupa brain transcripts (Coverage Plot)",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
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+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlM-BRN_S22.sorted.subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
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+         "key" : "Onthophagus taurus early female pupa brain transcripts (Coverage Plot)",
+         "label" : "Onthophagus taurus early female pupa brain transcripts (Coverage Plot)",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
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+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
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+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlF-BRN_S18.sorted.subset.bigwig"
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+      {
+         "category" : "Gene Silhouette Models/1. Gene Sets/Protein Coding",
+         "compress" : 0,
+         "key" : "Gene Silhouette Models v4",
+         "label" : "Gene_Silhouette_Models_v4",
+         "metadata" : {
+            "Analysis method" : "Gene Silhouette Algorithm, alpha version, unpublished",
+            "Analysis provider" : "Douglas B. Rusch, Centre for Genomics and Bioinformatics, Indiana University Bloomington",
+            "Other notes" : "Novel algorithm predicts genes based on mapped RNAseq reads; based on data from early pupae, brain, dorsal head and pronotal epidermis, and posterior abdominal epidermis only"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "container-16px",
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+               "CDS" : "gnomon_CDS",
+               "UTR" : "gnomon_UTR",
+               "exon" : "container-100pct",
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+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
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+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus M PD1 BRN+CHE+THE+GEN transcripts",
+         "label" : "O. taurus M PD1 BRN+CHE+THE+GEN transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
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+            "Tissues included" : "pooled brain, dorsal head epidermis, pronotum epidermis, posterior abdominal epidermis"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
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+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/mixed_transcripts_march_2016/ctrlM-ALL.merged.subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus F PD1 BRN+CHE+THE+GEN transcripts",
+         "label" : "O. taurus F PD1 BRN+CHE+THE+GEN transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
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+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Female",
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+            "Tissues included" : "pooled brain, dorsal head epidermis, pronotum epidermis, posterior abdominal epidermis"
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+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/mixed_transcripts_march_2016/ctrlF-ALL.merged_subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus M NC L3L+PP1+PD1+AD4",
+         "label" : "O. taurus M NC L3L+PP1+PD1+AD4",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version" : "Illumina HiSeq 100PE",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "whole body, pooled late 3 larvae, prepupa 1, pupa day 1, adult day 4"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
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+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/NC-L3L_PP1_PD1_AD4/NC_M_merged.subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
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+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus F NC L3L+PP1+PD1+AD4",
+         "label" : "O. taurus F NC L3L+PP1+PD1+AD4",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version" : "Illumina HiSeq 100PE",
+            "Sex" : "Female",
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+            "Tissues included" : "whole body, pooled late 3 larvae, prepupa 1, pupa day 1, adult day 4"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
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+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/NC-L3L_PP1_PD1_AD4/NC_F_merged.subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
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+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus embryonic reads",
+         "label" : "O. taurus embryonic",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "Western Australia, Busselton",
+            "NCBI TaxID" : "166361",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq500, 75SE",
+            "Sex" : "pooled",
+            "Strain" : "WA",
+            "Tissues included" : "whole embryos, pooled mixed stages"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/whole_embryos/Otau-embryos.subset.bigwig"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "O. taurus embryonic reads",
+         "label" : "O. taurus embryonic reads",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "Western Australia, Busselton",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
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+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other tissue notes" : "Mix of late larvae, prepupae, pupae and adult RNA; pool of 12 individuals",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
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+}
diff --git a/organisms/stage/stage-v2/12_-_Onthophagus_taurus_training/trackList.json b/organisms/stage/stage-v2/12_-_Onthophagus_taurus_training/trackList.json
new file mode 100644
index 0000000..3d98296
--- /dev/null
+++ b/organisms/stage/stage-v2/12_-_Onthophagus_taurus_training/trackList.json
@@ -0,0 +1,1603 @@
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+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Mollusca proteins as part of the MAKER automated annotation pipeline."
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+         "urlTemplate" : "tracks/protein2genome_Mollusca/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Nemata",
+         "label" : "protein2genome_Nemata",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline."
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+      },
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+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+         "key" : "protein2genome_Nematomorpha",
+         "label" : "protein2genome_Nematomorpha",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Nematomorpha proteins as part of the MAKER automated annotation pipeline."
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+            "arrowheadClass" : "webapollo-arrowhead",
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+         "key" : "protein2genome_Onychophora",
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+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Onychophora proteins as part of the MAKER automated annotation pipeline."
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+         "trackType" : null,
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+         "urlTemplate" : "tracks/protein2genome_Onychophora/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+         "key" : "protein2genome_Parazoa",
+         "label" : "protein2genome_Parazoa",
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+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline."
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+            "arrowheadClass" : "webapollo-arrowhead",
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+         "urlTemplate" : "tracks/protein2genome_Parazoa/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Placozoa",
+         "label" : "protein2genome_Placozoa",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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+            "arrowheadClass" : "webapollo-arrowhead",
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+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Placozoa/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Platyhelminthes",
+         "label" : "protein2genome_Platyhelminthes",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
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+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Platyhelminthes/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Priapulida",
+         "label" : "protein2genome_Priapulida",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Priapulida/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Tardigrada",
+         "label" : "protein2genome_Tardigrada",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Tardigrada/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Tunicata",
+         "label" : "protein2genome_Tunicata",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
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+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Tunicata/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_UNCATEGORISED",
+         "label" : "protein2genome_UNCATEGORISED",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
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+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
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+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_UNCATEGORISED/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/2. Evidence/Repeats",
+         "compress" : 0,
+         "key" : "repeatmasker",
+         "label" : "repeatmasker",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from RepeatMasker as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
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+               "match_part" : "repeat"
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+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/repeatmasker/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/2. Evidence/Repeats",
+         "compress" : 0,
+         "key" : "repeatrunner",
+         "label" : "repeatrunner",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Repeatrunner as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "repeat"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/repeatrunner/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/1. Gene Sets/Supplementary Gene Predictions",
+         "compress" : 0,
+         "key" : "snap_masked",
+         "label" : "snap_masked",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "snap"
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+         },
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+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/snap_masked/{refseq}/trackData.json"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Reference Assembly",
+         "key" : "Gaps in assembly",
+         "label" : "Gaps in assembly",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "white",
+            "pos_color" : "black"
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+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/onttau_genome.fa.gaps.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "0.5",
+         "category" : "Reference Assembly",
+         "key" : "GC Content",
+         "label" : "GC Content",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "rgba(255,255,0,50)",
+            "pos_color" : "rgba(0,0,255,50)"
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+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/onttau_genome.fa.gc.bigwig"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "Onthophagus taurus early male pupa brain transcripts",
+         "label" : "Onthophagus taurus early male pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlM-BRN_S22.sorted.subset.bam"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "Onthophagus taurus early female pupa brain transcripts",
+         "label" : "Onthophagus taurus early female pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Female",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlF-BRN_S18.sorted.subset.bam"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "Onthophagus taurus early male pupa brain transcripts (Coverage Plot)",
+         "label" : "Onthophagus taurus early male pupa brain transcripts (Coverage Plot)",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlM-BRN_S22.sorted.subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "Onthophagus taurus early female pupa brain transcripts (Coverage Plot)",
+         "label" : "Onthophagus taurus early female pupa brain transcripts (Coverage Plot)",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Female",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlF-BRN_S18.sorted.subset.bigwig"
+      },
+      {
+         "category" : "Gene Silhouette Models/1. Gene Sets/Protein Coding",
+         "compress" : 0,
+         "key" : "Gene Silhouette Models v4",
+         "label" : "Gene_Silhouette_Models_v4",
+         "metadata" : {
+            "Analysis method" : "Gene Silhouette Algorithm, alpha version, unpublished",
+            "Analysis provider" : "Douglas B. Rusch, Centre for Genomics and Bioinformatics, Indiana University Bloomington",
+            "Other notes" : "Novel algorithm predicts genes based on mapped RNAseq reads; based on data from early pupae, brain, dorsal head and pronotal epidermis, and posterior abdominal epidermis only"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "container-16px",
+            "subfeatureClasses" : {
+               "CDS" : "gnomon_CDS",
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+               "exon" : "container-100pct",
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+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
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+      },
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+}
diff --git a/organisms/stage/stage-v2/13_-_Onthophagus_taurus_training/trackList.json b/organisms/stage/stage-v2/13_-_Onthophagus_taurus_training/trackList.json
new file mode 100644
index 0000000..3d98296
--- /dev/null
+++ b/organisms/stage/stage-v2/13_-_Onthophagus_taurus_training/trackList.json
@@ -0,0 +1,1603 @@
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+            "Track legend" : "Results from Protein2genome alignments of a set of Echinodermata proteins as part of the MAKER automated annotation pipeline."
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+      },
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+            "Track legend" : "Results from Protein2genome alignments of a set of Nematomorpha proteins as part of the MAKER automated annotation pipeline."
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+      },
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+      },
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+            "Track legend" : "Results from Protein2genome alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline."
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+      },
+      {
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+         "key" : "protein2genome_Placozoa",
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+            "Track legend" : "Results from Protein2genome alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline."
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+      },
+      {
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+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
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+            "Track legend" : "Results from Protein2genome alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline."
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+            "arrowheadClass" : "webapollo-arrowhead",
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+         "urlTemplate" : "tracks/protein2genome_Platyhelminthes/{refseq}/trackData.json"
+      },
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+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
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+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline."
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+            "arrowheadClass" : "webapollo-arrowhead",
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+         "urlTemplate" : "tracks/protein2genome_Priapulida/{refseq}/trackData.json"
+      },
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+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+         "key" : "protein2genome_Tardigrada",
+         "label" : "protein2genome_Tardigrada",
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+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline."
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+            "arrowheadClass" : "webapollo-arrowhead",
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+         "urlTemplate" : "tracks/protein2genome_Tardigrada/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+         "key" : "protein2genome_Tunicata",
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+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
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+            "arrowheadClass" : "webapollo-arrowhead",
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+         "urlTemplate" : "tracks/protein2genome_Tunicata/{refseq}/trackData.json"
+      },
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+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+            "Track legend" : "Results from Protein2genome alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline."
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+         "urlTemplate" : "tracks/protein2genome_UNCATEGORISED/{refseq}/trackData.json"
+      },
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+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
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+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
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+         "urlTemplate" : "tracks/repeatmasker/{refseq}/trackData.json"
+      },
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+         "category" : "BCM_v0.5.3/2. Evidence/Repeats",
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+         "key" : "repeatrunner",
+         "label" : "repeatrunner",
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+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
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+            "Track legend" : "Results from Repeatrunner as part of the MAKER automated annotation pipeline."
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+      },
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+         "key" : "snap_masked",
+         "label" : "snap_masked",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
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+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline."
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+      },
+      {
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+         "bicolor_pivot" : "zero",
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+            "Track contact" : "The i5k workspace@NAL",
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+            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
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+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
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+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/onttau_genome.fa.gaps.bigwig"
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+         "autoscale" : "local",
+         "bicolor_pivot" : "0.5",
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+         "label" : "GC Content",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "rgba(255,255,0,50)",
+            "pos_color" : "rgba(0,0,255,50)"
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+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/onttau_genome.fa.gc.bigwig"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "Onthophagus taurus early male pupa brain transcripts",
+         "label" : "Onthophagus taurus early male pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlM-BRN_S22.sorted.subset.bam"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "Onthophagus taurus early female pupa brain transcripts",
+         "label" : "Onthophagus taurus early female pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
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+         "key" : "Onthophagus taurus early male pupa brain transcripts (Coverage Plot)",
+         "label" : "Onthophagus taurus early male pupa brain transcripts (Coverage Plot)",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
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+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
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+         "key" : "Onthophagus taurus early female pupa brain transcripts (Coverage Plot)",
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+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Female",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
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+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlF-BRN_S18.sorted.subset.bigwig"
+      },
+      {
+         "category" : "Gene Silhouette Models/1. Gene Sets/Protein Coding",
+         "compress" : 0,
+         "key" : "Gene Silhouette Models v4",
+         "label" : "Gene_Silhouette_Models_v4",
+         "metadata" : {
+            "Analysis method" : "Gene Silhouette Algorithm, alpha version, unpublished",
+            "Analysis provider" : "Douglas B. Rusch, Centre for Genomics and Bioinformatics, Indiana University Bloomington",
+            "Other notes" : "Novel algorithm predicts genes based on mapped RNAseq reads; based on data from early pupae, brain, dorsal head and pronotal epidermis, and posterior abdominal epidermis only"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "container-16px",
+            "subfeatureClasses" : {
+               "CDS" : "gnomon_CDS",
+               "UTR" : "gnomon_UTR",
+               "exon" : "container-100pct",
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+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/Gene_Silhouette_Models_v4/{refseq}/trackData.json"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus M PD1 BRN+CHE+THE+GEN transcripts",
+         "label" : "O. taurus M PD1 BRN+CHE+THE+GEN transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
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+            "Tissues included" : "pooled brain, dorsal head epidermis, pronotum epidermis, posterior abdominal epidermis"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/mixed_transcripts_march_2016/ctrlM-ALL.merged.subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
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+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus F PD1 BRN+CHE+THE+GEN transcripts",
+         "label" : "O. taurus F PD1 BRN+CHE+THE+GEN transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Female",
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+            "Tissues included" : "pooled brain, dorsal head epidermis, pronotum epidermis, posterior abdominal epidermis"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
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+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/mixed_transcripts_march_2016/ctrlF-ALL.merged_subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus M NC L3L+PP1+PD1+AD4",
+         "label" : "O. taurus M NC L3L+PP1+PD1+AD4",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version" : "Illumina HiSeq 100PE",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "whole body, pooled late 3 larvae, prepupa 1, pupa day 1, adult day 4"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/NC-L3L_PP1_PD1_AD4/NC_M_merged.subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus F NC L3L+PP1+PD1+AD4",
+         "label" : "O. taurus F NC L3L+PP1+PD1+AD4",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version" : "Illumina HiSeq 100PE",
+            "Sex" : "Female",
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+            "Tissues included" : "whole body, pooled late 3 larvae, prepupa 1, pupa day 1, adult day 4"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
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+         "urlTemplate" : "user_contributed_data/ezattara/NC-L3L_PP1_PD1_AD4/NC_F_merged.subset.bigwig"
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+      {
+         "autoscale" : "local",
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+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus embryonic reads",
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+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "Western Australia, Busselton",
+            "NCBI TaxID" : "166361",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq500, 75SE",
+            "Sex" : "pooled",
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+      },
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+         "label" : "O. taurus embryonic reads",
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+            "Analysis method" : "tophat2 v2.0.14",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
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+            "Sequencing platform and version" : "Illumina NextSeq500, 75SE",
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+         "urlTemplate" : "user_contributed_data/ezattara/whole_embryos/Otau-embryos.accepted_hits.sorted.subset.bam"
+      },
+      {
+         "category" : "Transcriptome/Splice Junctions",
+         "compress" : 0,
+         "key" : "O. taurus embryonic junctions",
+         "label" : "O. taurus embryonic junctions",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "Western Australia, Busselton",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq500, 75SE",
+            "Sex" : "pooled",
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+            }
+         },
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+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/O. taurus embryonic junctions/{refseq}/trackData.json"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "O. taurus whole body, mixed stage RNAseq, reduced coverage, females",
+         "label" : "O. taurus whole body, mixed stage RNAseq, reduced coverage, females",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "June-16-2016",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32, normalized coverage with samtools, picard and GATK",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other tissue notes" : "Mix of late larvae, prepupae, pupae and adult RNA; pool of 12 individuals",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina HiSeq 2000m 100PE",
+            "Sex" : "Female",
+            "Strain" : "NC",
+            "Tissues included" : "Whole body"
+         },
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+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "user_contributed_data/ezattara/reduced_coverage_june_2016/NC_F_merged.reduced.subset.bam"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "O. taurus whole body, mixed stage RNAseq, reduced coverage, males",
+         "label" : "O. taurus whole body, mixed stage RNAseq, reduced coverage, males",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "June-16-2016",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32, normalized coverage with samtools, picard and GATK",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other tissue notes" : "Mix of late larvae, prepupae, pupae and adult RNA; pool of 12 individuals",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina HiSeq 2000m 100PE",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "Whole body"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "user_contributed_data/ezattara/reduced_coverage_june_2016/NC_M_merged.reduced.subset.bam"
+      }
+   ]
+}
diff --git a/organisms/stage/stage-v2/14_-_Onthophagus_taurus_training/trackList.json b/organisms/stage/stage-v2/14_-_Onthophagus_taurus_training/trackList.json
new file mode 100644
index 0000000..3d98296
--- /dev/null
+++ b/organisms/stage/stage-v2/14_-_Onthophagus_taurus_training/trackList.json
@@ -0,0 +1,1603 @@
+{
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+   "names" : {
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+      "url" : "names/"
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+   "plugins" : [
+      {
+         "location" : "./plugins/WebApollo",
+         "name" : "WebApollo"
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+      {
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+               "rRNA" : {
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+         "compress" : 0,
+         "key" : "OTAU_v0.5.3-Models",
+         "label" : "onttau_current_models",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
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+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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+            "arrowheadClass" : "webapollo-arrowhead",
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+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Tardigrada/{refseq}/trackData.json"
+      },
+      {
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+         "compress" : 0,
+         "key" : "protein2genome_Tunicata",
+         "label" : "protein2genome_Tunicata",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
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+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Tunicata/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_UNCATEGORISED",
+         "label" : "protein2genome_UNCATEGORISED",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
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+               "match_part" : "protein2genome"
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+         "urlTemplate" : "tracks/protein2genome_UNCATEGORISED/{refseq}/trackData.json"
+      },
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+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from RepeatMasker as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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+            "arrowheadClass" : "webapollo-arrowhead",
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+      },
+      {
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+         "compress" : 0,
+         "key" : "repeatrunner",
+         "label" : "repeatrunner",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Repeatrunner as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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+            "arrowheadClass" : "webapollo-arrowhead",
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+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/repeatrunner/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/1. Gene Sets/Supplementary Gene Predictions",
+         "compress" : 0,
+         "key" : "snap_masked",
+         "label" : "snap_masked",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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+            "arrowheadClass" : "webapollo-arrowhead",
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+      {
+         "autoscale" : "local",
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+         "category" : "Reference Assembly",
+         "key" : "Gaps in assembly",
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+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
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+            "neg_color" : "white",
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+         "urlTemplate" : "bigwig/onttau_genome.fa.gaps.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "0.5",
+         "category" : "Reference Assembly",
+         "key" : "GC Content",
+         "label" : "GC Content",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "rgba(255,255,0,50)",
+            "pos_color" : "rgba(0,0,255,50)"
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+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/onttau_genome.fa.gc.bigwig"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "Onthophagus taurus early male pupa brain transcripts",
+         "label" : "Onthophagus taurus early male pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlM-BRN_S22.sorted.subset.bam"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "Onthophagus taurus early female pupa brain transcripts",
+         "label" : "Onthophagus taurus early female pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Female",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlF-BRN_S18.sorted.subset.bam"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "Onthophagus taurus early male pupa brain transcripts (Coverage Plot)",
+         "label" : "Onthophagus taurus early male pupa brain transcripts (Coverage Plot)",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
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+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
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+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlM-BRN_S22.sorted.subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
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+         "key" : "Onthophagus taurus early female pupa brain transcripts (Coverage Plot)",
+         "label" : "Onthophagus taurus early female pupa brain transcripts (Coverage Plot)",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
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+            "Tissues included" : "Brain"
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+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
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+         "category" : "Gene Silhouette Models/1. Gene Sets/Protein Coding",
+         "compress" : 0,
+         "key" : "Gene Silhouette Models v4",
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+         "metadata" : {
+            "Analysis method" : "Gene Silhouette Algorithm, alpha version, unpublished",
+            "Analysis provider" : "Douglas B. Rusch, Centre for Genomics and Bioinformatics, Indiana University Bloomington",
+            "Other notes" : "Novel algorithm predicts genes based on mapped RNAseq reads; based on data from early pupae, brain, dorsal head and pronotal epidermis, and posterior abdominal epidermis only"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "container-16px",
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+               "CDS" : "gnomon_CDS",
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+               "exon" : "container-100pct",
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+      {
+         "autoscale" : "local",
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+         "key" : "O. taurus M PD1 BRN+CHE+THE+GEN transcripts",
+         "label" : "O. taurus M PD1 BRN+CHE+THE+GEN transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
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+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
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+            "Tissues included" : "pooled brain, dorsal head epidermis, pronotum epidermis, posterior abdominal epidermis"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
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+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/mixed_transcripts_march_2016/ctrlM-ALL.merged.subset.bigwig"
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+      {
+         "autoscale" : "local",
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+         "key" : "O. taurus F PD1 BRN+CHE+THE+GEN transcripts",
+         "label" : "O. taurus F PD1 BRN+CHE+THE+GEN transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
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+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
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+            "Tissues included" : "pooled brain, dorsal head epidermis, pronotum epidermis, posterior abdominal epidermis"
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+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/mixed_transcripts_march_2016/ctrlF-ALL.merged_subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus M NC L3L+PP1+PD1+AD4",
+         "label" : "O. taurus M NC L3L+PP1+PD1+AD4",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version" : "Illumina HiSeq 100PE",
+            "Sex" : "Male",
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+            "Tissues included" : "whole body, pooled late 3 larvae, prepupa 1, pupa day 1, adult day 4"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
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+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/NC-L3L_PP1_PD1_AD4/NC_M_merged.subset.bigwig"
+      },
+      {
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+         "key" : "O. taurus F NC L3L+PP1+PD1+AD4",
+         "label" : "O. taurus F NC L3L+PP1+PD1+AD4",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
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+            "Other organism notes" : "Large female",
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+            "Sequencing platform and version" : "Illumina HiSeq 100PE",
+            "Sex" : "Female",
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+         },
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+      {
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+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus embryonic reads",
+         "label" : "O. taurus embryonic",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "Western Australia, Busselton",
+            "NCBI TaxID" : "166361",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq500, 75SE",
+            "Sex" : "pooled",
+            "Strain" : "WA",
+            "Tissues included" : "whole embryos, pooled mixed stages"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
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+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/whole_embryos/Otau-embryos.subset.bigwig"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "O. taurus embryonic reads",
+         "label" : "O. taurus embryonic reads",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "Western Australia, Busselton",
+            "NCBI TaxID" : "166361",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq500, 75SE",
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+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
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+      },
+      {
+         "category" : "Transcriptome/Splice Junctions",
+         "compress" : 0,
+         "key" : "O. taurus embryonic junctions",
+         "label" : "O. taurus embryonic junctions",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "Western Australia, Busselton",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
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+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq500, 75SE",
+            "Sex" : "pooled",
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+            "Tissues included" : "whole embryos, pooled mixed stages"
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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+}
diff --git a/organisms/stage/stage-v2/15_-_Onthophagus_taurus_training/trackList.json b/organisms/stage/stage-v2/15_-_Onthophagus_taurus_training/trackList.json
new file mode 100644
index 0000000..3d98296
--- /dev/null
+++ b/organisms/stage/stage-v2/15_-_Onthophagus_taurus_training/trackList.json
@@ -0,0 +1,1603 @@
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+         "key" : "protein2genome_Nematomorpha",
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+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
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+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Nematomorpha proteins as part of the MAKER automated annotation pipeline."
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+         "urlTemplate" : "tracks/protein2genome_Nematomorpha/{refseq}/trackData.json"
+      },
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+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Onychophora",
+         "label" : "protein2genome_Onychophora",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Onychophora proteins as part of the MAKER automated annotation pipeline."
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+            "arrowheadClass" : "webapollo-arrowhead",
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+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Onychophora/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Parazoa",
+         "label" : "protein2genome_Parazoa",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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+            "arrowheadClass" : "webapollo-arrowhead",
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+               "match_part" : "protein2genome"
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+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Parazoa/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Placozoa",
+         "label" : "protein2genome_Placozoa",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
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+               "match_part" : "protein2genome"
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+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Placozoa/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Platyhelminthes",
+         "label" : "protein2genome_Platyhelminthes",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
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+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Platyhelminthes/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Priapulida",
+         "label" : "protein2genome_Priapulida",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Priapulida/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Tardigrada",
+         "label" : "protein2genome_Tardigrada",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Tardigrada/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Tunicata",
+         "label" : "protein2genome_Tunicata",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Tunicata/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_UNCATEGORISED",
+         "label" : "protein2genome_UNCATEGORISED",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_UNCATEGORISED/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/2. Evidence/Repeats",
+         "compress" : 0,
+         "key" : "repeatmasker",
+         "label" : "repeatmasker",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from RepeatMasker as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "repeat"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/repeatmasker/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/2. Evidence/Repeats",
+         "compress" : 0,
+         "key" : "repeatrunner",
+         "label" : "repeatrunner",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Repeatrunner as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "repeat"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/repeatrunner/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/1. Gene Sets/Supplementary Gene Predictions",
+         "compress" : 0,
+         "key" : "snap_masked",
+         "label" : "snap_masked",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "snap"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/snap_masked/{refseq}/trackData.json"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Reference Assembly",
+         "key" : "Gaps in assembly",
+         "label" : "Gaps in assembly",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "white",
+            "pos_color" : "black"
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+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/onttau_genome.fa.gaps.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "0.5",
+         "category" : "Reference Assembly",
+         "key" : "GC Content",
+         "label" : "GC Content",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "rgba(255,255,0,50)",
+            "pos_color" : "rgba(0,0,255,50)"
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+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/onttau_genome.fa.gc.bigwig"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "Onthophagus taurus early male pupa brain transcripts",
+         "label" : "Onthophagus taurus early male pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlM-BRN_S22.sorted.subset.bam"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "Onthophagus taurus early female pupa brain transcripts",
+         "label" : "Onthophagus taurus early female pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Female",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlF-BRN_S18.sorted.subset.bam"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "Onthophagus taurus early male pupa brain transcripts (Coverage Plot)",
+         "label" : "Onthophagus taurus early male pupa brain transcripts (Coverage Plot)",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlM-BRN_S22.sorted.subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "Onthophagus taurus early female pupa brain transcripts (Coverage Plot)",
+         "label" : "Onthophagus taurus early female pupa brain transcripts (Coverage Plot)",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Female",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlF-BRN_S18.sorted.subset.bigwig"
+      },
+      {
+         "category" : "Gene Silhouette Models/1. Gene Sets/Protein Coding",
+         "compress" : 0,
+         "key" : "Gene Silhouette Models v4",
+         "label" : "Gene_Silhouette_Models_v4",
+         "metadata" : {
+            "Analysis method" : "Gene Silhouette Algorithm, alpha version, unpublished",
+            "Analysis provider" : "Douglas B. Rusch, Centre for Genomics and Bioinformatics, Indiana University Bloomington",
+            "Other notes" : "Novel algorithm predicts genes based on mapped RNAseq reads; based on data from early pupae, brain, dorsal head and pronotal epidermis, and posterior abdominal epidermis only"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "container-16px",
+            "subfeatureClasses" : {
+               "CDS" : "gnomon_CDS",
+               "UTR" : "gnomon_UTR",
+               "exon" : "container-100pct",
+               "wholeCDS" : null
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
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+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus M PD1 BRN+CHE+THE+GEN transcripts",
+         "label" : "O. taurus M PD1 BRN+CHE+THE+GEN transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "pooled brain, dorsal head epidermis, pronotum epidermis, posterior abdominal epidermis"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/mixed_transcripts_march_2016/ctrlM-ALL.merged.subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus F PD1 BRN+CHE+THE+GEN transcripts",
+         "label" : "O. taurus F PD1 BRN+CHE+THE+GEN transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
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+}
diff --git a/organisms/stage/stage-v2/16_-_Onthophagus_taurus_training/trackList.json b/organisms/stage/stage-v2/16_-_Onthophagus_taurus_training/trackList.json
new file mode 100644
index 0000000..3d98296
--- /dev/null
+++ b/organisms/stage/stage-v2/16_-_Onthophagus_taurus_training/trackList.json
@@ -0,0 +1,1603 @@
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+            }
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+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Chelicerata/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Cnidaria",
+         "label" : "protein2genome_Cnidaria",
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+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Cnidaria proteins as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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+            "arrowheadClass" : "webapollo-arrowhead",
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+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Cnidaria/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+         "key" : "protein2genome_Craniata",
+         "label" : "protein2genome_Craniata",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Craniata proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
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+               "match_part" : "protein2genome"
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+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Craniata/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Crustacea",
+         "label" : "protein2genome_Crustacea",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Crustacea proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
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+               "match_part" : "protein2genome"
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+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Crustacea/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Echinodermata",
+         "label" : "protein2genome_Echinodermata",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Echinodermata proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Echinodermata/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+         "key" : "protein2genome_Mollusca",
+         "label" : "protein2genome_Mollusca",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Mollusca proteins as part of the MAKER automated annotation pipeline."
+         },
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+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
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+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Mollusca/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Nemata",
+         "label" : "protein2genome_Nemata",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
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+               "match_part" : "protein2genome"
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+         },
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+         "urlTemplate" : "tracks/protein2genome_Nemata/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Nematomorpha",
+         "label" : "protein2genome_Nematomorpha",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Nematomorpha proteins as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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+            "arrowheadClass" : "webapollo-arrowhead",
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+               "match_part" : "protein2genome"
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+         "urlTemplate" : "tracks/protein2genome_Nematomorpha/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Onychophora",
+         "label" : "protein2genome_Onychophora",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Onychophora proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
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+               "match_part" : "protein2genome"
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+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Onychophora/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Parazoa",
+         "label" : "protein2genome_Parazoa",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Parazoa/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Placozoa",
+         "label" : "protein2genome_Placozoa",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Placozoa/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Platyhelminthes",
+         "label" : "protein2genome_Platyhelminthes",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Platyhelminthes/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Priapulida",
+         "label" : "protein2genome_Priapulida",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Priapulida/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Tardigrada",
+         "label" : "protein2genome_Tardigrada",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Tardigrada/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Tunicata",
+         "label" : "protein2genome_Tunicata",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Tunicata/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_UNCATEGORISED",
+         "label" : "protein2genome_UNCATEGORISED",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_UNCATEGORISED/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/2. Evidence/Repeats",
+         "compress" : 0,
+         "key" : "repeatmasker",
+         "label" : "repeatmasker",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from RepeatMasker as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "repeat"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/repeatmasker/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/2. Evidence/Repeats",
+         "compress" : 0,
+         "key" : "repeatrunner",
+         "label" : "repeatrunner",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Repeatrunner as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "repeat"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/repeatrunner/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/1. Gene Sets/Supplementary Gene Predictions",
+         "compress" : 0,
+         "key" : "snap_masked",
+         "label" : "snap_masked",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "snap"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/snap_masked/{refseq}/trackData.json"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Reference Assembly",
+         "key" : "Gaps in assembly",
+         "label" : "Gaps in assembly",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "white",
+            "pos_color" : "black"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/onttau_genome.fa.gaps.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "0.5",
+         "category" : "Reference Assembly",
+         "key" : "GC Content",
+         "label" : "GC Content",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "rgba(255,255,0,50)",
+            "pos_color" : "rgba(0,0,255,50)"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/onttau_genome.fa.gc.bigwig"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "Onthophagus taurus early male pupa brain transcripts",
+         "label" : "Onthophagus taurus early male pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlM-BRN_S22.sorted.subset.bam"
+      },
+      {
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+            "Other notes" : "Part of a larger project still unpublished",
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+         "metadata" : {
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+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other tissue notes" : "Mix of late larvae, prepupae, pupae and adult RNA; pool of 12 individuals",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
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+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
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+            "Other methods" : "Trimmomatic 0.32, normalized coverage with samtools, picard and GATK",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other tissue notes" : "Mix of late larvae, prepupae, pupae and adult RNA; pool of 12 individuals",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina HiSeq 2000m 100PE",
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+}
diff --git a/organisms/stage/stage-v2/17_-_Onthophagus_taurus_training/trackList.json b/organisms/stage/stage-v2/17_-_Onthophagus_taurus_training/trackList.json
new file mode 100644
index 0000000..3d98296
--- /dev/null
+++ b/organisms/stage/stage-v2/17_-_Onthophagus_taurus_training/trackList.json
@@ -0,0 +1,1603 @@
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+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
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+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Repeatrunner as part of the MAKER automated annotation pipeline."
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+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline."
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+            "Track contact" : "The i5k workspace@NAL",
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+            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
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+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+         },
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+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "Onthophagus taurus early male pupa brain transcripts",
+         "label" : "Onthophagus taurus early male pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
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+            "Tissues included" : "Brain"
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+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlM-BRN_S22.sorted.subset.bam"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "Onthophagus taurus early female pupa brain transcripts",
+         "label" : "Onthophagus taurus early female pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Female",
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+            "Tissues included" : "Brain"
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+      },
+      {
+         "autoscale" : "local",
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+         "key" : "Onthophagus taurus early male pupa brain transcripts (Coverage Plot)",
+         "label" : "Onthophagus taurus early male pupa brain transcripts (Coverage Plot)",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
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+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
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+            "Tissues included" : "Brain"
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+      },
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+         "key" : "Onthophagus taurus early female pupa brain transcripts (Coverage Plot)",
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+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
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+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
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+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
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+         "key" : "Gene Silhouette Models v4",
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+         "metadata" : {
+            "Analysis method" : "Gene Silhouette Algorithm, alpha version, unpublished",
+            "Analysis provider" : "Douglas B. Rusch, Centre for Genomics and Bioinformatics, Indiana University Bloomington",
+            "Other notes" : "Novel algorithm predicts genes based on mapped RNAseq reads; based on data from early pupae, brain, dorsal head and pronotal epidermis, and posterior abdominal epidermis only"
+         },
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+               "CDS" : "gnomon_CDS",
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+         "key" : "O. taurus M PD1 BRN+CHE+THE+GEN transcripts",
+         "label" : "O. taurus M PD1 BRN+CHE+THE+GEN transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
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+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/mixed_transcripts_march_2016/ctrlM-ALL.merged.subset.bigwig"
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+      {
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+         "key" : "O. taurus F PD1 BRN+CHE+THE+GEN transcripts",
+         "label" : "O. taurus F PD1 BRN+CHE+THE+GEN transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
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+      },
+      {
+         "autoscale" : "local",
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+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus M NC L3L+PP1+PD1+AD4",
+         "label" : "O. taurus M NC L3L+PP1+PD1+AD4",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
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+         "metadata" : {
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+            "Sequencing platform and version" : "Illumina HiSeq 100PE",
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+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
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+         "label" : "O. taurus embryonic reads",
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+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
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+         "key" : "O. taurus embryonic junctions",
+         "label" : "O. taurus embryonic junctions",
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+            "Analysis method" : "tophat2 v2.0.14",
+            "Date completed" : "Nov-15",
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+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
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+         "label" : "O. taurus whole body, mixed stage RNAseq, reduced coverage, females",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "June-16-2016",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other tissue notes" : "Mix of late larvae, prepupae, pupae and adult RNA; pool of 12 individuals",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina HiSeq 2000m 100PE",
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+         "urlTemplate" : "user_contributed_data/ezattara/reduced_coverage_june_2016/NC_F_merged.reduced.subset.bam"
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+      {
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+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
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+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32, normalized coverage with samtools, picard and GATK",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other tissue notes" : "Mix of late larvae, prepupae, pupae and adult RNA; pool of 12 individuals",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina HiSeq 2000m 100PE",
+            "Sex" : "Male",
+            "Strain" : "NC",
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diff --git a/organisms/stage/stage-v2/18_-_Onthophagus_taurus_training/trackList.json b/organisms/stage/stage-v2/18_-_Onthophagus_taurus_training/trackList.json
new file mode 100644
index 0000000..3d98296
--- /dev/null
+++ b/organisms/stage/stage-v2/18_-_Onthophagus_taurus_training/trackList.json
@@ -0,0 +1,1603 @@
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+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Parazoa",
+         "label" : "protein2genome_Parazoa",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
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+            "Track legend" : "Results from Protein2genome alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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+            "arrowheadClass" : "webapollo-arrowhead",
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+               "match_part" : "protein2genome"
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+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Parazoa/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Placozoa",
+         "label" : "protein2genome_Placozoa",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
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+               "match_part" : "protein2genome"
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+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Placozoa/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Platyhelminthes",
+         "label" : "protein2genome_Platyhelminthes",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
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+               "match_part" : "protein2genome"
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+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Platyhelminthes/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Priapulida",
+         "label" : "protein2genome_Priapulida",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Priapulida/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Tardigrada",
+         "label" : "protein2genome_Tardigrada",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Tardigrada/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Tunicata",
+         "label" : "protein2genome_Tunicata",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Tunicata/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_UNCATEGORISED",
+         "label" : "protein2genome_UNCATEGORISED",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_UNCATEGORISED/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/2. Evidence/Repeats",
+         "compress" : 0,
+         "key" : "repeatmasker",
+         "label" : "repeatmasker",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from RepeatMasker as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "repeat"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/repeatmasker/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/2. Evidence/Repeats",
+         "compress" : 0,
+         "key" : "repeatrunner",
+         "label" : "repeatrunner",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Repeatrunner as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "repeat"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/repeatrunner/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/1. Gene Sets/Supplementary Gene Predictions",
+         "compress" : 0,
+         "key" : "snap_masked",
+         "label" : "snap_masked",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "snap"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/snap_masked/{refseq}/trackData.json"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Reference Assembly",
+         "key" : "Gaps in assembly",
+         "label" : "Gaps in assembly",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "white",
+            "pos_color" : "black"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/onttau_genome.fa.gaps.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "0.5",
+         "category" : "Reference Assembly",
+         "key" : "GC Content",
+         "label" : "GC Content",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "rgba(255,255,0,50)",
+            "pos_color" : "rgba(0,0,255,50)"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/onttau_genome.fa.gc.bigwig"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "Onthophagus taurus early male pupa brain transcripts",
+         "label" : "Onthophagus taurus early male pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlM-BRN_S22.sorted.subset.bam"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "Onthophagus taurus early female pupa brain transcripts",
+         "label" : "Onthophagus taurus early female pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Female",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlF-BRN_S18.sorted.subset.bam"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "Onthophagus taurus early male pupa brain transcripts (Coverage Plot)",
+         "label" : "Onthophagus taurus early male pupa brain transcripts (Coverage Plot)",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlM-BRN_S22.sorted.subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "Onthophagus taurus early female pupa brain transcripts (Coverage Plot)",
+         "label" : "Onthophagus taurus early female pupa brain transcripts (Coverage Plot)",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Female",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlF-BRN_S18.sorted.subset.bigwig"
+      },
+      {
+         "category" : "Gene Silhouette Models/1. Gene Sets/Protein Coding",
+         "compress" : 0,
+         "key" : "Gene Silhouette Models v4",
+         "label" : "Gene_Silhouette_Models_v4",
+         "metadata" : {
+            "Analysis method" : "Gene Silhouette Algorithm, alpha version, unpublished",
+            "Analysis provider" : "Douglas B. Rusch, Centre for Genomics and Bioinformatics, Indiana University Bloomington",
+            "Other notes" : "Novel algorithm predicts genes based on mapped RNAseq reads; based on data from early pupae, brain, dorsal head and pronotal epidermis, and posterior abdominal epidermis only"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "container-16px",
+            "subfeatureClasses" : {
+               "CDS" : "gnomon_CDS",
+               "UTR" : "gnomon_UTR",
+               "exon" : "container-100pct",
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+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
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+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus M PD1 BRN+CHE+THE+GEN transcripts",
+         "label" : "O. taurus M PD1 BRN+CHE+THE+GEN transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "pooled brain, dorsal head epidermis, pronotum epidermis, posterior abdominal epidermis"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/mixed_transcripts_march_2016/ctrlM-ALL.merged.subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus F PD1 BRN+CHE+THE+GEN transcripts",
+         "label" : "O. taurus F PD1 BRN+CHE+THE+GEN transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Female",
+            "Strain" : "NC",
+            "Tissues included" : "pooled brain, dorsal head epidermis, pronotum epidermis, posterior abdominal epidermis"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
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+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/mixed_transcripts_march_2016/ctrlF-ALL.merged_subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus M NC L3L+PP1+PD1+AD4",
+         "label" : "O. taurus M NC L3L+PP1+PD1+AD4",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version" : "Illumina HiSeq 100PE",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "whole body, pooled late 3 larvae, prepupa 1, pupa day 1, adult day 4"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
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+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
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+}
diff --git a/organisms/stage/stage-v2/19_-_Onthophagus_taurus_training/trackList.json b/organisms/stage/stage-v2/19_-_Onthophagus_taurus_training/trackList.json
new file mode 100644
index 0000000..3d98296
--- /dev/null
+++ b/organisms/stage/stage-v2/19_-_Onthophagus_taurus_training/trackList.json
@@ -0,0 +1,1603 @@
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+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Craniata proteins as part of the MAKER automated annotation pipeline."
+         },
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+            "arrowheadClass" : "webapollo-arrowhead",
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+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Craniata/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Crustacea",
+         "label" : "protein2genome_Crustacea",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Crustacea proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Crustacea/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Echinodermata",
+         "label" : "protein2genome_Echinodermata",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Echinodermata proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Echinodermata/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Mollusca",
+         "label" : "protein2genome_Mollusca",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Mollusca proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
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+               "match_part" : "protein2genome"
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+         },
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+         "urlTemplate" : "tracks/protein2genome_Mollusca/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Nemata",
+         "label" : "protein2genome_Nemata",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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+            "arrowheadClass" : "webapollo-arrowhead",
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+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Nematomorpha",
+         "label" : "protein2genome_Nematomorpha",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Nematomorpha proteins as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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+            "arrowheadClass" : "webapollo-arrowhead",
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+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Onychophora",
+         "label" : "protein2genome_Onychophora",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Onychophora proteins as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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+            "arrowheadClass" : "webapollo-arrowhead",
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+               "match_part" : "protein2genome"
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+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Onychophora/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Parazoa",
+         "label" : "protein2genome_Parazoa",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
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+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Parazoa/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Placozoa",
+         "label" : "protein2genome_Placozoa",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Placozoa/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Platyhelminthes",
+         "label" : "protein2genome_Platyhelminthes",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Platyhelminthes/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Priapulida",
+         "label" : "protein2genome_Priapulida",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Priapulida/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Tardigrada",
+         "label" : "protein2genome_Tardigrada",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Tardigrada/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Tunicata",
+         "label" : "protein2genome_Tunicata",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Tunicata/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_UNCATEGORISED",
+         "label" : "protein2genome_UNCATEGORISED",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_UNCATEGORISED/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/2. Evidence/Repeats",
+         "compress" : 0,
+         "key" : "repeatmasker",
+         "label" : "repeatmasker",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from RepeatMasker as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "repeat"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/repeatmasker/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/2. Evidence/Repeats",
+         "compress" : 0,
+         "key" : "repeatrunner",
+         "label" : "repeatrunner",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Repeatrunner as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "repeat"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/repeatrunner/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/1. Gene Sets/Supplementary Gene Predictions",
+         "compress" : 0,
+         "key" : "snap_masked",
+         "label" : "snap_masked",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "snap"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/snap_masked/{refseq}/trackData.json"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Reference Assembly",
+         "key" : "Gaps in assembly",
+         "label" : "Gaps in assembly",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "white",
+            "pos_color" : "black"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/onttau_genome.fa.gaps.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "0.5",
+         "category" : "Reference Assembly",
+         "key" : "GC Content",
+         "label" : "GC Content",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "rgba(255,255,0,50)",
+            "pos_color" : "rgba(0,0,255,50)"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/onttau_genome.fa.gc.bigwig"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "Onthophagus taurus early male pupa brain transcripts",
+         "label" : "Onthophagus taurus early male pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlM-BRN_S22.sorted.subset.bam"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "Onthophagus taurus early female pupa brain transcripts",
+         "label" : "Onthophagus taurus early female pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Female",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlF-BRN_S18.sorted.subset.bam"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "Onthophagus taurus early male pupa brain transcripts (Coverage Plot)",
+         "label" : "Onthophagus taurus early male pupa brain transcripts (Coverage Plot)",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
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+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
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+}
diff --git a/organisms/stage/stage-v2/1_-_Onthophagus_taurus_training/trackList.json b/organisms/stage/stage-v2/1_-_Onthophagus_taurus_training/trackList.json
new file mode 100644
index 0000000..3d98296
--- /dev/null
+++ b/organisms/stage/stage-v2/1_-_Onthophagus_taurus_training/trackList.json
@@ -0,0 +1,1603 @@
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+         "key" : "repeatrunner",
+         "label" : "repeatrunner",
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+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Repeatrunner as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
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+      },
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+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline."
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+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Reference Assembly",
+         "key" : "Gaps in assembly",
+         "label" : "Gaps in assembly",
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+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
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+      },
+      {
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+         "key" : "GC Content",
+         "label" : "GC Content",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+         },
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+         "urlTemplate" : "bigwig/onttau_genome.fa.gc.bigwig"
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+      {
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+         "key" : "Onthophagus taurus early male pupa brain transcripts",
+         "label" : "Onthophagus taurus early male pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
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+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlM-BRN_S22.sorted.subset.bam"
+      },
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+         "key" : "Onthophagus taurus early female pupa brain transcripts",
+         "label" : "Onthophagus taurus early female pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
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+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
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+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
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+         "label" : "Onthophagus taurus early male pupa brain transcripts (Coverage Plot)",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
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+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
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+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
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+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
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+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
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+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
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+      {
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+         "compress" : 0,
+         "key" : "Gene Silhouette Models v4",
+         "label" : "Gene_Silhouette_Models_v4",
+         "metadata" : {
+            "Analysis method" : "Gene Silhouette Algorithm, alpha version, unpublished",
+            "Analysis provider" : "Douglas B. Rusch, Centre for Genomics and Bioinformatics, Indiana University Bloomington",
+            "Other notes" : "Novel algorithm predicts genes based on mapped RNAseq reads; based on data from early pupae, brain, dorsal head and pronotal epidermis, and posterior abdominal epidermis only"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "container-16px",
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+               "CDS" : "gnomon_CDS",
+               "UTR" : "gnomon_UTR",
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+      {
+         "autoscale" : "local",
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+         "key" : "O. taurus M PD1 BRN+CHE+THE+GEN transcripts",
+         "label" : "O. taurus M PD1 BRN+CHE+THE+GEN transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
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+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
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+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
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+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/mixed_transcripts_march_2016/ctrlM-ALL.merged.subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
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+         "key" : "O. taurus F PD1 BRN+CHE+THE+GEN transcripts",
+         "label" : "O. taurus F PD1 BRN+CHE+THE+GEN transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
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+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
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+            "Tissues included" : "pooled brain, dorsal head epidermis, pronotum epidermis, posterior abdominal epidermis"
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+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/mixed_transcripts_march_2016/ctrlF-ALL.merged_subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus M NC L3L+PP1+PD1+AD4",
+         "label" : "O. taurus M NC L3L+PP1+PD1+AD4",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version" : "Illumina HiSeq 100PE",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "whole body, pooled late 3 larvae, prepupa 1, pupa day 1, adult day 4"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
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+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/NC-L3L_PP1_PD1_AD4/NC_M_merged.subset.bigwig"
+      },
+      {
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+         "key" : "O. taurus F NC L3L+PP1+PD1+AD4",
+         "label" : "O. taurus F NC L3L+PP1+PD1+AD4",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version" : "Illumina HiSeq 100PE",
+            "Sex" : "Female",
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+            "Tissues included" : "whole body, pooled late 3 larvae, prepupa 1, pupa day 1, adult day 4"
+         },
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+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus embryonic reads",
+         "label" : "O. taurus embryonic",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "Western Australia, Busselton",
+            "NCBI TaxID" : "166361",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq500, 75SE",
+            "Sex" : "pooled",
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+         "label" : "O. taurus embryonic reads",
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+            "Analysis method" : "tophat2 v2.0.14",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
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+         "compress" : 0,
+         "key" : "O. taurus embryonic junctions",
+         "label" : "O. taurus embryonic junctions",
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+            "Analysis method" : "tophat2 v2.0.14",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
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+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "O. taurus whole body, mixed stage RNAseq, reduced coverage, females",
+         "label" : "O. taurus whole body, mixed stage RNAseq, reduced coverage, females",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "June-16-2016",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32, normalized coverage with samtools, picard and GATK",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other tissue notes" : "Mix of late larvae, prepupae, pupae and adult RNA; pool of 12 individuals",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina HiSeq 2000m 100PE",
+            "Sex" : "Female",
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+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "user_contributed_data/ezattara/reduced_coverage_june_2016/NC_F_merged.reduced.subset.bam"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "O. taurus whole body, mixed stage RNAseq, reduced coverage, males",
+         "label" : "O. taurus whole body, mixed stage RNAseq, reduced coverage, males",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "June-16-2016",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32, normalized coverage with samtools, picard and GATK",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other tissue notes" : "Mix of late larvae, prepupae, pupae and adult RNA; pool of 12 individuals",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina HiSeq 2000m 100PE",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "Whole body"
+         },
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+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "user_contributed_data/ezattara/reduced_coverage_june_2016/NC_M_merged.reduced.subset.bam"
+      }
+   ]
+}
diff --git a/organisms/stage/stage-v2/20_-_Onthophagus_taurus_training/trackList.json b/organisms/stage/stage-v2/20_-_Onthophagus_taurus_training/trackList.json
new file mode 100644
index 0000000..3d98296
--- /dev/null
+++ b/organisms/stage/stage-v2/20_-_Onthophagus_taurus_training/trackList.json
@@ -0,0 +1,1603 @@
+{
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+   "names" : {
+      "type" : "Hash",
+      "url" : "names/"
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+   "plugins" : [
+      {
+         "location" : "./plugins/WebApollo",
+         "name" : "WebApollo"
+      }
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+   "tracks" : [
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+            }
+         },
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+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Placozoa/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Platyhelminthes",
+         "label" : "protein2genome_Platyhelminthes",
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+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
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+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline."
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+            "arrowheadClass" : "webapollo-arrowhead",
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+               "match_part" : "protein2genome"
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+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Platyhelminthes/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Priapulida",
+         "label" : "protein2genome_Priapulida",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
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+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Priapulida/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Tardigrada",
+         "label" : "protein2genome_Tardigrada",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
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+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Tardigrada/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Tunicata",
+         "label" : "protein2genome_Tunicata",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
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+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Tunicata/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_UNCATEGORISED",
+         "label" : "protein2genome_UNCATEGORISED",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_UNCATEGORISED/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/2. Evidence/Repeats",
+         "compress" : 0,
+         "key" : "repeatmasker",
+         "label" : "repeatmasker",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from RepeatMasker as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
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+            "subfeatureClasses" : {
+               "match_part" : "repeat"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/repeatmasker/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/2. Evidence/Repeats",
+         "compress" : 0,
+         "key" : "repeatrunner",
+         "label" : "repeatrunner",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Repeatrunner as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "repeat"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/repeatrunner/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/1. Gene Sets/Supplementary Gene Predictions",
+         "compress" : 0,
+         "key" : "snap_masked",
+         "label" : "snap_masked",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
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+               "match_part" : "snap"
+            }
+         },
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+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/snap_masked/{refseq}/trackData.json"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Reference Assembly",
+         "key" : "Gaps in assembly",
+         "label" : "Gaps in assembly",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "white",
+            "pos_color" : "black"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/onttau_genome.fa.gaps.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "0.5",
+         "category" : "Reference Assembly",
+         "key" : "GC Content",
+         "label" : "GC Content",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "rgba(255,255,0,50)",
+            "pos_color" : "rgba(0,0,255,50)"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/onttau_genome.fa.gc.bigwig"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "Onthophagus taurus early male pupa brain transcripts",
+         "label" : "Onthophagus taurus early male pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlM-BRN_S22.sorted.subset.bam"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "Onthophagus taurus early female pupa brain transcripts",
+         "label" : "Onthophagus taurus early female pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Female",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlF-BRN_S18.sorted.subset.bam"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "Onthophagus taurus early male pupa brain transcripts (Coverage Plot)",
+         "label" : "Onthophagus taurus early male pupa brain transcripts (Coverage Plot)",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlM-BRN_S22.sorted.subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "Onthophagus taurus early female pupa brain transcripts (Coverage Plot)",
+         "label" : "Onthophagus taurus early female pupa brain transcripts (Coverage Plot)",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
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+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
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+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlF-BRN_S18.sorted.subset.bigwig"
+      },
+      {
+         "category" : "Gene Silhouette Models/1. Gene Sets/Protein Coding",
+         "compress" : 0,
+         "key" : "Gene Silhouette Models v4",
+         "label" : "Gene_Silhouette_Models_v4",
+         "metadata" : {
+            "Analysis method" : "Gene Silhouette Algorithm, alpha version, unpublished",
+            "Analysis provider" : "Douglas B. Rusch, Centre for Genomics and Bioinformatics, Indiana University Bloomington",
+            "Other notes" : "Novel algorithm predicts genes based on mapped RNAseq reads; based on data from early pupae, brain, dorsal head and pronotal epidermis, and posterior abdominal epidermis only"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "container-16px",
+            "subfeatureClasses" : {
+               "CDS" : "gnomon_CDS",
+               "UTR" : "gnomon_UTR",
+               "exon" : "container-100pct",
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+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
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+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus M PD1 BRN+CHE+THE+GEN transcripts",
+         "label" : "O. taurus M PD1 BRN+CHE+THE+GEN transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "pooled brain, dorsal head epidermis, pronotum epidermis, posterior abdominal epidermis"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/mixed_transcripts_march_2016/ctrlM-ALL.merged.subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus F PD1 BRN+CHE+THE+GEN transcripts",
+         "label" : "O. taurus F PD1 BRN+CHE+THE+GEN transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Female",
+            "Strain" : "NC",
+            "Tissues included" : "pooled brain, dorsal head epidermis, pronotum epidermis, posterior abdominal epidermis"
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+         "style" : {
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+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/mixed_transcripts_march_2016/ctrlF-ALL.merged_subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus M NC L3L+PP1+PD1+AD4",
+         "label" : "O. taurus M NC L3L+PP1+PD1+AD4",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version" : "Illumina HiSeq 100PE",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "whole body, pooled late 3 larvae, prepupa 1, pupa day 1, adult day 4"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
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+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/NC-L3L_PP1_PD1_AD4/NC_M_merged.subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus F NC L3L+PP1+PD1+AD4",
+         "label" : "O. taurus F NC L3L+PP1+PD1+AD4",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version" : "Illumina HiSeq 100PE",
+            "Sex" : "Female",
+            "Strain" : "NC",
+            "Tissues included" : "whole body, pooled late 3 larvae, prepupa 1, pupa day 1, adult day 4"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/NC-L3L_PP1_PD1_AD4/NC_F_merged.subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus embryonic reads",
+         "label" : "O. taurus embryonic",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "Western Australia, Busselton",
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+}
diff --git a/organisms/stage/stage-v2/21_-_Onthophagus_taurus_training/trackList.json b/organisms/stage/stage-v2/21_-_Onthophagus_taurus_training/trackList.json
new file mode 100644
index 0000000..3d98296
--- /dev/null
+++ b/organisms/stage/stage-v2/21_-_Onthophagus_taurus_training/trackList.json
@@ -0,0 +1,1603 @@
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+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Echinodermata proteins as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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+            "arrowheadClass" : "webapollo-arrowhead",
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+               "match_part" : "protein2genome"
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+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Echinodermata/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Mollusca",
+         "label" : "protein2genome_Mollusca",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Mollusca proteins as part of the MAKER automated annotation pipeline."
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+            "arrowheadClass" : "webapollo-arrowhead",
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+         "urlTemplate" : "tracks/protein2genome_Mollusca/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+         "key" : "protein2genome_Nemata",
+         "label" : "protein2genome_Nemata",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline."
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+            "arrowheadClass" : "webapollo-arrowhead",
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+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+         "key" : "protein2genome_Nematomorpha",
+         "label" : "protein2genome_Nematomorpha",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Nematomorpha proteins as part of the MAKER automated annotation pipeline."
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+            "arrowheadClass" : "webapollo-arrowhead",
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+      {
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+         "key" : "protein2genome_Onychophora",
+         "label" : "protein2genome_Onychophora",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Onychophora proteins as part of the MAKER automated annotation pipeline."
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+            "arrowheadClass" : "webapollo-arrowhead",
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+         "urlTemplate" : "tracks/protein2genome_Onychophora/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Parazoa",
+         "label" : "protein2genome_Parazoa",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
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+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Parazoa/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Placozoa",
+         "label" : "protein2genome_Placozoa",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
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+               "match_part" : "protein2genome"
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+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Placozoa/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Platyhelminthes",
+         "label" : "protein2genome_Platyhelminthes",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Platyhelminthes/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Priapulida",
+         "label" : "protein2genome_Priapulida",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Priapulida/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Tardigrada",
+         "label" : "protein2genome_Tardigrada",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Tardigrada/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Tunicata",
+         "label" : "protein2genome_Tunicata",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Tunicata/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_UNCATEGORISED",
+         "label" : "protein2genome_UNCATEGORISED",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_UNCATEGORISED/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/2. Evidence/Repeats",
+         "compress" : 0,
+         "key" : "repeatmasker",
+         "label" : "repeatmasker",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from RepeatMasker as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "repeat"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/repeatmasker/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/2. Evidence/Repeats",
+         "compress" : 0,
+         "key" : "repeatrunner",
+         "label" : "repeatrunner",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Repeatrunner as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "repeat"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/repeatrunner/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/1. Gene Sets/Supplementary Gene Predictions",
+         "compress" : 0,
+         "key" : "snap_masked",
+         "label" : "snap_masked",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "snap"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/snap_masked/{refseq}/trackData.json"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Reference Assembly",
+         "key" : "Gaps in assembly",
+         "label" : "Gaps in assembly",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "white",
+            "pos_color" : "black"
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+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/onttau_genome.fa.gaps.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "0.5",
+         "category" : "Reference Assembly",
+         "key" : "GC Content",
+         "label" : "GC Content",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "rgba(255,255,0,50)",
+            "pos_color" : "rgba(0,0,255,50)"
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+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/onttau_genome.fa.gc.bigwig"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "Onthophagus taurus early male pupa brain transcripts",
+         "label" : "Onthophagus taurus early male pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlM-BRN_S22.sorted.subset.bam"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "Onthophagus taurus early female pupa brain transcripts",
+         "label" : "Onthophagus taurus early female pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Female",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlF-BRN_S18.sorted.subset.bam"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "Onthophagus taurus early male pupa brain transcripts (Coverage Plot)",
+         "label" : "Onthophagus taurus early male pupa brain transcripts (Coverage Plot)",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
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+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlM-BRN_S22.sorted.subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "Onthophagus taurus early female pupa brain transcripts (Coverage Plot)",
+         "label" : "Onthophagus taurus early female pupa brain transcripts (Coverage Plot)",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Female",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
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+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlF-BRN_S18.sorted.subset.bigwig"
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+}
diff --git a/organisms/stage/stage-v2/22_-_Onthophagus_taurus_training/trackList.json b/organisms/stage/stage-v2/22_-_Onthophagus_taurus_training/trackList.json
new file mode 100644
index 0000000..3d98296
--- /dev/null
+++ b/organisms/stage/stage-v2/22_-_Onthophagus_taurus_training/trackList.json
@@ -0,0 +1,1603 @@
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+         "label" : "Gaps in assembly",
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+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "white",
+            "pos_color" : "black"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/onttau_genome.fa.gaps.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "0.5",
+         "category" : "Reference Assembly",
+         "key" : "GC Content",
+         "label" : "GC Content",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "rgba(255,255,0,50)",
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+         "urlTemplate" : "bigwig/onttau_genome.fa.gc.bigwig"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "Onthophagus taurus early male pupa brain transcripts",
+         "label" : "Onthophagus taurus early male pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
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+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlM-BRN_S22.sorted.subset.bam"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "Onthophagus taurus early female pupa brain transcripts",
+         "label" : "Onthophagus taurus early female pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
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+         "key" : "Onthophagus taurus early male pupa brain transcripts (Coverage Plot)",
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+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
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+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
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+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
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+         "key" : "Onthophagus taurus early female pupa brain transcripts (Coverage Plot)",
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+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Female",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
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+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
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+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlF-BRN_S18.sorted.subset.bigwig"
+      },
+      {
+         "category" : "Gene Silhouette Models/1. Gene Sets/Protein Coding",
+         "compress" : 0,
+         "key" : "Gene Silhouette Models v4",
+         "label" : "Gene_Silhouette_Models_v4",
+         "metadata" : {
+            "Analysis method" : "Gene Silhouette Algorithm, alpha version, unpublished",
+            "Analysis provider" : "Douglas B. Rusch, Centre for Genomics and Bioinformatics, Indiana University Bloomington",
+            "Other notes" : "Novel algorithm predicts genes based on mapped RNAseq reads; based on data from early pupae, brain, dorsal head and pronotal epidermis, and posterior abdominal epidermis only"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "trellis-arrowhead",
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+               "CDS" : "gnomon_CDS",
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+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus M PD1 BRN+CHE+THE+GEN transcripts",
+         "label" : "O. taurus M PD1 BRN+CHE+THE+GEN transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
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+            "Tissues included" : "pooled brain, dorsal head epidermis, pronotum epidermis, posterior abdominal epidermis"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
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+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/mixed_transcripts_march_2016/ctrlM-ALL.merged.subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus F PD1 BRN+CHE+THE+GEN transcripts",
+         "label" : "O. taurus F PD1 BRN+CHE+THE+GEN transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Female",
+            "Strain" : "NC",
+            "Tissues included" : "pooled brain, dorsal head epidermis, pronotum epidermis, posterior abdominal epidermis"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
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+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/mixed_transcripts_march_2016/ctrlF-ALL.merged_subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus M NC L3L+PP1+PD1+AD4",
+         "label" : "O. taurus M NC L3L+PP1+PD1+AD4",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version" : "Illumina HiSeq 100PE",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "whole body, pooled late 3 larvae, prepupa 1, pupa day 1, adult day 4"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/NC-L3L_PP1_PD1_AD4/NC_M_merged.subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus F NC L3L+PP1+PD1+AD4",
+         "label" : "O. taurus F NC L3L+PP1+PD1+AD4",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version" : "Illumina HiSeq 100PE",
+            "Sex" : "Female",
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+            "Tissues included" : "whole body, pooled late 3 larvae, prepupa 1, pupa day 1, adult day 4"
+         },
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+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus embryonic reads",
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+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "Western Australia, Busselton",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
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+            "Sex" : "pooled",
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+         "label" : "O. taurus embryonic reads",
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+            "Analysis method" : "tophat2 v2.0.14",
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+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
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+         "key" : "O. taurus embryonic junctions",
+         "label" : "O. taurus embryonic junctions",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "Western Australia, Busselton",
+            "NCBI TaxID" : "166361",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq500, 75SE",
+            "Sex" : "pooled",
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+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/O. taurus embryonic junctions/{refseq}/trackData.json"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "O. taurus whole body, mixed stage RNAseq, reduced coverage, females",
+         "label" : "O. taurus whole body, mixed stage RNAseq, reduced coverage, females",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "June-16-2016",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32, normalized coverage with samtools, picard and GATK",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other tissue notes" : "Mix of late larvae, prepupae, pupae and adult RNA; pool of 12 individuals",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina HiSeq 2000m 100PE",
+            "Sex" : "Female",
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+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "user_contributed_data/ezattara/reduced_coverage_june_2016/NC_F_merged.reduced.subset.bam"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "O. taurus whole body, mixed stage RNAseq, reduced coverage, males",
+         "label" : "O. taurus whole body, mixed stage RNAseq, reduced coverage, males",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "June-16-2016",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32, normalized coverage with samtools, picard and GATK",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other tissue notes" : "Mix of late larvae, prepupae, pupae and adult RNA; pool of 12 individuals",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina HiSeq 2000m 100PE",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "Whole body"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "user_contributed_data/ezattara/reduced_coverage_june_2016/NC_M_merged.reduced.subset.bam"
+      }
+   ]
+}
diff --git a/organisms/stage/stage-v2/23_-_Onthophagus_taurus_training/trackList.json b/organisms/stage/stage-v2/23_-_Onthophagus_taurus_training/trackList.json
new file mode 100644
index 0000000..3d98296
--- /dev/null
+++ b/organisms/stage/stage-v2/23_-_Onthophagus_taurus_training/trackList.json
@@ -0,0 +1,1603 @@
+{
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+   "names" : {
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+      "url" : "names/"
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+   "plugins" : [
+      {
+         "location" : "./plugins/WebApollo",
+         "name" : "WebApollo"
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+               "rRNA" : {
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+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Priapulida/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Tardigrada",
+         "label" : "protein2genome_Tardigrada",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
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+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Tardigrada/{refseq}/trackData.json"
+      },
+      {
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+         "key" : "protein2genome_Tunicata",
+         "label" : "protein2genome_Tunicata",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
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+         "urlTemplate" : "tracks/protein2genome_Tunicata/{refseq}/trackData.json"
+      },
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+         "compress" : 0,
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+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline."
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+         "style" : {
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+      },
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+         "label" : "repeatmasker",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from RepeatMasker as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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+            "arrowheadClass" : "webapollo-arrowhead",
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+         "urlTemplate" : "tracks/repeatmasker/{refseq}/trackData.json"
+      },
+      {
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+         "compress" : 0,
+         "key" : "repeatrunner",
+         "label" : "repeatrunner",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Repeatrunner as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
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+         },
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+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/repeatrunner/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/1. Gene Sets/Supplementary Gene Predictions",
+         "compress" : 0,
+         "key" : "snap_masked",
+         "label" : "snap_masked",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
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+               "match_part" : "snap"
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+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Reference Assembly",
+         "key" : "Gaps in assembly",
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+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
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+            "neg_color" : "white",
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+         "urlTemplate" : "bigwig/onttau_genome.fa.gaps.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "0.5",
+         "category" : "Reference Assembly",
+         "key" : "GC Content",
+         "label" : "GC Content",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "rgba(255,255,0,50)",
+            "pos_color" : "rgba(0,0,255,50)"
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+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/onttau_genome.fa.gc.bigwig"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "Onthophagus taurus early male pupa brain transcripts",
+         "label" : "Onthophagus taurus early male pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlM-BRN_S22.sorted.subset.bam"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "Onthophagus taurus early female pupa brain transcripts",
+         "label" : "Onthophagus taurus early female pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Female",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlF-BRN_S18.sorted.subset.bam"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "Onthophagus taurus early male pupa brain transcripts (Coverage Plot)",
+         "label" : "Onthophagus taurus early male pupa brain transcripts (Coverage Plot)",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
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+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
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+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlM-BRN_S22.sorted.subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
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+         "key" : "Onthophagus taurus early female pupa brain transcripts (Coverage Plot)",
+         "label" : "Onthophagus taurus early female pupa brain transcripts (Coverage Plot)",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
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+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
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+      {
+         "category" : "Gene Silhouette Models/1. Gene Sets/Protein Coding",
+         "compress" : 0,
+         "key" : "Gene Silhouette Models v4",
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+         "metadata" : {
+            "Analysis method" : "Gene Silhouette Algorithm, alpha version, unpublished",
+            "Analysis provider" : "Douglas B. Rusch, Centre for Genomics and Bioinformatics, Indiana University Bloomington",
+            "Other notes" : "Novel algorithm predicts genes based on mapped RNAseq reads; based on data from early pupae, brain, dorsal head and pronotal epidermis, and posterior abdominal epidermis only"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "container-16px",
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+               "CDS" : "gnomon_CDS",
+               "UTR" : "gnomon_UTR",
+               "exon" : "container-100pct",
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+            }
+         },
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+         "type" : "FeatureTrack",
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+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
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+         "key" : "O. taurus M PD1 BRN+CHE+THE+GEN transcripts",
+         "label" : "O. taurus M PD1 BRN+CHE+THE+GEN transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
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+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
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+            "Tissues included" : "pooled brain, dorsal head epidermis, pronotum epidermis, posterior abdominal epidermis"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
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+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/mixed_transcripts_march_2016/ctrlM-ALL.merged.subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus F PD1 BRN+CHE+THE+GEN transcripts",
+         "label" : "O. taurus F PD1 BRN+CHE+THE+GEN transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
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+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
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+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
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+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus M NC L3L+PP1+PD1+AD4",
+         "label" : "O. taurus M NC L3L+PP1+PD1+AD4",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version" : "Illumina HiSeq 100PE",
+            "Sex" : "Male",
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+            "Tissues included" : "whole body, pooled late 3 larvae, prepupa 1, pupa day 1, adult day 4"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
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+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/NC-L3L_PP1_PD1_AD4/NC_M_merged.subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
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+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus F NC L3L+PP1+PD1+AD4",
+         "label" : "O. taurus F NC L3L+PP1+PD1+AD4",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
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+            "Other organism notes" : "Large female",
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+            "Sequencing platform and version" : "Illumina HiSeq 100PE",
+            "Sex" : "Female",
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+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
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+         "urlTemplate" : "user_contributed_data/ezattara/NC-L3L_PP1_PD1_AD4/NC_F_merged.subset.bigwig"
+      },
+      {
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+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus embryonic reads",
+         "label" : "O. taurus embryonic",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "Western Australia, Busselton",
+            "NCBI TaxID" : "166361",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq500, 75SE",
+            "Sex" : "pooled",
+            "Strain" : "WA",
+            "Tissues included" : "whole embryos, pooled mixed stages"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/whole_embryos/Otau-embryos.subset.bigwig"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "O. taurus embryonic reads",
+         "label" : "O. taurus embryonic reads",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "Western Australia, Busselton",
+            "NCBI TaxID" : "166361",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq500, 75SE",
+            "Sex" : "pooled",
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+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "user_contributed_data/ezattara/whole_embryos/Otau-embryos.accepted_hits.sorted.subset.bam"
+      },
+      {
+         "category" : "Transcriptome/Splice Junctions",
+         "compress" : 0,
+         "key" : "O. taurus embryonic junctions",
+         "label" : "O. taurus embryonic junctions",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "Western Australia, Busselton",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
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+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
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+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
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+            "Other methods" : "Trimmomatic 0.32, normalized coverage with samtools, picard and GATK",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other tissue notes" : "Mix of late larvae, prepupae, pupae and adult RNA; pool of 12 individuals",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
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+}
diff --git a/organisms/stage/stage-v2/24_-_Onthophagus_taurus_training/trackList.json b/organisms/stage/stage-v2/24_-_Onthophagus_taurus_training/trackList.json
new file mode 100644
index 0000000..3d98296
--- /dev/null
+++ b/organisms/stage/stage-v2/24_-_Onthophagus_taurus_training/trackList.json
@@ -0,0 +1,1603 @@
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+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline."
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+         "urlTemplate" : "tracks/protein2genome_Nemata/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+         "key" : "protein2genome_Nematomorpha",
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+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Nematomorpha proteins as part of the MAKER automated annotation pipeline."
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+            "arrowheadClass" : "webapollo-arrowhead",
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+         "urlTemplate" : "tracks/protein2genome_Nematomorpha/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Onychophora",
+         "label" : "protein2genome_Onychophora",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Onychophora proteins as part of the MAKER automated annotation pipeline."
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+            "arrowheadClass" : "webapollo-arrowhead",
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+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Onychophora/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Parazoa",
+         "label" : "protein2genome_Parazoa",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline."
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+            "arrowheadClass" : "webapollo-arrowhead",
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+         "urlTemplate" : "tracks/protein2genome_Parazoa/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Placozoa",
+         "label" : "protein2genome_Placozoa",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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+            "arrowheadClass" : "webapollo-arrowhead",
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+               "match_part" : "protein2genome"
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+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Placozoa/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Platyhelminthes",
+         "label" : "protein2genome_Platyhelminthes",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
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+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Platyhelminthes/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Priapulida",
+         "label" : "protein2genome_Priapulida",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Priapulida/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Tardigrada",
+         "label" : "protein2genome_Tardigrada",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Tardigrada/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Tunicata",
+         "label" : "protein2genome_Tunicata",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
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+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Tunicata/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_UNCATEGORISED",
+         "label" : "protein2genome_UNCATEGORISED",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
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+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_UNCATEGORISED/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/2. Evidence/Repeats",
+         "compress" : 0,
+         "key" : "repeatmasker",
+         "label" : "repeatmasker",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from RepeatMasker as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
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+            "subfeatureClasses" : {
+               "match_part" : "repeat"
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+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/repeatmasker/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/2. Evidence/Repeats",
+         "compress" : 0,
+         "key" : "repeatrunner",
+         "label" : "repeatrunner",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Repeatrunner as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "repeat"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/repeatrunner/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/1. Gene Sets/Supplementary Gene Predictions",
+         "compress" : 0,
+         "key" : "snap_masked",
+         "label" : "snap_masked",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "snap"
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+         },
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+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/snap_masked/{refseq}/trackData.json"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Reference Assembly",
+         "key" : "Gaps in assembly",
+         "label" : "Gaps in assembly",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "white",
+            "pos_color" : "black"
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+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/onttau_genome.fa.gaps.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "0.5",
+         "category" : "Reference Assembly",
+         "key" : "GC Content",
+         "label" : "GC Content",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "rgba(255,255,0,50)",
+            "pos_color" : "rgba(0,0,255,50)"
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+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/onttau_genome.fa.gc.bigwig"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "Onthophagus taurus early male pupa brain transcripts",
+         "label" : "Onthophagus taurus early male pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlM-BRN_S22.sorted.subset.bam"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "Onthophagus taurus early female pupa brain transcripts",
+         "label" : "Onthophagus taurus early female pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Female",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlF-BRN_S18.sorted.subset.bam"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "Onthophagus taurus early male pupa brain transcripts (Coverage Plot)",
+         "label" : "Onthophagus taurus early male pupa brain transcripts (Coverage Plot)",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlM-BRN_S22.sorted.subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "Onthophagus taurus early female pupa brain transcripts (Coverage Plot)",
+         "label" : "Onthophagus taurus early female pupa brain transcripts (Coverage Plot)",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Female",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlF-BRN_S18.sorted.subset.bigwig"
+      },
+      {
+         "category" : "Gene Silhouette Models/1. Gene Sets/Protein Coding",
+         "compress" : 0,
+         "key" : "Gene Silhouette Models v4",
+         "label" : "Gene_Silhouette_Models_v4",
+         "metadata" : {
+            "Analysis method" : "Gene Silhouette Algorithm, alpha version, unpublished",
+            "Analysis provider" : "Douglas B. Rusch, Centre for Genomics and Bioinformatics, Indiana University Bloomington",
+            "Other notes" : "Novel algorithm predicts genes based on mapped RNAseq reads; based on data from early pupae, brain, dorsal head and pronotal epidermis, and posterior abdominal epidermis only"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "container-16px",
+            "subfeatureClasses" : {
+               "CDS" : "gnomon_CDS",
+               "UTR" : "gnomon_UTR",
+               "exon" : "container-100pct",
+               "wholeCDS" : null
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/Gene_Silhouette_Models_v4/{refseq}/trackData.json"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus M PD1 BRN+CHE+THE+GEN transcripts",
+         "label" : "O. taurus M PD1 BRN+CHE+THE+GEN transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "pooled brain, dorsal head epidermis, pronotum epidermis, posterior abdominal epidermis"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
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diff --git a/organisms/stage/stage-v2/25_-_Onthophagus_taurus_training/trackList.json b/organisms/stage/stage-v2/25_-_Onthophagus_taurus_training/trackList.json
new file mode 100644
index 0000000..3d98296
--- /dev/null
+++ b/organisms/stage/stage-v2/25_-_Onthophagus_taurus_training/trackList.json
@@ -0,0 +1,1603 @@
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+         "key" : "protein2genome_Chelicerata",
+         "label" : "protein2genome_Chelicerata",
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+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Chelicerata proteins as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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+            "arrowheadClass" : "webapollo-arrowhead",
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+         "urlTemplate" : "tracks/protein2genome_Chelicerata/{refseq}/trackData.json"
+      },
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+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+         "key" : "protein2genome_Cnidaria",
+         "label" : "protein2genome_Cnidaria",
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+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Cnidaria proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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+         "urlTemplate" : "tracks/protein2genome_Cnidaria/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+         "key" : "protein2genome_Craniata",
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+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Craniata proteins as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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+            "arrowheadClass" : "webapollo-arrowhead",
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+         "urlTemplate" : "tracks/protein2genome_Craniata/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+         "key" : "protein2genome_Crustacea",
+         "label" : "protein2genome_Crustacea",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Crustacea proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
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+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Crustacea/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Echinodermata",
+         "label" : "protein2genome_Echinodermata",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Echinodermata proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
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+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Echinodermata/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+         "key" : "protein2genome_Mollusca",
+         "label" : "protein2genome_Mollusca",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Mollusca proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
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+         },
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+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Nemata",
+         "label" : "protein2genome_Nemata",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline."
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+            "arrowheadClass" : "webapollo-arrowhead",
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+         },
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+         "urlTemplate" : "tracks/protein2genome_Nemata/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+         "key" : "protein2genome_Nematomorpha",
+         "label" : "protein2genome_Nematomorpha",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Nematomorpha proteins as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
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+               "match_part" : "protein2genome"
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+         },
+         "trackType" : null,
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+         "urlTemplate" : "tracks/protein2genome_Nematomorpha/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+         "key" : "protein2genome_Onychophora",
+         "label" : "protein2genome_Onychophora",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Onychophora proteins as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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+            "arrowheadClass" : "webapollo-arrowhead",
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+               "match_part" : "protein2genome"
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+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Onychophora/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Parazoa",
+         "label" : "protein2genome_Parazoa",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
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+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Parazoa/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Placozoa",
+         "label" : "protein2genome_Placozoa",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
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+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Placozoa/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Platyhelminthes",
+         "label" : "protein2genome_Platyhelminthes",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
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+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Platyhelminthes/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Priapulida",
+         "label" : "protein2genome_Priapulida",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
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+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Priapulida/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Tardigrada",
+         "label" : "protein2genome_Tardigrada",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Tardigrada/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Tunicata",
+         "label" : "protein2genome_Tunicata",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
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+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Tunicata/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_UNCATEGORISED",
+         "label" : "protein2genome_UNCATEGORISED",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_UNCATEGORISED/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/2. Evidence/Repeats",
+         "compress" : 0,
+         "key" : "repeatmasker",
+         "label" : "repeatmasker",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from RepeatMasker as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "repeat"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/repeatmasker/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/2. Evidence/Repeats",
+         "compress" : 0,
+         "key" : "repeatrunner",
+         "label" : "repeatrunner",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Repeatrunner as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "repeat"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/repeatrunner/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/1. Gene Sets/Supplementary Gene Predictions",
+         "compress" : 0,
+         "key" : "snap_masked",
+         "label" : "snap_masked",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "snap"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/snap_masked/{refseq}/trackData.json"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Reference Assembly",
+         "key" : "Gaps in assembly",
+         "label" : "Gaps in assembly",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "white",
+            "pos_color" : "black"
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+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/onttau_genome.fa.gaps.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "0.5",
+         "category" : "Reference Assembly",
+         "key" : "GC Content",
+         "label" : "GC Content",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "rgba(255,255,0,50)",
+            "pos_color" : "rgba(0,0,255,50)"
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+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/onttau_genome.fa.gc.bigwig"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "Onthophagus taurus early male pupa brain transcripts",
+         "label" : "Onthophagus taurus early male pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
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+            "Analysis method" : "Gene Silhouette Algorithm, alpha version, unpublished",
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+            "Other notes" : "Novel algorithm predicts genes based on mapped RNAseq reads; based on data from early pupae, brain, dorsal head and pronotal epidermis, and posterior abdominal epidermis only"
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+         "metadata" : {
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+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other tissue notes" : "Mix of late larvae, prepupae, pupae and adult RNA; pool of 12 individuals",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
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+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
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+            "Other methods" : "Trimmomatic 0.32, normalized coverage with samtools, picard and GATK",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other tissue notes" : "Mix of late larvae, prepupae, pupae and adult RNA; pool of 12 individuals",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina HiSeq 2000m 100PE",
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+}
diff --git a/organisms/stage/stage-v2/26_-_Onthophagus_taurus_training/trackList.json b/organisms/stage/stage-v2/26_-_Onthophagus_taurus_training/trackList.json
new file mode 100644
index 0000000..3d98296
--- /dev/null
+++ b/organisms/stage/stage-v2/26_-_Onthophagus_taurus_training/trackList.json
@@ -0,0 +1,1603 @@
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+         "urlTemplate" : "tracks/protein2genome_Tunicata/{refseq}/trackData.json"
+      },
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+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
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+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from RepeatMasker as part of the MAKER automated annotation pipeline."
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+         "key" : "repeatrunner",
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+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Repeatrunner as part of the MAKER automated annotation pipeline."
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+      },
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+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline."
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+         "category" : "Reference Assembly",
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+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
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+      {
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+         "category" : "Reference Assembly",
+         "key" : "GC Content",
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+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
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+            "neg_color" : "rgba(255,255,0,50)",
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+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/onttau_genome.fa.gc.bigwig"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "Onthophagus taurus early male pupa brain transcripts",
+         "label" : "Onthophagus taurus early male pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
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+            "Tissues included" : "Brain"
+         },
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+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlM-BRN_S22.sorted.subset.bam"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "Onthophagus taurus early female pupa brain transcripts",
+         "label" : "Onthophagus taurus early female pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Female",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlF-BRN_S18.sorted.subset.bam"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
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+         "key" : "Onthophagus taurus early male pupa brain transcripts (Coverage Plot)",
+         "label" : "Onthophagus taurus early male pupa brain transcripts (Coverage Plot)",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
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+            "Tissues included" : "Brain"
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+      },
+      {
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+         "key" : "Onthophagus taurus early female pupa brain transcripts (Coverage Plot)",
+         "label" : "Onthophagus taurus early female pupa brain transcripts (Coverage Plot)",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
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+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
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+            "Tissues included" : "Brain"
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+         "compress" : 0,
+         "key" : "Gene Silhouette Models v4",
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+         "metadata" : {
+            "Analysis method" : "Gene Silhouette Algorithm, alpha version, unpublished",
+            "Analysis provider" : "Douglas B. Rusch, Centre for Genomics and Bioinformatics, Indiana University Bloomington",
+            "Other notes" : "Novel algorithm predicts genes based on mapped RNAseq reads; based on data from early pupae, brain, dorsal head and pronotal epidermis, and posterior abdominal epidermis only"
+         },
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+               "CDS" : "gnomon_CDS",
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+      {
+         "autoscale" : "local",
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+         "key" : "O. taurus M PD1 BRN+CHE+THE+GEN transcripts",
+         "label" : "O. taurus M PD1 BRN+CHE+THE+GEN transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
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+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
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+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/mixed_transcripts_march_2016/ctrlM-ALL.merged.subset.bigwig"
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+      {
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+         "key" : "O. taurus F PD1 BRN+CHE+THE+GEN transcripts",
+         "label" : "O. taurus F PD1 BRN+CHE+THE+GEN transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
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+      },
+      {
+         "autoscale" : "local",
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+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus M NC L3L+PP1+PD1+AD4",
+         "label" : "O. taurus M NC L3L+PP1+PD1+AD4",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version" : "Illumina HiSeq 100PE",
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+         },
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+      {
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+         "label" : "O. taurus F NC L3L+PP1+PD1+AD4",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
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+            "Sequencing platform and version" : "Illumina HiSeq 100PE",
+            "Sex" : "Female",
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+         },
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+            "Analysis method" : "tophat2 v2.0.14",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
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+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
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+            "Sex" : "pooled",
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+         "urlTemplate" : "user_contributed_data/ezattara/whole_embryos/Otau-embryos.subset.bigwig"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
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+         "label" : "O. taurus embryonic reads",
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+            "Analysis method" : "tophat2 v2.0.14",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "Western Australia, Busselton",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
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+            "Sequencing platform and version" : "Illumina NextSeq500, 75SE",
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+         "category" : "Transcriptome/Splice Junctions",
+         "compress" : 0,
+         "key" : "O. taurus embryonic junctions",
+         "label" : "O. taurus embryonic junctions",
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+            "Analysis method" : "tophat2 v2.0.14",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
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+            "Sex" : "pooled",
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+            }
+         },
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+         "type" : "FeatureTrack",
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+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "O. taurus whole body, mixed stage RNAseq, reduced coverage, females",
+         "label" : "O. taurus whole body, mixed stage RNAseq, reduced coverage, females",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "June-16-2016",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32, normalized coverage with samtools, picard and GATK",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other tissue notes" : "Mix of late larvae, prepupae, pupae and adult RNA; pool of 12 individuals",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina HiSeq 2000m 100PE",
+            "Sex" : "Female",
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+            "Tissues included" : "Whole body"
+         },
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+         "key" : "O. taurus whole body, mixed stage RNAseq, reduced coverage, males",
+         "label" : "O. taurus whole body, mixed stage RNAseq, reduced coverage, males",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "June-16-2016",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32, normalized coverage with samtools, picard and GATK",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other tissue notes" : "Mix of late larvae, prepupae, pupae and adult RNA; pool of 12 individuals",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina HiSeq 2000m 100PE",
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+}
diff --git a/organisms/stage/stage-v2/27_-_Onthophagus_taurus_training/trackList.json b/organisms/stage/stage-v2/27_-_Onthophagus_taurus_training/trackList.json
new file mode 100644
index 0000000..3d98296
--- /dev/null
+++ b/organisms/stage/stage-v2/27_-_Onthophagus_taurus_training/trackList.json
@@ -0,0 +1,1603 @@
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+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Onychophora proteins as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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+            "arrowheadClass" : "webapollo-arrowhead",
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+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Onychophora/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Parazoa",
+         "label" : "protein2genome_Parazoa",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
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+               "match_part" : "protein2genome"
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+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Parazoa/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Placozoa",
+         "label" : "protein2genome_Placozoa",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
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+               "match_part" : "protein2genome"
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+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Placozoa/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Platyhelminthes",
+         "label" : "protein2genome_Platyhelminthes",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
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+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Platyhelminthes/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Priapulida",
+         "label" : "protein2genome_Priapulida",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Priapulida/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Tardigrada",
+         "label" : "protein2genome_Tardigrada",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Tardigrada/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Tunicata",
+         "label" : "protein2genome_Tunicata",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Tunicata/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_UNCATEGORISED",
+         "label" : "protein2genome_UNCATEGORISED",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_UNCATEGORISED/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/2. Evidence/Repeats",
+         "compress" : 0,
+         "key" : "repeatmasker",
+         "label" : "repeatmasker",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from RepeatMasker as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "repeat"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/repeatmasker/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/2. Evidence/Repeats",
+         "compress" : 0,
+         "key" : "repeatrunner",
+         "label" : "repeatrunner",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Repeatrunner as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "repeat"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/repeatrunner/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/1. Gene Sets/Supplementary Gene Predictions",
+         "compress" : 0,
+         "key" : "snap_masked",
+         "label" : "snap_masked",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "snap"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/snap_masked/{refseq}/trackData.json"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Reference Assembly",
+         "key" : "Gaps in assembly",
+         "label" : "Gaps in assembly",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "white",
+            "pos_color" : "black"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/onttau_genome.fa.gaps.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "0.5",
+         "category" : "Reference Assembly",
+         "key" : "GC Content",
+         "label" : "GC Content",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "rgba(255,255,0,50)",
+            "pos_color" : "rgba(0,0,255,50)"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/onttau_genome.fa.gc.bigwig"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "Onthophagus taurus early male pupa brain transcripts",
+         "label" : "Onthophagus taurus early male pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlM-BRN_S22.sorted.subset.bam"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "Onthophagus taurus early female pupa brain transcripts",
+         "label" : "Onthophagus taurus early female pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Female",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlF-BRN_S18.sorted.subset.bam"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "Onthophagus taurus early male pupa brain transcripts (Coverage Plot)",
+         "label" : "Onthophagus taurus early male pupa brain transcripts (Coverage Plot)",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlM-BRN_S22.sorted.subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "Onthophagus taurus early female pupa brain transcripts (Coverage Plot)",
+         "label" : "Onthophagus taurus early female pupa brain transcripts (Coverage Plot)",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Female",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlF-BRN_S18.sorted.subset.bigwig"
+      },
+      {
+         "category" : "Gene Silhouette Models/1. Gene Sets/Protein Coding",
+         "compress" : 0,
+         "key" : "Gene Silhouette Models v4",
+         "label" : "Gene_Silhouette_Models_v4",
+         "metadata" : {
+            "Analysis method" : "Gene Silhouette Algorithm, alpha version, unpublished",
+            "Analysis provider" : "Douglas B. Rusch, Centre for Genomics and Bioinformatics, Indiana University Bloomington",
+            "Other notes" : "Novel algorithm predicts genes based on mapped RNAseq reads; based on data from early pupae, brain, dorsal head and pronotal epidermis, and posterior abdominal epidermis only"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "container-16px",
+            "subfeatureClasses" : {
+               "CDS" : "gnomon_CDS",
+               "UTR" : "gnomon_UTR",
+               "exon" : "container-100pct",
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+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
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+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus M PD1 BRN+CHE+THE+GEN transcripts",
+         "label" : "O. taurus M PD1 BRN+CHE+THE+GEN transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "pooled brain, dorsal head epidermis, pronotum epidermis, posterior abdominal epidermis"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/mixed_transcripts_march_2016/ctrlM-ALL.merged.subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus F PD1 BRN+CHE+THE+GEN transcripts",
+         "label" : "O. taurus F PD1 BRN+CHE+THE+GEN transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Female",
+            "Strain" : "NC",
+            "Tissues included" : "pooled brain, dorsal head epidermis, pronotum epidermis, posterior abdominal epidermis"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
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+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/mixed_transcripts_march_2016/ctrlF-ALL.merged_subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus M NC L3L+PP1+PD1+AD4",
+         "label" : "O. taurus M NC L3L+PP1+PD1+AD4",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
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+}
diff --git a/organisms/stage/stage-v2/28_-_Onthophagus_taurus_training/trackList.json b/organisms/stage/stage-v2/28_-_Onthophagus_taurus_training/trackList.json
new file mode 100644
index 0000000..3d98296
--- /dev/null
+++ b/organisms/stage/stage-v2/28_-_Onthophagus_taurus_training/trackList.json
@@ -0,0 +1,1603 @@
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+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Craniata",
+         "label" : "protein2genome_Craniata",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Craniata proteins as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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+            "arrowheadClass" : "webapollo-arrowhead",
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+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Craniata/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Crustacea",
+         "label" : "protein2genome_Crustacea",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Crustacea proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
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+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Crustacea/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Echinodermata",
+         "label" : "protein2genome_Echinodermata",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Echinodermata proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
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+               "match_part" : "protein2genome"
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+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Echinodermata/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+         "key" : "protein2genome_Mollusca",
+         "label" : "protein2genome_Mollusca",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Mollusca proteins as part of the MAKER automated annotation pipeline."
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+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
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+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Mollusca/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Nemata",
+         "label" : "protein2genome_Nemata",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline."
+         },
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+            "arrowheadClass" : "webapollo-arrowhead",
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+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+         "key" : "protein2genome_Nematomorpha",
+         "label" : "protein2genome_Nematomorpha",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Nematomorpha proteins as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
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+               "match_part" : "protein2genome"
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+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Nematomorpha/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+         "key" : "protein2genome_Onychophora",
+         "label" : "protein2genome_Onychophora",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Onychophora proteins as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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+            "arrowheadClass" : "webapollo-arrowhead",
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+               "match_part" : "protein2genome"
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+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Onychophora/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Parazoa",
+         "label" : "protein2genome_Parazoa",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
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+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Parazoa/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Placozoa",
+         "label" : "protein2genome_Placozoa",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Placozoa/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Platyhelminthes",
+         "label" : "protein2genome_Platyhelminthes",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Platyhelminthes/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Priapulida",
+         "label" : "protein2genome_Priapulida",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Priapulida/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Tardigrada",
+         "label" : "protein2genome_Tardigrada",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Tardigrada/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Tunicata",
+         "label" : "protein2genome_Tunicata",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Tunicata/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_UNCATEGORISED",
+         "label" : "protein2genome_UNCATEGORISED",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_UNCATEGORISED/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/2. Evidence/Repeats",
+         "compress" : 0,
+         "key" : "repeatmasker",
+         "label" : "repeatmasker",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from RepeatMasker as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "repeat"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/repeatmasker/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/2. Evidence/Repeats",
+         "compress" : 0,
+         "key" : "repeatrunner",
+         "label" : "repeatrunner",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Repeatrunner as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "repeat"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/repeatrunner/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/1. Gene Sets/Supplementary Gene Predictions",
+         "compress" : 0,
+         "key" : "snap_masked",
+         "label" : "snap_masked",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "snap"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/snap_masked/{refseq}/trackData.json"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Reference Assembly",
+         "key" : "Gaps in assembly",
+         "label" : "Gaps in assembly",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "white",
+            "pos_color" : "black"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/onttau_genome.fa.gaps.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "0.5",
+         "category" : "Reference Assembly",
+         "key" : "GC Content",
+         "label" : "GC Content",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "rgba(255,255,0,50)",
+            "pos_color" : "rgba(0,0,255,50)"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/onttau_genome.fa.gc.bigwig"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "Onthophagus taurus early male pupa brain transcripts",
+         "label" : "Onthophagus taurus early male pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlM-BRN_S22.sorted.subset.bam"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "Onthophagus taurus early female pupa brain transcripts",
+         "label" : "Onthophagus taurus early female pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Female",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlF-BRN_S18.sorted.subset.bam"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
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+            "Analysis method" : "tophat2 v2.1.0",
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+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
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+            "Sex" : "Male",
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+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
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+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
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+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32, normalized coverage with samtools, picard and GATK",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other tissue notes" : "Mix of late larvae, prepupae, pupae and adult RNA; pool of 12 individuals",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
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+}
diff --git a/organisms/stage/stage-v2/29_-_Onthophagus_taurus_training/trackList.json b/organisms/stage/stage-v2/29_-_Onthophagus_taurus_training/trackList.json
new file mode 100644
index 0000000..3d98296
--- /dev/null
+++ b/organisms/stage/stage-v2/29_-_Onthophagus_taurus_training/trackList.json
@@ -0,0 +1,1603 @@
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+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from RepeatMasker as part of the MAKER automated annotation pipeline."
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+         "key" : "repeatrunner",
+         "label" : "repeatrunner",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Repeatrunner as part of the MAKER automated annotation pipeline."
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+         "compress" : 0,
+         "key" : "snap_masked",
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+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Reference Assembly",
+         "key" : "Gaps in assembly",
+         "label" : "Gaps in assembly",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
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+            "neg_color" : "white",
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+         "urlTemplate" : "bigwig/onttau_genome.fa.gaps.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "0.5",
+         "category" : "Reference Assembly",
+         "key" : "GC Content",
+         "label" : "GC Content",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+         },
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+         "urlTemplate" : "bigwig/onttau_genome.fa.gc.bigwig"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "Onthophagus taurus early male pupa brain transcripts",
+         "label" : "Onthophagus taurus early male pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
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+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlM-BRN_S22.sorted.subset.bam"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "Onthophagus taurus early female pupa brain transcripts",
+         "label" : "Onthophagus taurus early female pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Female",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
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+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
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+         "key" : "Onthophagus taurus early male pupa brain transcripts (Coverage Plot)",
+         "label" : "Onthophagus taurus early male pupa brain transcripts (Coverage Plot)",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
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+            "Tissues included" : "Brain"
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+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
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+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlM-BRN_S22.sorted.subset.bigwig"
+      },
+      {
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+         "key" : "Onthophagus taurus early female pupa brain transcripts (Coverage Plot)",
+         "label" : "Onthophagus taurus early female pupa brain transcripts (Coverage Plot)",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
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+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
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+      },
+      {
+         "category" : "Gene Silhouette Models/1. Gene Sets/Protein Coding",
+         "compress" : 0,
+         "key" : "Gene Silhouette Models v4",
+         "label" : "Gene_Silhouette_Models_v4",
+         "metadata" : {
+            "Analysis method" : "Gene Silhouette Algorithm, alpha version, unpublished",
+            "Analysis provider" : "Douglas B. Rusch, Centre for Genomics and Bioinformatics, Indiana University Bloomington",
+            "Other notes" : "Novel algorithm predicts genes based on mapped RNAseq reads; based on data from early pupae, brain, dorsal head and pronotal epidermis, and posterior abdominal epidermis only"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "container-16px",
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+               "CDS" : "gnomon_CDS",
+               "UTR" : "gnomon_UTR",
+               "exon" : "container-100pct",
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+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
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+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus M PD1 BRN+CHE+THE+GEN transcripts",
+         "label" : "O. taurus M PD1 BRN+CHE+THE+GEN transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "pooled brain, dorsal head epidermis, pronotum epidermis, posterior abdominal epidermis"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/mixed_transcripts_march_2016/ctrlM-ALL.merged.subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus F PD1 BRN+CHE+THE+GEN transcripts",
+         "label" : "O. taurus F PD1 BRN+CHE+THE+GEN transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Female",
+            "Strain" : "NC",
+            "Tissues included" : "pooled brain, dorsal head epidermis, pronotum epidermis, posterior abdominal epidermis"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
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+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/mixed_transcripts_march_2016/ctrlF-ALL.merged_subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus M NC L3L+PP1+PD1+AD4",
+         "label" : "O. taurus M NC L3L+PP1+PD1+AD4",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version" : "Illumina HiSeq 100PE",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "whole body, pooled late 3 larvae, prepupa 1, pupa day 1, adult day 4"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/NC-L3L_PP1_PD1_AD4/NC_M_merged.subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus F NC L3L+PP1+PD1+AD4",
+         "label" : "O. taurus F NC L3L+PP1+PD1+AD4",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version" : "Illumina HiSeq 100PE",
+            "Sex" : "Female",
+            "Strain" : "NC",
+            "Tissues included" : "whole body, pooled late 3 larvae, prepupa 1, pupa day 1, adult day 4"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
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+         },
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+         "urlTemplate" : "user_contributed_data/ezattara/NC-L3L_PP1_PD1_AD4/NC_F_merged.subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus embryonic reads",
+         "label" : "O. taurus embryonic",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "Western Australia, Busselton",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq500, 75SE",
+            "Sex" : "pooled",
+            "Strain" : "WA",
+            "Tissues included" : "whole embryos, pooled mixed stages"
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+         "style" : {
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+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/whole_embryos/Otau-embryos.subset.bigwig"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "O. taurus embryonic reads",
+         "label" : "O. taurus embryonic reads",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "Western Australia, Busselton",
+            "NCBI TaxID" : "166361",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq500, 75SE",
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+         },
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+         "urlTemplate" : "user_contributed_data/ezattara/whole_embryos/Otau-embryos.accepted_hits.sorted.subset.bam"
+      },
+      {
+         "category" : "Transcriptome/Splice Junctions",
+         "compress" : 0,
+         "key" : "O. taurus embryonic junctions",
+         "label" : "O. taurus embryonic junctions",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "Western Australia, Busselton",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq500, 75SE",
+            "Sex" : "pooled",
+            "Strain" : "WA",
+            "Tissues included" : "whole embryos, pooled mixed stages"
+         },
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+               "CDS" : "junction-cds",
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+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/O. taurus embryonic junctions/{refseq}/trackData.json"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "O. taurus whole body, mixed stage RNAseq, reduced coverage, females",
+         "label" : "O. taurus whole body, mixed stage RNAseq, reduced coverage, females",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "June-16-2016",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32, normalized coverage with samtools, picard and GATK",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other tissue notes" : "Mix of late larvae, prepupae, pupae and adult RNA; pool of 12 individuals",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina HiSeq 2000m 100PE",
+            "Sex" : "Female",
+            "Strain" : "NC",
+            "Tissues included" : "Whole body"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "user_contributed_data/ezattara/reduced_coverage_june_2016/NC_F_merged.reduced.subset.bam"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "O. taurus whole body, mixed stage RNAseq, reduced coverage, males",
+         "label" : "O. taurus whole body, mixed stage RNAseq, reduced coverage, males",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "June-16-2016",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32, normalized coverage with samtools, picard and GATK",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other tissue notes" : "Mix of late larvae, prepupae, pupae and adult RNA; pool of 12 individuals",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina HiSeq 2000m 100PE",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "Whole body"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "user_contributed_data/ezattara/reduced_coverage_june_2016/NC_M_merged.reduced.subset.bam"
+      }
+   ]
+}
diff --git a/organisms/stage/stage-v2/2_-_Onthophagus_taurus_training/trackList.json b/organisms/stage/stage-v2/2_-_Onthophagus_taurus_training/trackList.json
new file mode 100644
index 0000000..3d98296
--- /dev/null
+++ b/organisms/stage/stage-v2/2_-_Onthophagus_taurus_training/trackList.json
@@ -0,0 +1,1603 @@
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+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Placozoa",
+         "label" : "protein2genome_Placozoa",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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+            "arrowheadClass" : "webapollo-arrowhead",
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+               "match_part" : "protein2genome"
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+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Placozoa/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Platyhelminthes",
+         "label" : "protein2genome_Platyhelminthes",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Platyhelminthes/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Priapulida",
+         "label" : "protein2genome_Priapulida",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Priapulida/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Tardigrada",
+         "label" : "protein2genome_Tardigrada",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Tardigrada/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Tunicata",
+         "label" : "protein2genome_Tunicata",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Tunicata/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_UNCATEGORISED",
+         "label" : "protein2genome_UNCATEGORISED",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_UNCATEGORISED/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/2. Evidence/Repeats",
+         "compress" : 0,
+         "key" : "repeatmasker",
+         "label" : "repeatmasker",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from RepeatMasker as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "repeat"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/repeatmasker/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/2. Evidence/Repeats",
+         "compress" : 0,
+         "key" : "repeatrunner",
+         "label" : "repeatrunner",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Repeatrunner as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "repeat"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/repeatrunner/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/1. Gene Sets/Supplementary Gene Predictions",
+         "compress" : 0,
+         "key" : "snap_masked",
+         "label" : "snap_masked",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "snap"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/snap_masked/{refseq}/trackData.json"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Reference Assembly",
+         "key" : "Gaps in assembly",
+         "label" : "Gaps in assembly",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "white",
+            "pos_color" : "black"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/onttau_genome.fa.gaps.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "0.5",
+         "category" : "Reference Assembly",
+         "key" : "GC Content",
+         "label" : "GC Content",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "rgba(255,255,0,50)",
+            "pos_color" : "rgba(0,0,255,50)"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/onttau_genome.fa.gc.bigwig"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "Onthophagus taurus early male pupa brain transcripts",
+         "label" : "Onthophagus taurus early male pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlM-BRN_S22.sorted.subset.bam"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "Onthophagus taurus early female pupa brain transcripts",
+         "label" : "Onthophagus taurus early female pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Female",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlF-BRN_S18.sorted.subset.bam"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "Onthophagus taurus early male pupa brain transcripts (Coverage Plot)",
+         "label" : "Onthophagus taurus early male pupa brain transcripts (Coverage Plot)",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlM-BRN_S22.sorted.subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "Onthophagus taurus early female pupa brain transcripts (Coverage Plot)",
+         "label" : "Onthophagus taurus early female pupa brain transcripts (Coverage Plot)",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
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+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
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+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlF-BRN_S18.sorted.subset.bigwig"
+      },
+      {
+         "category" : "Gene Silhouette Models/1. Gene Sets/Protein Coding",
+         "compress" : 0,
+         "key" : "Gene Silhouette Models v4",
+         "label" : "Gene_Silhouette_Models_v4",
+         "metadata" : {
+            "Analysis method" : "Gene Silhouette Algorithm, alpha version, unpublished",
+            "Analysis provider" : "Douglas B. Rusch, Centre for Genomics and Bioinformatics, Indiana University Bloomington",
+            "Other notes" : "Novel algorithm predicts genes based on mapped RNAseq reads; based on data from early pupae, brain, dorsal head and pronotal epidermis, and posterior abdominal epidermis only"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "container-16px",
+            "subfeatureClasses" : {
+               "CDS" : "gnomon_CDS",
+               "UTR" : "gnomon_UTR",
+               "exon" : "container-100pct",
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+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
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+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus M PD1 BRN+CHE+THE+GEN transcripts",
+         "label" : "O. taurus M PD1 BRN+CHE+THE+GEN transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "pooled brain, dorsal head epidermis, pronotum epidermis, posterior abdominal epidermis"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/mixed_transcripts_march_2016/ctrlM-ALL.merged.subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus F PD1 BRN+CHE+THE+GEN transcripts",
+         "label" : "O. taurus F PD1 BRN+CHE+THE+GEN transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Female",
+            "Strain" : "NC",
+            "Tissues included" : "pooled brain, dorsal head epidermis, pronotum epidermis, posterior abdominal epidermis"
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+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/mixed_transcripts_march_2016/ctrlF-ALL.merged_subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus M NC L3L+PP1+PD1+AD4",
+         "label" : "O. taurus M NC L3L+PP1+PD1+AD4",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version" : "Illumina HiSeq 100PE",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "whole body, pooled late 3 larvae, prepupa 1, pupa day 1, adult day 4"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
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+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/NC-L3L_PP1_PD1_AD4/NC_M_merged.subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus F NC L3L+PP1+PD1+AD4",
+         "label" : "O. taurus F NC L3L+PP1+PD1+AD4",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version" : "Illumina HiSeq 100PE",
+            "Sex" : "Female",
+            "Strain" : "NC",
+            "Tissues included" : "whole body, pooled late 3 larvae, prepupa 1, pupa day 1, adult day 4"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
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diff --git a/organisms/stage/stage-v2/30_-_Onthophagus_taurus_training/trackList.json b/organisms/stage/stage-v2/30_-_Onthophagus_taurus_training/trackList.json
new file mode 100644
index 0000000..3d98296
--- /dev/null
+++ b/organisms/stage/stage-v2/30_-_Onthophagus_taurus_training/trackList.json
@@ -0,0 +1,1603 @@
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+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Crustacea/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Echinodermata",
+         "label" : "protein2genome_Echinodermata",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Echinodermata proteins as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Echinodermata/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Mollusca",
+         "label" : "protein2genome_Mollusca",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Mollusca proteins as part of the MAKER automated annotation pipeline."
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+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
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+         "urlTemplate" : "tracks/protein2genome_Mollusca/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Nemata",
+         "label" : "protein2genome_Nemata",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline."
+         },
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+            "arrowheadClass" : "webapollo-arrowhead",
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+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+         "key" : "protein2genome_Nematomorpha",
+         "label" : "protein2genome_Nematomorpha",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Nematomorpha proteins as part of the MAKER automated annotation pipeline."
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+            "arrowheadClass" : "webapollo-arrowhead",
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+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Onychophora",
+         "label" : "protein2genome_Onychophora",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Onychophora proteins as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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+            "arrowheadClass" : "webapollo-arrowhead",
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+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Onychophora/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Parazoa",
+         "label" : "protein2genome_Parazoa",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
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+               "match_part" : "protein2genome"
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+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Parazoa/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Placozoa",
+         "label" : "protein2genome_Placozoa",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
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+               "match_part" : "protein2genome"
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+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Placozoa/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Platyhelminthes",
+         "label" : "protein2genome_Platyhelminthes",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Platyhelminthes/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Priapulida",
+         "label" : "protein2genome_Priapulida",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Priapulida/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Tardigrada",
+         "label" : "protein2genome_Tardigrada",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Tardigrada/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Tunicata",
+         "label" : "protein2genome_Tunicata",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Tunicata/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_UNCATEGORISED",
+         "label" : "protein2genome_UNCATEGORISED",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_UNCATEGORISED/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/2. Evidence/Repeats",
+         "compress" : 0,
+         "key" : "repeatmasker",
+         "label" : "repeatmasker",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from RepeatMasker as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "repeat"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/repeatmasker/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/2. Evidence/Repeats",
+         "compress" : 0,
+         "key" : "repeatrunner",
+         "label" : "repeatrunner",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Repeatrunner as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "repeat"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/repeatrunner/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/1. Gene Sets/Supplementary Gene Predictions",
+         "compress" : 0,
+         "key" : "snap_masked",
+         "label" : "snap_masked",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "snap"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/snap_masked/{refseq}/trackData.json"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Reference Assembly",
+         "key" : "Gaps in assembly",
+         "label" : "Gaps in assembly",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "white",
+            "pos_color" : "black"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/onttau_genome.fa.gaps.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "0.5",
+         "category" : "Reference Assembly",
+         "key" : "GC Content",
+         "label" : "GC Content",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "rgba(255,255,0,50)",
+            "pos_color" : "rgba(0,0,255,50)"
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+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/onttau_genome.fa.gc.bigwig"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "Onthophagus taurus early male pupa brain transcripts",
+         "label" : "Onthophagus taurus early male pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlM-BRN_S22.sorted.subset.bam"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "Onthophagus taurus early female pupa brain transcripts",
+         "label" : "Onthophagus taurus early female pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Female",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlF-BRN_S18.sorted.subset.bam"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "Onthophagus taurus early male pupa brain transcripts (Coverage Plot)",
+         "label" : "Onthophagus taurus early male pupa brain transcripts (Coverage Plot)",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlM-BRN_S22.sorted.subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "Onthophagus taurus early female pupa brain transcripts (Coverage Plot)",
+         "label" : "Onthophagus taurus early female pupa brain transcripts (Coverage Plot)",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
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+}
diff --git a/organisms/stage/stage-v2/31_-_Onthophagus_taurus_training/trackList.json b/organisms/stage/stage-v2/31_-_Onthophagus_taurus_training/trackList.json
new file mode 100644
index 0000000..3d98296
--- /dev/null
+++ b/organisms/stage/stage-v2/31_-_Onthophagus_taurus_training/trackList.json
@@ -0,0 +1,1603 @@
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+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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+            "arrowheadClass" : "webapollo-arrowhead",
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+               "match_part" : "snap"
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+         },
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+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/snap_masked/{refseq}/trackData.json"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Reference Assembly",
+         "key" : "Gaps in assembly",
+         "label" : "Gaps in assembly",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "white",
+            "pos_color" : "black"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/onttau_genome.fa.gaps.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "0.5",
+         "category" : "Reference Assembly",
+         "key" : "GC Content",
+         "label" : "GC Content",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "rgba(255,255,0,50)",
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+         "urlTemplate" : "bigwig/onttau_genome.fa.gc.bigwig"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "Onthophagus taurus early male pupa brain transcripts",
+         "label" : "Onthophagus taurus early male pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
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+            "Tissues included" : "Brain"
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+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlM-BRN_S22.sorted.subset.bam"
+      },
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+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "Onthophagus taurus early female pupa brain transcripts",
+         "label" : "Onthophagus taurus early female pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
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+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
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+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
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+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
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+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
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+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
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+      },
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+         "key" : "Onthophagus taurus early female pupa brain transcripts (Coverage Plot)",
+         "label" : "Onthophagus taurus early female pupa brain transcripts (Coverage Plot)",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Female",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
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+      },
+      {
+         "category" : "Gene Silhouette Models/1. Gene Sets/Protein Coding",
+         "compress" : 0,
+         "key" : "Gene Silhouette Models v4",
+         "label" : "Gene_Silhouette_Models_v4",
+         "metadata" : {
+            "Analysis method" : "Gene Silhouette Algorithm, alpha version, unpublished",
+            "Analysis provider" : "Douglas B. Rusch, Centre for Genomics and Bioinformatics, Indiana University Bloomington",
+            "Other notes" : "Novel algorithm predicts genes based on mapped RNAseq reads; based on data from early pupae, brain, dorsal head and pronotal epidermis, and posterior abdominal epidermis only"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "container-16px",
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+               "CDS" : "gnomon_CDS",
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+         },
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+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus M PD1 BRN+CHE+THE+GEN transcripts",
+         "label" : "O. taurus M PD1 BRN+CHE+THE+GEN transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
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+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
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+            "Sex" : "Male",
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+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
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+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/mixed_transcripts_march_2016/ctrlM-ALL.merged.subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus F PD1 BRN+CHE+THE+GEN transcripts",
+         "label" : "O. taurus F PD1 BRN+CHE+THE+GEN transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Female",
+            "Strain" : "NC",
+            "Tissues included" : "pooled brain, dorsal head epidermis, pronotum epidermis, posterior abdominal epidermis"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
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+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/mixed_transcripts_march_2016/ctrlF-ALL.merged_subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus M NC L3L+PP1+PD1+AD4",
+         "label" : "O. taurus M NC L3L+PP1+PD1+AD4",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version" : "Illumina HiSeq 100PE",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "whole body, pooled late 3 larvae, prepupa 1, pupa day 1, adult day 4"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
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+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/NC-L3L_PP1_PD1_AD4/NC_M_merged.subset.bigwig"
+      },
+      {
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+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus F NC L3L+PP1+PD1+AD4",
+         "label" : "O. taurus F NC L3L+PP1+PD1+AD4",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version" : "Illumina HiSeq 100PE",
+            "Sex" : "Female",
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+            "Tissues included" : "whole body, pooled late 3 larvae, prepupa 1, pupa day 1, adult day 4"
+         },
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+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus embryonic reads",
+         "label" : "O. taurus embryonic",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "Western Australia, Busselton",
+            "NCBI TaxID" : "166361",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq500, 75SE",
+            "Sex" : "pooled",
+            "Strain" : "WA",
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+      {
+         "category" : "Transcriptome/Mapped Reads",
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+         "label" : "O. taurus embryonic reads",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "Western Australia, Busselton",
+            "NCBI TaxID" : "166361",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
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+            "Sequencing platform and version" : "Illumina NextSeq500, 75SE",
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+      {
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+         "compress" : 0,
+         "key" : "O. taurus embryonic junctions",
+         "label" : "O. taurus embryonic junctions",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "Western Australia, Busselton",
+            "NCBI TaxID" : "166361",
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+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
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+         },
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+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/O. taurus embryonic junctions/{refseq}/trackData.json"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "O. taurus whole body, mixed stage RNAseq, reduced coverage, females",
+         "label" : "O. taurus whole body, mixed stage RNAseq, reduced coverage, females",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "June-16-2016",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32, normalized coverage with samtools, picard and GATK",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other tissue notes" : "Mix of late larvae, prepupae, pupae and adult RNA; pool of 12 individuals",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina HiSeq 2000m 100PE",
+            "Sex" : "Female",
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+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "user_contributed_data/ezattara/reduced_coverage_june_2016/NC_F_merged.reduced.subset.bam"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "O. taurus whole body, mixed stage RNAseq, reduced coverage, males",
+         "label" : "O. taurus whole body, mixed stage RNAseq, reduced coverage, males",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "June-16-2016",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32, normalized coverage with samtools, picard and GATK",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other tissue notes" : "Mix of late larvae, prepupae, pupae and adult RNA; pool of 12 individuals",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina HiSeq 2000m 100PE",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "Whole body"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "user_contributed_data/ezattara/reduced_coverage_june_2016/NC_M_merged.reduced.subset.bam"
+      }
+   ]
+}
diff --git a/organisms/stage/stage-v2/32_-_Onthophagus_taurus_training/trackList.json b/organisms/stage/stage-v2/32_-_Onthophagus_taurus_training/trackList.json
new file mode 100644
index 0000000..3d98296
--- /dev/null
+++ b/organisms/stage/stage-v2/32_-_Onthophagus_taurus_training/trackList.json
@@ -0,0 +1,1603 @@
+{
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+   "names" : {
+      "type" : "Hash",
+      "url" : "names/"
+   },
+   "plugins" : [
+      {
+         "location" : "./plugins/WebApollo",
+         "name" : "WebApollo"
+      }
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+   "share_link" : 0,
+   "tracks" : [
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+         "urlTemplate" : "seq/onttau_genome.fa",
+         "useAsRefSeqStore" : 1
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+      {
+         "autocomplete" : "none",
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+         "key" : "User-created Annotations",
+         "label" : "Annotations",
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+                  "renderClassName" : "gray-center-30pct"
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+               "ncRNA" : {
+                  "className" : "brightgreen-80pct",
+                  "renderClassName" : "gray-center-30pct"
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+               "pseudogene" : {
+                  "className" : "light-purple-80pct",
+                  "renderClassName" : "gray-center-30pct"
+               },
+               "rRNA" : {
+                  "className" : "brightgreen-80pct",
+                  "renderClassName" : "gray-center-30pct"
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+               "repeat_region" : {
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+         "urlTemplate" : "tracks/protein2genome_Platyhelminthes/{refseq}/trackData.json"
+      },
+      {
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+         "compress" : 0,
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+         "label" : "protein2genome_Priapulida",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
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+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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+            "arrowheadClass" : "webapollo-arrowhead",
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+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Priapulida/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Tardigrada",
+         "label" : "protein2genome_Tardigrada",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
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+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Tardigrada/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Tunicata",
+         "label" : "protein2genome_Tunicata",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
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+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Tunicata/{refseq}/trackData.json"
+      },
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+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+         "key" : "protein2genome_UNCATEGORISED",
+         "label" : "protein2genome_UNCATEGORISED",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline."
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+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
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+               "match_part" : "protein2genome"
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+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_UNCATEGORISED/{refseq}/trackData.json"
+      },
+      {
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+         "compress" : 0,
+         "key" : "repeatmasker",
+         "label" : "repeatmasker",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from RepeatMasker as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
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+         "urlTemplate" : "tracks/repeatmasker/{refseq}/trackData.json"
+      },
+      {
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+         "compress" : 0,
+         "key" : "repeatrunner",
+         "label" : "repeatrunner",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Repeatrunner as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
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+            "subfeatureClasses" : {
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+            }
+         },
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+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/repeatrunner/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/1. Gene Sets/Supplementary Gene Predictions",
+         "compress" : 0,
+         "key" : "snap_masked",
+         "label" : "snap_masked",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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+            "arrowheadClass" : "webapollo-arrowhead",
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+               "match_part" : "snap"
+            }
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+         "urlTemplate" : "tracks/snap_masked/{refseq}/trackData.json"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Reference Assembly",
+         "key" : "Gaps in assembly",
+         "label" : "Gaps in assembly",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "white",
+            "pos_color" : "black"
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+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/onttau_genome.fa.gaps.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "0.5",
+         "category" : "Reference Assembly",
+         "key" : "GC Content",
+         "label" : "GC Content",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "rgba(255,255,0,50)",
+            "pos_color" : "rgba(0,0,255,50)"
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+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/onttau_genome.fa.gc.bigwig"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "Onthophagus taurus early male pupa brain transcripts",
+         "label" : "Onthophagus taurus early male pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlM-BRN_S22.sorted.subset.bam"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "Onthophagus taurus early female pupa brain transcripts",
+         "label" : "Onthophagus taurus early female pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Female",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlF-BRN_S18.sorted.subset.bam"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
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+         "key" : "Onthophagus taurus early male pupa brain transcripts (Coverage Plot)",
+         "label" : "Onthophagus taurus early male pupa brain transcripts (Coverage Plot)",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
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+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
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+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlM-BRN_S22.sorted.subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
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+         "key" : "Onthophagus taurus early female pupa brain transcripts (Coverage Plot)",
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+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
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+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
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+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlF-BRN_S18.sorted.subset.bigwig"
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+      {
+         "category" : "Gene Silhouette Models/1. Gene Sets/Protein Coding",
+         "compress" : 0,
+         "key" : "Gene Silhouette Models v4",
+         "label" : "Gene_Silhouette_Models_v4",
+         "metadata" : {
+            "Analysis method" : "Gene Silhouette Algorithm, alpha version, unpublished",
+            "Analysis provider" : "Douglas B. Rusch, Centre for Genomics and Bioinformatics, Indiana University Bloomington",
+            "Other notes" : "Novel algorithm predicts genes based on mapped RNAseq reads; based on data from early pupae, brain, dorsal head and pronotal epidermis, and posterior abdominal epidermis only"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "container-16px",
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+               "CDS" : "gnomon_CDS",
+               "UTR" : "gnomon_UTR",
+               "exon" : "container-100pct",
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+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
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+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus M PD1 BRN+CHE+THE+GEN transcripts",
+         "label" : "O. taurus M PD1 BRN+CHE+THE+GEN transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
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+            "Tissues included" : "pooled brain, dorsal head epidermis, pronotum epidermis, posterior abdominal epidermis"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
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+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/mixed_transcripts_march_2016/ctrlM-ALL.merged.subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus F PD1 BRN+CHE+THE+GEN transcripts",
+         "label" : "O. taurus F PD1 BRN+CHE+THE+GEN transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Female",
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+            "Tissues included" : "pooled brain, dorsal head epidermis, pronotum epidermis, posterior abdominal epidermis"
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+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/mixed_transcripts_march_2016/ctrlF-ALL.merged_subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus M NC L3L+PP1+PD1+AD4",
+         "label" : "O. taurus M NC L3L+PP1+PD1+AD4",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version" : "Illumina HiSeq 100PE",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "whole body, pooled late 3 larvae, prepupa 1, pupa day 1, adult day 4"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
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+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/NC-L3L_PP1_PD1_AD4/NC_M_merged.subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus F NC L3L+PP1+PD1+AD4",
+         "label" : "O. taurus F NC L3L+PP1+PD1+AD4",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version" : "Illumina HiSeq 100PE",
+            "Sex" : "Female",
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+            "Tissues included" : "whole body, pooled late 3 larvae, prepupa 1, pupa day 1, adult day 4"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
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+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/NC-L3L_PP1_PD1_AD4/NC_F_merged.subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus embryonic reads",
+         "label" : "O. taurus embryonic",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "Western Australia, Busselton",
+            "NCBI TaxID" : "166361",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq500, 75SE",
+            "Sex" : "pooled",
+            "Strain" : "WA",
+            "Tissues included" : "whole embryos, pooled mixed stages"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/whole_embryos/Otau-embryos.subset.bigwig"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "O. taurus embryonic reads",
+         "label" : "O. taurus embryonic reads",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "Western Australia, Busselton",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
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+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
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+}
diff --git a/organisms/stage/stage-v2/33_-_Onthophagus_taurus_training/trackList.json b/organisms/stage/stage-v2/33_-_Onthophagus_taurus_training/trackList.json
new file mode 100644
index 0000000..3d98296
--- /dev/null
+++ b/organisms/stage/stage-v2/33_-_Onthophagus_taurus_training/trackList.json
@@ -0,0 +1,1603 @@
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+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Mollusca proteins as part of the MAKER automated annotation pipeline."
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+         "urlTemplate" : "tracks/protein2genome_Mollusca/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Nemata",
+         "label" : "protein2genome_Nemata",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline."
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+      },
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+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+         "key" : "protein2genome_Nematomorpha",
+         "label" : "protein2genome_Nematomorpha",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Nematomorpha proteins as part of the MAKER automated annotation pipeline."
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+            "arrowheadClass" : "webapollo-arrowhead",
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+         "key" : "protein2genome_Onychophora",
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+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Onychophora proteins as part of the MAKER automated annotation pipeline."
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+         "trackType" : null,
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+         "urlTemplate" : "tracks/protein2genome_Onychophora/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+         "key" : "protein2genome_Parazoa",
+         "label" : "protein2genome_Parazoa",
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+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline."
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+            "arrowheadClass" : "webapollo-arrowhead",
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+         "urlTemplate" : "tracks/protein2genome_Parazoa/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Placozoa",
+         "label" : "protein2genome_Placozoa",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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+            "arrowheadClass" : "webapollo-arrowhead",
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+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Placozoa/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Platyhelminthes",
+         "label" : "protein2genome_Platyhelminthes",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
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+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Platyhelminthes/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Priapulida",
+         "label" : "protein2genome_Priapulida",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Priapulida/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Tardigrada",
+         "label" : "protein2genome_Tardigrada",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Tardigrada/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Tunicata",
+         "label" : "protein2genome_Tunicata",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
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+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Tunicata/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_UNCATEGORISED",
+         "label" : "protein2genome_UNCATEGORISED",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
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+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
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+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_UNCATEGORISED/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/2. Evidence/Repeats",
+         "compress" : 0,
+         "key" : "repeatmasker",
+         "label" : "repeatmasker",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from RepeatMasker as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
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+               "match_part" : "repeat"
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+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/repeatmasker/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/2. Evidence/Repeats",
+         "compress" : 0,
+         "key" : "repeatrunner",
+         "label" : "repeatrunner",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Repeatrunner as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "repeat"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/repeatrunner/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/1. Gene Sets/Supplementary Gene Predictions",
+         "compress" : 0,
+         "key" : "snap_masked",
+         "label" : "snap_masked",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "snap"
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+         },
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+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/snap_masked/{refseq}/trackData.json"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Reference Assembly",
+         "key" : "Gaps in assembly",
+         "label" : "Gaps in assembly",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "white",
+            "pos_color" : "black"
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+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/onttau_genome.fa.gaps.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "0.5",
+         "category" : "Reference Assembly",
+         "key" : "GC Content",
+         "label" : "GC Content",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "rgba(255,255,0,50)",
+            "pos_color" : "rgba(0,0,255,50)"
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+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/onttau_genome.fa.gc.bigwig"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "Onthophagus taurus early male pupa brain transcripts",
+         "label" : "Onthophagus taurus early male pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlM-BRN_S22.sorted.subset.bam"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "Onthophagus taurus early female pupa brain transcripts",
+         "label" : "Onthophagus taurus early female pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Female",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlF-BRN_S18.sorted.subset.bam"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "Onthophagus taurus early male pupa brain transcripts (Coverage Plot)",
+         "label" : "Onthophagus taurus early male pupa brain transcripts (Coverage Plot)",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlM-BRN_S22.sorted.subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "Onthophagus taurus early female pupa brain transcripts (Coverage Plot)",
+         "label" : "Onthophagus taurus early female pupa brain transcripts (Coverage Plot)",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Female",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlF-BRN_S18.sorted.subset.bigwig"
+      },
+      {
+         "category" : "Gene Silhouette Models/1. Gene Sets/Protein Coding",
+         "compress" : 0,
+         "key" : "Gene Silhouette Models v4",
+         "label" : "Gene_Silhouette_Models_v4",
+         "metadata" : {
+            "Analysis method" : "Gene Silhouette Algorithm, alpha version, unpublished",
+            "Analysis provider" : "Douglas B. Rusch, Centre for Genomics and Bioinformatics, Indiana University Bloomington",
+            "Other notes" : "Novel algorithm predicts genes based on mapped RNAseq reads; based on data from early pupae, brain, dorsal head and pronotal epidermis, and posterior abdominal epidermis only"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "container-16px",
+            "subfeatureClasses" : {
+               "CDS" : "gnomon_CDS",
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+               "exon" : "container-100pct",
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+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
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+      },
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+}
diff --git a/organisms/stage/stage-v2/34_-_Onthophagus_taurus_training/trackList.json b/organisms/stage/stage-v2/34_-_Onthophagus_taurus_training/trackList.json
new file mode 100644
index 0000000..3d98296
--- /dev/null
+++ b/organisms/stage/stage-v2/34_-_Onthophagus_taurus_training/trackList.json
@@ -0,0 +1,1603 @@
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+            "Track legend" : "Results from Protein2genome alignments of a set of Echinodermata proteins as part of the MAKER automated annotation pipeline."
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+      },
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+            "Track legend" : "Results from Protein2genome alignments of a set of Nematomorpha proteins as part of the MAKER automated annotation pipeline."
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+      },
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+      },
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+            "Track legend" : "Results from Protein2genome alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline."
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+      },
+      {
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+         "key" : "protein2genome_Placozoa",
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+            "Track legend" : "Results from Protein2genome alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline."
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+      },
+      {
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+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
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+            "Track legend" : "Results from Protein2genome alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline."
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+            "arrowheadClass" : "webapollo-arrowhead",
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+         "urlTemplate" : "tracks/protein2genome_Platyhelminthes/{refseq}/trackData.json"
+      },
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+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
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+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline."
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+            "arrowheadClass" : "webapollo-arrowhead",
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+         "urlTemplate" : "tracks/protein2genome_Priapulida/{refseq}/trackData.json"
+      },
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+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+         "key" : "protein2genome_Tardigrada",
+         "label" : "protein2genome_Tardigrada",
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+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline."
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+            "arrowheadClass" : "webapollo-arrowhead",
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+         "urlTemplate" : "tracks/protein2genome_Tardigrada/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+         "key" : "protein2genome_Tunicata",
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+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
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+            "arrowheadClass" : "webapollo-arrowhead",
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+         "urlTemplate" : "tracks/protein2genome_Tunicata/{refseq}/trackData.json"
+      },
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+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+            "Track legend" : "Results from Protein2genome alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline."
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+         "urlTemplate" : "tracks/protein2genome_UNCATEGORISED/{refseq}/trackData.json"
+      },
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+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
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+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
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+         "urlTemplate" : "tracks/repeatmasker/{refseq}/trackData.json"
+      },
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+         "category" : "BCM_v0.5.3/2. Evidence/Repeats",
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+         "key" : "repeatrunner",
+         "label" : "repeatrunner",
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+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
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+            "Track legend" : "Results from Repeatrunner as part of the MAKER automated annotation pipeline."
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+      },
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+         "key" : "snap_masked",
+         "label" : "snap_masked",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
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+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline."
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+      },
+      {
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+         "bicolor_pivot" : "zero",
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+            "Track contact" : "The i5k workspace@NAL",
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+            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
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+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
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+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/onttau_genome.fa.gaps.bigwig"
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+         "autoscale" : "local",
+         "bicolor_pivot" : "0.5",
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+         "label" : "GC Content",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "rgba(255,255,0,50)",
+            "pos_color" : "rgba(0,0,255,50)"
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+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/onttau_genome.fa.gc.bigwig"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "Onthophagus taurus early male pupa brain transcripts",
+         "label" : "Onthophagus taurus early male pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlM-BRN_S22.sorted.subset.bam"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "Onthophagus taurus early female pupa brain transcripts",
+         "label" : "Onthophagus taurus early female pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
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+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
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+         "key" : "Onthophagus taurus early male pupa brain transcripts (Coverage Plot)",
+         "label" : "Onthophagus taurus early male pupa brain transcripts (Coverage Plot)",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
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+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
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+         "key" : "Onthophagus taurus early female pupa brain transcripts (Coverage Plot)",
+         "label" : "Onthophagus taurus early female pupa brain transcripts (Coverage Plot)",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Female",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
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+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlF-BRN_S18.sorted.subset.bigwig"
+      },
+      {
+         "category" : "Gene Silhouette Models/1. Gene Sets/Protein Coding",
+         "compress" : 0,
+         "key" : "Gene Silhouette Models v4",
+         "label" : "Gene_Silhouette_Models_v4",
+         "metadata" : {
+            "Analysis method" : "Gene Silhouette Algorithm, alpha version, unpublished",
+            "Analysis provider" : "Douglas B. Rusch, Centre for Genomics and Bioinformatics, Indiana University Bloomington",
+            "Other notes" : "Novel algorithm predicts genes based on mapped RNAseq reads; based on data from early pupae, brain, dorsal head and pronotal epidermis, and posterior abdominal epidermis only"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "container-16px",
+            "subfeatureClasses" : {
+               "CDS" : "gnomon_CDS",
+               "UTR" : "gnomon_UTR",
+               "exon" : "container-100pct",
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+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/Gene_Silhouette_Models_v4/{refseq}/trackData.json"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus M PD1 BRN+CHE+THE+GEN transcripts",
+         "label" : "O. taurus M PD1 BRN+CHE+THE+GEN transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
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+            "Tissues included" : "pooled brain, dorsal head epidermis, pronotum epidermis, posterior abdominal epidermis"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/mixed_transcripts_march_2016/ctrlM-ALL.merged.subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus F PD1 BRN+CHE+THE+GEN transcripts",
+         "label" : "O. taurus F PD1 BRN+CHE+THE+GEN transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Female",
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+            "Tissues included" : "pooled brain, dorsal head epidermis, pronotum epidermis, posterior abdominal epidermis"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
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+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/mixed_transcripts_march_2016/ctrlF-ALL.merged_subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
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+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus M NC L3L+PP1+PD1+AD4",
+         "label" : "O. taurus M NC L3L+PP1+PD1+AD4",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version" : "Illumina HiSeq 100PE",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "whole body, pooled late 3 larvae, prepupa 1, pupa day 1, adult day 4"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/NC-L3L_PP1_PD1_AD4/NC_M_merged.subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus F NC L3L+PP1+PD1+AD4",
+         "label" : "O. taurus F NC L3L+PP1+PD1+AD4",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version" : "Illumina HiSeq 100PE",
+            "Sex" : "Female",
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+            "Tissues included" : "whole body, pooled late 3 larvae, prepupa 1, pupa day 1, adult day 4"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
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+         "urlTemplate" : "user_contributed_data/ezattara/NC-L3L_PP1_PD1_AD4/NC_F_merged.subset.bigwig"
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+      {
+         "autoscale" : "local",
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+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus embryonic reads",
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+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "Western Australia, Busselton",
+            "NCBI TaxID" : "166361",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq500, 75SE",
+            "Sex" : "pooled",
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+         "label" : "O. taurus embryonic reads",
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+            "Analysis method" : "tophat2 v2.0.14",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "Western Australia, Busselton",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
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+            "Sequencing platform and version" : "Illumina NextSeq500, 75SE",
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+         "urlTemplate" : "user_contributed_data/ezattara/whole_embryos/Otau-embryos.accepted_hits.sorted.subset.bam"
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+      {
+         "category" : "Transcriptome/Splice Junctions",
+         "compress" : 0,
+         "key" : "O. taurus embryonic junctions",
+         "label" : "O. taurus embryonic junctions",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "Western Australia, Busselton",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq500, 75SE",
+            "Sex" : "pooled",
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+            }
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+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/O. taurus embryonic junctions/{refseq}/trackData.json"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "O. taurus whole body, mixed stage RNAseq, reduced coverage, females",
+         "label" : "O. taurus whole body, mixed stage RNAseq, reduced coverage, females",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "June-16-2016",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32, normalized coverage with samtools, picard and GATK",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other tissue notes" : "Mix of late larvae, prepupae, pupae and adult RNA; pool of 12 individuals",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina HiSeq 2000m 100PE",
+            "Sex" : "Female",
+            "Strain" : "NC",
+            "Tissues included" : "Whole body"
+         },
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+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "user_contributed_data/ezattara/reduced_coverage_june_2016/NC_F_merged.reduced.subset.bam"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "O. taurus whole body, mixed stage RNAseq, reduced coverage, males",
+         "label" : "O. taurus whole body, mixed stage RNAseq, reduced coverage, males",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "June-16-2016",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32, normalized coverage with samtools, picard and GATK",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other tissue notes" : "Mix of late larvae, prepupae, pupae and adult RNA; pool of 12 individuals",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina HiSeq 2000m 100PE",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "Whole body"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "user_contributed_data/ezattara/reduced_coverage_june_2016/NC_M_merged.reduced.subset.bam"
+      }
+   ]
+}
diff --git a/organisms/stage/stage-v2/35_-_Onthophagus_taurus_training/trackList.json b/organisms/stage/stage-v2/35_-_Onthophagus_taurus_training/trackList.json
new file mode 100644
index 0000000..3d98296
--- /dev/null
+++ b/organisms/stage/stage-v2/35_-_Onthophagus_taurus_training/trackList.json
@@ -0,0 +1,1603 @@
+{
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+   "names" : {
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+      "url" : "names/"
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+   "plugins" : [
+      {
+         "location" : "./plugins/WebApollo",
+         "name" : "WebApollo"
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+      {
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+               "rRNA" : {
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+         "compress" : 0,
+         "key" : "OTAU_v0.5.3-Models",
+         "label" : "onttau_current_models",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
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+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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+            "arrowheadClass" : "webapollo-arrowhead",
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+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Tardigrada/{refseq}/trackData.json"
+      },
+      {
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+         "compress" : 0,
+         "key" : "protein2genome_Tunicata",
+         "label" : "protein2genome_Tunicata",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
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+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Tunicata/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_UNCATEGORISED",
+         "label" : "protein2genome_UNCATEGORISED",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
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+               "match_part" : "protein2genome"
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+         "urlTemplate" : "tracks/protein2genome_UNCATEGORISED/{refseq}/trackData.json"
+      },
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+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from RepeatMasker as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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+            "arrowheadClass" : "webapollo-arrowhead",
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+      },
+      {
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+         "compress" : 0,
+         "key" : "repeatrunner",
+         "label" : "repeatrunner",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Repeatrunner as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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+            "arrowheadClass" : "webapollo-arrowhead",
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+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/repeatrunner/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/1. Gene Sets/Supplementary Gene Predictions",
+         "compress" : 0,
+         "key" : "snap_masked",
+         "label" : "snap_masked",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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+            "arrowheadClass" : "webapollo-arrowhead",
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+      {
+         "autoscale" : "local",
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+         "category" : "Reference Assembly",
+         "key" : "Gaps in assembly",
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+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
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+            "neg_color" : "white",
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+         "urlTemplate" : "bigwig/onttau_genome.fa.gaps.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "0.5",
+         "category" : "Reference Assembly",
+         "key" : "GC Content",
+         "label" : "GC Content",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "rgba(255,255,0,50)",
+            "pos_color" : "rgba(0,0,255,50)"
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+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/onttau_genome.fa.gc.bigwig"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "Onthophagus taurus early male pupa brain transcripts",
+         "label" : "Onthophagus taurus early male pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlM-BRN_S22.sorted.subset.bam"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "Onthophagus taurus early female pupa brain transcripts",
+         "label" : "Onthophagus taurus early female pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Female",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlF-BRN_S18.sorted.subset.bam"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "Onthophagus taurus early male pupa brain transcripts (Coverage Plot)",
+         "label" : "Onthophagus taurus early male pupa brain transcripts (Coverage Plot)",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
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+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
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+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlM-BRN_S22.sorted.subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
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+         "key" : "Onthophagus taurus early female pupa brain transcripts (Coverage Plot)",
+         "label" : "Onthophagus taurus early female pupa brain transcripts (Coverage Plot)",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
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+            "Tissues included" : "Brain"
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+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
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+         "category" : "Gene Silhouette Models/1. Gene Sets/Protein Coding",
+         "compress" : 0,
+         "key" : "Gene Silhouette Models v4",
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+         "metadata" : {
+            "Analysis method" : "Gene Silhouette Algorithm, alpha version, unpublished",
+            "Analysis provider" : "Douglas B. Rusch, Centre for Genomics and Bioinformatics, Indiana University Bloomington",
+            "Other notes" : "Novel algorithm predicts genes based on mapped RNAseq reads; based on data from early pupae, brain, dorsal head and pronotal epidermis, and posterior abdominal epidermis only"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "container-16px",
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+               "CDS" : "gnomon_CDS",
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+               "exon" : "container-100pct",
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+      {
+         "autoscale" : "local",
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+         "key" : "O. taurus M PD1 BRN+CHE+THE+GEN transcripts",
+         "label" : "O. taurus M PD1 BRN+CHE+THE+GEN transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
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+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
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+            "Tissues included" : "pooled brain, dorsal head epidermis, pronotum epidermis, posterior abdominal epidermis"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
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+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/mixed_transcripts_march_2016/ctrlM-ALL.merged.subset.bigwig"
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+      {
+         "autoscale" : "local",
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+         "key" : "O. taurus F PD1 BRN+CHE+THE+GEN transcripts",
+         "label" : "O. taurus F PD1 BRN+CHE+THE+GEN transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
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+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
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+            "Tissues included" : "pooled brain, dorsal head epidermis, pronotum epidermis, posterior abdominal epidermis"
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+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/mixed_transcripts_march_2016/ctrlF-ALL.merged_subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus M NC L3L+PP1+PD1+AD4",
+         "label" : "O. taurus M NC L3L+PP1+PD1+AD4",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version" : "Illumina HiSeq 100PE",
+            "Sex" : "Male",
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+            "Tissues included" : "whole body, pooled late 3 larvae, prepupa 1, pupa day 1, adult day 4"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
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+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/NC-L3L_PP1_PD1_AD4/NC_M_merged.subset.bigwig"
+      },
+      {
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+         "key" : "O. taurus F NC L3L+PP1+PD1+AD4",
+         "label" : "O. taurus F NC L3L+PP1+PD1+AD4",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
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+            "Other organism notes" : "Large female",
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+            "Sequencing platform and version" : "Illumina HiSeq 100PE",
+            "Sex" : "Female",
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+         },
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+      {
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+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus embryonic reads",
+         "label" : "O. taurus embryonic",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "Western Australia, Busselton",
+            "NCBI TaxID" : "166361",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq500, 75SE",
+            "Sex" : "pooled",
+            "Strain" : "WA",
+            "Tissues included" : "whole embryos, pooled mixed stages"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
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+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/whole_embryos/Otau-embryos.subset.bigwig"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "O. taurus embryonic reads",
+         "label" : "O. taurus embryonic reads",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "Western Australia, Busselton",
+            "NCBI TaxID" : "166361",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq500, 75SE",
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+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
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+      },
+      {
+         "category" : "Transcriptome/Splice Junctions",
+         "compress" : 0,
+         "key" : "O. taurus embryonic junctions",
+         "label" : "O. taurus embryonic junctions",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "Western Australia, Busselton",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
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+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq500, 75SE",
+            "Sex" : "pooled",
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+            "Tissues included" : "whole embryos, pooled mixed stages"
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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+}
diff --git a/organisms/stage/stage-v2/36_-_Onthophagus_taurus_training/trackList.json b/organisms/stage/stage-v2/36_-_Onthophagus_taurus_training/trackList.json
new file mode 100644
index 0000000..3d98296
--- /dev/null
+++ b/organisms/stage/stage-v2/36_-_Onthophagus_taurus_training/trackList.json
@@ -0,0 +1,1603 @@
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+         "key" : "protein2genome_Nematomorpha",
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+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
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+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Nematomorpha proteins as part of the MAKER automated annotation pipeline."
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+         "urlTemplate" : "tracks/protein2genome_Nematomorpha/{refseq}/trackData.json"
+      },
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+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Onychophora",
+         "label" : "protein2genome_Onychophora",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Onychophora proteins as part of the MAKER automated annotation pipeline."
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+            "arrowheadClass" : "webapollo-arrowhead",
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+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Onychophora/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Parazoa",
+         "label" : "protein2genome_Parazoa",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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+            "arrowheadClass" : "webapollo-arrowhead",
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+               "match_part" : "protein2genome"
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+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Parazoa/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Placozoa",
+         "label" : "protein2genome_Placozoa",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
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+               "match_part" : "protein2genome"
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+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Placozoa/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Platyhelminthes",
+         "label" : "protein2genome_Platyhelminthes",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
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+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Platyhelminthes/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Priapulida",
+         "label" : "protein2genome_Priapulida",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Priapulida/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Tardigrada",
+         "label" : "protein2genome_Tardigrada",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Tardigrada/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Tunicata",
+         "label" : "protein2genome_Tunicata",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Tunicata/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_UNCATEGORISED",
+         "label" : "protein2genome_UNCATEGORISED",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_UNCATEGORISED/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/2. Evidence/Repeats",
+         "compress" : 0,
+         "key" : "repeatmasker",
+         "label" : "repeatmasker",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from RepeatMasker as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "repeat"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/repeatmasker/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/2. Evidence/Repeats",
+         "compress" : 0,
+         "key" : "repeatrunner",
+         "label" : "repeatrunner",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Repeatrunner as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "repeat"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/repeatrunner/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/1. Gene Sets/Supplementary Gene Predictions",
+         "compress" : 0,
+         "key" : "snap_masked",
+         "label" : "snap_masked",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "snap"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/snap_masked/{refseq}/trackData.json"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Reference Assembly",
+         "key" : "Gaps in assembly",
+         "label" : "Gaps in assembly",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "white",
+            "pos_color" : "black"
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+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/onttau_genome.fa.gaps.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "0.5",
+         "category" : "Reference Assembly",
+         "key" : "GC Content",
+         "label" : "GC Content",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "rgba(255,255,0,50)",
+            "pos_color" : "rgba(0,0,255,50)"
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+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/onttau_genome.fa.gc.bigwig"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "Onthophagus taurus early male pupa brain transcripts",
+         "label" : "Onthophagus taurus early male pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlM-BRN_S22.sorted.subset.bam"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "Onthophagus taurus early female pupa brain transcripts",
+         "label" : "Onthophagus taurus early female pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Female",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlF-BRN_S18.sorted.subset.bam"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "Onthophagus taurus early male pupa brain transcripts (Coverage Plot)",
+         "label" : "Onthophagus taurus early male pupa brain transcripts (Coverage Plot)",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlM-BRN_S22.sorted.subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "Onthophagus taurus early female pupa brain transcripts (Coverage Plot)",
+         "label" : "Onthophagus taurus early female pupa brain transcripts (Coverage Plot)",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Female",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlF-BRN_S18.sorted.subset.bigwig"
+      },
+      {
+         "category" : "Gene Silhouette Models/1. Gene Sets/Protein Coding",
+         "compress" : 0,
+         "key" : "Gene Silhouette Models v4",
+         "label" : "Gene_Silhouette_Models_v4",
+         "metadata" : {
+            "Analysis method" : "Gene Silhouette Algorithm, alpha version, unpublished",
+            "Analysis provider" : "Douglas B. Rusch, Centre for Genomics and Bioinformatics, Indiana University Bloomington",
+            "Other notes" : "Novel algorithm predicts genes based on mapped RNAseq reads; based on data from early pupae, brain, dorsal head and pronotal epidermis, and posterior abdominal epidermis only"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "container-16px",
+            "subfeatureClasses" : {
+               "CDS" : "gnomon_CDS",
+               "UTR" : "gnomon_UTR",
+               "exon" : "container-100pct",
+               "wholeCDS" : null
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
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+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus M PD1 BRN+CHE+THE+GEN transcripts",
+         "label" : "O. taurus M PD1 BRN+CHE+THE+GEN transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "pooled brain, dorsal head epidermis, pronotum epidermis, posterior abdominal epidermis"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/mixed_transcripts_march_2016/ctrlM-ALL.merged.subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus F PD1 BRN+CHE+THE+GEN transcripts",
+         "label" : "O. taurus F PD1 BRN+CHE+THE+GEN transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
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+}
diff --git a/organisms/stage/stage-v2/37_-_Onthophagus_taurus_training/trackList.json b/organisms/stage/stage-v2/37_-_Onthophagus_taurus_training/trackList.json
new file mode 100644
index 0000000..3d98296
--- /dev/null
+++ b/organisms/stage/stage-v2/37_-_Onthophagus_taurus_training/trackList.json
@@ -0,0 +1,1603 @@
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+            }
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+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Chelicerata/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Cnidaria",
+         "label" : "protein2genome_Cnidaria",
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+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Cnidaria proteins as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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+            "arrowheadClass" : "webapollo-arrowhead",
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+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Cnidaria/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+         "key" : "protein2genome_Craniata",
+         "label" : "protein2genome_Craniata",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Craniata proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
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+               "match_part" : "protein2genome"
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+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Craniata/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Crustacea",
+         "label" : "protein2genome_Crustacea",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Crustacea proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
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+               "match_part" : "protein2genome"
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+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Crustacea/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Echinodermata",
+         "label" : "protein2genome_Echinodermata",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Echinodermata proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Echinodermata/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+         "key" : "protein2genome_Mollusca",
+         "label" : "protein2genome_Mollusca",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Mollusca proteins as part of the MAKER automated annotation pipeline."
+         },
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+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
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+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Mollusca/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Nemata",
+         "label" : "protein2genome_Nemata",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
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+               "match_part" : "protein2genome"
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+         },
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+         "urlTemplate" : "tracks/protein2genome_Nemata/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Nematomorpha",
+         "label" : "protein2genome_Nematomorpha",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Nematomorpha proteins as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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+            "arrowheadClass" : "webapollo-arrowhead",
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+               "match_part" : "protein2genome"
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+         "urlTemplate" : "tracks/protein2genome_Nematomorpha/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Onychophora",
+         "label" : "protein2genome_Onychophora",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Onychophora proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
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+               "match_part" : "protein2genome"
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+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Onychophora/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Parazoa",
+         "label" : "protein2genome_Parazoa",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Parazoa/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Placozoa",
+         "label" : "protein2genome_Placozoa",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Placozoa/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Platyhelminthes",
+         "label" : "protein2genome_Platyhelminthes",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Platyhelminthes/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Priapulida",
+         "label" : "protein2genome_Priapulida",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Priapulida/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Tardigrada",
+         "label" : "protein2genome_Tardigrada",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Tardigrada/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Tunicata",
+         "label" : "protein2genome_Tunicata",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Tunicata/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_UNCATEGORISED",
+         "label" : "protein2genome_UNCATEGORISED",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_UNCATEGORISED/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/2. Evidence/Repeats",
+         "compress" : 0,
+         "key" : "repeatmasker",
+         "label" : "repeatmasker",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from RepeatMasker as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "repeat"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/repeatmasker/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/2. Evidence/Repeats",
+         "compress" : 0,
+         "key" : "repeatrunner",
+         "label" : "repeatrunner",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Repeatrunner as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "repeat"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/repeatrunner/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/1. Gene Sets/Supplementary Gene Predictions",
+         "compress" : 0,
+         "key" : "snap_masked",
+         "label" : "snap_masked",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "snap"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/snap_masked/{refseq}/trackData.json"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Reference Assembly",
+         "key" : "Gaps in assembly",
+         "label" : "Gaps in assembly",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "white",
+            "pos_color" : "black"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/onttau_genome.fa.gaps.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "0.5",
+         "category" : "Reference Assembly",
+         "key" : "GC Content",
+         "label" : "GC Content",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "rgba(255,255,0,50)",
+            "pos_color" : "rgba(0,0,255,50)"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/onttau_genome.fa.gc.bigwig"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "Onthophagus taurus early male pupa brain transcripts",
+         "label" : "Onthophagus taurus early male pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlM-BRN_S22.sorted.subset.bam"
+      },
+      {
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+            "Other notes" : "Part of a larger project still unpublished",
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+         "metadata" : {
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+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other tissue notes" : "Mix of late larvae, prepupae, pupae and adult RNA; pool of 12 individuals",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
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+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
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+            "Other methods" : "Trimmomatic 0.32, normalized coverage with samtools, picard and GATK",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other tissue notes" : "Mix of late larvae, prepupae, pupae and adult RNA; pool of 12 individuals",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina HiSeq 2000m 100PE",
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+}
diff --git a/organisms/stage/stage-v2/38_-_Onthophagus_taurus_training/trackList.json b/organisms/stage/stage-v2/38_-_Onthophagus_taurus_training/trackList.json
new file mode 100644
index 0000000..3d98296
--- /dev/null
+++ b/organisms/stage/stage-v2/38_-_Onthophagus_taurus_training/trackList.json
@@ -0,0 +1,1603 @@
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+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
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+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Repeatrunner as part of the MAKER automated annotation pipeline."
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+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline."
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+            "Track contact" : "The i5k workspace@NAL",
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+            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
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+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+         },
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+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "Onthophagus taurus early male pupa brain transcripts",
+         "label" : "Onthophagus taurus early male pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
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+            "Tissues included" : "Brain"
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+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlM-BRN_S22.sorted.subset.bam"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "Onthophagus taurus early female pupa brain transcripts",
+         "label" : "Onthophagus taurus early female pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Female",
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+            "Tissues included" : "Brain"
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+      },
+      {
+         "autoscale" : "local",
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+         "key" : "Onthophagus taurus early male pupa brain transcripts (Coverage Plot)",
+         "label" : "Onthophagus taurus early male pupa brain transcripts (Coverage Plot)",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
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+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
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+            "Tissues included" : "Brain"
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+      },
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+         "key" : "Onthophagus taurus early female pupa brain transcripts (Coverage Plot)",
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+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
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+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
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+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
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+         "key" : "Gene Silhouette Models v4",
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+         "metadata" : {
+            "Analysis method" : "Gene Silhouette Algorithm, alpha version, unpublished",
+            "Analysis provider" : "Douglas B. Rusch, Centre for Genomics and Bioinformatics, Indiana University Bloomington",
+            "Other notes" : "Novel algorithm predicts genes based on mapped RNAseq reads; based on data from early pupae, brain, dorsal head and pronotal epidermis, and posterior abdominal epidermis only"
+         },
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+               "CDS" : "gnomon_CDS",
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+         "key" : "O. taurus M PD1 BRN+CHE+THE+GEN transcripts",
+         "label" : "O. taurus M PD1 BRN+CHE+THE+GEN transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
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+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/mixed_transcripts_march_2016/ctrlM-ALL.merged.subset.bigwig"
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+      {
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+         "key" : "O. taurus F PD1 BRN+CHE+THE+GEN transcripts",
+         "label" : "O. taurus F PD1 BRN+CHE+THE+GEN transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
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+      },
+      {
+         "autoscale" : "local",
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+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus M NC L3L+PP1+PD1+AD4",
+         "label" : "O. taurus M NC L3L+PP1+PD1+AD4",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
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+         "metadata" : {
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+            "Sequencing platform and version" : "Illumina HiSeq 100PE",
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+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
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+         "label" : "O. taurus embryonic reads",
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+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
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+         "key" : "O. taurus embryonic junctions",
+         "label" : "O. taurus embryonic junctions",
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+            "Analysis method" : "tophat2 v2.0.14",
+            "Date completed" : "Nov-15",
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+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
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+         "label" : "O. taurus whole body, mixed stage RNAseq, reduced coverage, females",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "June-16-2016",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other tissue notes" : "Mix of late larvae, prepupae, pupae and adult RNA; pool of 12 individuals",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina HiSeq 2000m 100PE",
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+         "urlTemplate" : "user_contributed_data/ezattara/reduced_coverage_june_2016/NC_F_merged.reduced.subset.bam"
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+      {
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+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
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+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32, normalized coverage with samtools, picard and GATK",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other tissue notes" : "Mix of late larvae, prepupae, pupae and adult RNA; pool of 12 individuals",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina HiSeq 2000m 100PE",
+            "Sex" : "Male",
+            "Strain" : "NC",
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diff --git a/organisms/stage/stage-v2/39_-_Onthophagus_taurus_training/trackList.json b/organisms/stage/stage-v2/39_-_Onthophagus_taurus_training/trackList.json
new file mode 100644
index 0000000..3d98296
--- /dev/null
+++ b/organisms/stage/stage-v2/39_-_Onthophagus_taurus_training/trackList.json
@@ -0,0 +1,1603 @@
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+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Parazoa",
+         "label" : "protein2genome_Parazoa",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
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+            "Track legend" : "Results from Protein2genome alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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+            "arrowheadClass" : "webapollo-arrowhead",
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+               "match_part" : "protein2genome"
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+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Parazoa/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Placozoa",
+         "label" : "protein2genome_Placozoa",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
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+               "match_part" : "protein2genome"
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+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Placozoa/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Platyhelminthes",
+         "label" : "protein2genome_Platyhelminthes",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
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+               "match_part" : "protein2genome"
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+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Platyhelminthes/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Priapulida",
+         "label" : "protein2genome_Priapulida",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Priapulida/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Tardigrada",
+         "label" : "protein2genome_Tardigrada",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Tardigrada/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Tunicata",
+         "label" : "protein2genome_Tunicata",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Tunicata/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_UNCATEGORISED",
+         "label" : "protein2genome_UNCATEGORISED",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_UNCATEGORISED/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/2. Evidence/Repeats",
+         "compress" : 0,
+         "key" : "repeatmasker",
+         "label" : "repeatmasker",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from RepeatMasker as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "repeat"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/repeatmasker/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/2. Evidence/Repeats",
+         "compress" : 0,
+         "key" : "repeatrunner",
+         "label" : "repeatrunner",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Repeatrunner as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "repeat"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/repeatrunner/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/1. Gene Sets/Supplementary Gene Predictions",
+         "compress" : 0,
+         "key" : "snap_masked",
+         "label" : "snap_masked",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "snap"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/snap_masked/{refseq}/trackData.json"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Reference Assembly",
+         "key" : "Gaps in assembly",
+         "label" : "Gaps in assembly",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "white",
+            "pos_color" : "black"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/onttau_genome.fa.gaps.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "0.5",
+         "category" : "Reference Assembly",
+         "key" : "GC Content",
+         "label" : "GC Content",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "rgba(255,255,0,50)",
+            "pos_color" : "rgba(0,0,255,50)"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/onttau_genome.fa.gc.bigwig"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "Onthophagus taurus early male pupa brain transcripts",
+         "label" : "Onthophagus taurus early male pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlM-BRN_S22.sorted.subset.bam"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "Onthophagus taurus early female pupa brain transcripts",
+         "label" : "Onthophagus taurus early female pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Female",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlF-BRN_S18.sorted.subset.bam"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "Onthophagus taurus early male pupa brain transcripts (Coverage Plot)",
+         "label" : "Onthophagus taurus early male pupa brain transcripts (Coverage Plot)",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlM-BRN_S22.sorted.subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "Onthophagus taurus early female pupa brain transcripts (Coverage Plot)",
+         "label" : "Onthophagus taurus early female pupa brain transcripts (Coverage Plot)",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Female",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlF-BRN_S18.sorted.subset.bigwig"
+      },
+      {
+         "category" : "Gene Silhouette Models/1. Gene Sets/Protein Coding",
+         "compress" : 0,
+         "key" : "Gene Silhouette Models v4",
+         "label" : "Gene_Silhouette_Models_v4",
+         "metadata" : {
+            "Analysis method" : "Gene Silhouette Algorithm, alpha version, unpublished",
+            "Analysis provider" : "Douglas B. Rusch, Centre for Genomics and Bioinformatics, Indiana University Bloomington",
+            "Other notes" : "Novel algorithm predicts genes based on mapped RNAseq reads; based on data from early pupae, brain, dorsal head and pronotal epidermis, and posterior abdominal epidermis only"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "container-16px",
+            "subfeatureClasses" : {
+               "CDS" : "gnomon_CDS",
+               "UTR" : "gnomon_UTR",
+               "exon" : "container-100pct",
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+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
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+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus M PD1 BRN+CHE+THE+GEN transcripts",
+         "label" : "O. taurus M PD1 BRN+CHE+THE+GEN transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "pooled brain, dorsal head epidermis, pronotum epidermis, posterior abdominal epidermis"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/mixed_transcripts_march_2016/ctrlM-ALL.merged.subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus F PD1 BRN+CHE+THE+GEN transcripts",
+         "label" : "O. taurus F PD1 BRN+CHE+THE+GEN transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Female",
+            "Strain" : "NC",
+            "Tissues included" : "pooled brain, dorsal head epidermis, pronotum epidermis, posterior abdominal epidermis"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
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+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/mixed_transcripts_march_2016/ctrlF-ALL.merged_subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus M NC L3L+PP1+PD1+AD4",
+         "label" : "O. taurus M NC L3L+PP1+PD1+AD4",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version" : "Illumina HiSeq 100PE",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "whole body, pooled late 3 larvae, prepupa 1, pupa day 1, adult day 4"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
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+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
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+}
diff --git a/organisms/stage/stage-v2/3_-_Onthophagus_taurus_training/trackList.json b/organisms/stage/stage-v2/3_-_Onthophagus_taurus_training/trackList.json
new file mode 100644
index 0000000..3d98296
--- /dev/null
+++ b/organisms/stage/stage-v2/3_-_Onthophagus_taurus_training/trackList.json
@@ -0,0 +1,1603 @@
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+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Craniata proteins as part of the MAKER automated annotation pipeline."
+         },
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+            "arrowheadClass" : "webapollo-arrowhead",
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+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Craniata/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Crustacea",
+         "label" : "protein2genome_Crustacea",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Crustacea proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Crustacea/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Echinodermata",
+         "label" : "protein2genome_Echinodermata",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Echinodermata proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Echinodermata/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Mollusca",
+         "label" : "protein2genome_Mollusca",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Mollusca proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
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+               "match_part" : "protein2genome"
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+         },
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+         "urlTemplate" : "tracks/protein2genome_Mollusca/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Nemata",
+         "label" : "protein2genome_Nemata",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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+            "arrowheadClass" : "webapollo-arrowhead",
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+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Nematomorpha",
+         "label" : "protein2genome_Nematomorpha",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Nematomorpha proteins as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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+            "arrowheadClass" : "webapollo-arrowhead",
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+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Onychophora",
+         "label" : "protein2genome_Onychophora",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Onychophora proteins as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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+            "arrowheadClass" : "webapollo-arrowhead",
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+               "match_part" : "protein2genome"
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+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Onychophora/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Parazoa",
+         "label" : "protein2genome_Parazoa",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
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+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Parazoa/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Placozoa",
+         "label" : "protein2genome_Placozoa",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Placozoa/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Platyhelminthes",
+         "label" : "protein2genome_Platyhelminthes",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Platyhelminthes/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Priapulida",
+         "label" : "protein2genome_Priapulida",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Priapulida/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Tardigrada",
+         "label" : "protein2genome_Tardigrada",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Tardigrada/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Tunicata",
+         "label" : "protein2genome_Tunicata",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Tunicata/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_UNCATEGORISED",
+         "label" : "protein2genome_UNCATEGORISED",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_UNCATEGORISED/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/2. Evidence/Repeats",
+         "compress" : 0,
+         "key" : "repeatmasker",
+         "label" : "repeatmasker",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from RepeatMasker as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "repeat"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/repeatmasker/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/2. Evidence/Repeats",
+         "compress" : 0,
+         "key" : "repeatrunner",
+         "label" : "repeatrunner",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Repeatrunner as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "repeat"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/repeatrunner/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/1. Gene Sets/Supplementary Gene Predictions",
+         "compress" : 0,
+         "key" : "snap_masked",
+         "label" : "snap_masked",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "snap"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/snap_masked/{refseq}/trackData.json"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Reference Assembly",
+         "key" : "Gaps in assembly",
+         "label" : "Gaps in assembly",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "white",
+            "pos_color" : "black"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/onttau_genome.fa.gaps.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "0.5",
+         "category" : "Reference Assembly",
+         "key" : "GC Content",
+         "label" : "GC Content",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "rgba(255,255,0,50)",
+            "pos_color" : "rgba(0,0,255,50)"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/onttau_genome.fa.gc.bigwig"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "Onthophagus taurus early male pupa brain transcripts",
+         "label" : "Onthophagus taurus early male pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlM-BRN_S22.sorted.subset.bam"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "Onthophagus taurus early female pupa brain transcripts",
+         "label" : "Onthophagus taurus early female pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Female",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlF-BRN_S18.sorted.subset.bam"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "Onthophagus taurus early male pupa brain transcripts (Coverage Plot)",
+         "label" : "Onthophagus taurus early male pupa brain transcripts (Coverage Plot)",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
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+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
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+}
diff --git a/organisms/stage/stage-v2/40_-_Onthophagus_taurus_training/trackList.json b/organisms/stage/stage-v2/40_-_Onthophagus_taurus_training/trackList.json
new file mode 100644
index 0000000..3d98296
--- /dev/null
+++ b/organisms/stage/stage-v2/40_-_Onthophagus_taurus_training/trackList.json
@@ -0,0 +1,1603 @@
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+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Repeatrunner as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
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+      },
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+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline."
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+      },
+      {
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+         "bicolor_pivot" : "zero",
+         "category" : "Reference Assembly",
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+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
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+      },
+      {
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+         "key" : "GC Content",
+         "label" : "GC Content",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+         },
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+         "urlTemplate" : "bigwig/onttau_genome.fa.gc.bigwig"
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+         "key" : "Onthophagus taurus early male pupa brain transcripts",
+         "label" : "Onthophagus taurus early male pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
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+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlM-BRN_S22.sorted.subset.bam"
+      },
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+         "key" : "Onthophagus taurus early female pupa brain transcripts",
+         "label" : "Onthophagus taurus early female pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
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+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
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+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
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+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
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+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
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+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
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+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
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+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
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+         "compress" : 0,
+         "key" : "Gene Silhouette Models v4",
+         "label" : "Gene_Silhouette_Models_v4",
+         "metadata" : {
+            "Analysis method" : "Gene Silhouette Algorithm, alpha version, unpublished",
+            "Analysis provider" : "Douglas B. Rusch, Centre for Genomics and Bioinformatics, Indiana University Bloomington",
+            "Other notes" : "Novel algorithm predicts genes based on mapped RNAseq reads; based on data from early pupae, brain, dorsal head and pronotal epidermis, and posterior abdominal epidermis only"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "container-16px",
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+               "CDS" : "gnomon_CDS",
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+      {
+         "autoscale" : "local",
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+         "key" : "O. taurus M PD1 BRN+CHE+THE+GEN transcripts",
+         "label" : "O. taurus M PD1 BRN+CHE+THE+GEN transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
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+         },
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+         "style" : {
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+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/mixed_transcripts_march_2016/ctrlM-ALL.merged.subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
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+         "key" : "O. taurus F PD1 BRN+CHE+THE+GEN transcripts",
+         "label" : "O. taurus F PD1 BRN+CHE+THE+GEN transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
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+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
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+            "Tissues included" : "pooled brain, dorsal head epidermis, pronotum epidermis, posterior abdominal epidermis"
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+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/mixed_transcripts_march_2016/ctrlF-ALL.merged_subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus M NC L3L+PP1+PD1+AD4",
+         "label" : "O. taurus M NC L3L+PP1+PD1+AD4",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version" : "Illumina HiSeq 100PE",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "whole body, pooled late 3 larvae, prepupa 1, pupa day 1, adult day 4"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
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+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/NC-L3L_PP1_PD1_AD4/NC_M_merged.subset.bigwig"
+      },
+      {
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+         "key" : "O. taurus F NC L3L+PP1+PD1+AD4",
+         "label" : "O. taurus F NC L3L+PP1+PD1+AD4",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version" : "Illumina HiSeq 100PE",
+            "Sex" : "Female",
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+            "Tissues included" : "whole body, pooled late 3 larvae, prepupa 1, pupa day 1, adult day 4"
+         },
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+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus embryonic reads",
+         "label" : "O. taurus embryonic",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "Western Australia, Busselton",
+            "NCBI TaxID" : "166361",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
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+            "Sex" : "pooled",
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+         "label" : "O. taurus embryonic reads",
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+            "Analysis method" : "tophat2 v2.0.14",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
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+         "compress" : 0,
+         "key" : "O. taurus embryonic junctions",
+         "label" : "O. taurus embryonic junctions",
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+            "Analysis method" : "tophat2 v2.0.14",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
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+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "O. taurus whole body, mixed stage RNAseq, reduced coverage, females",
+         "label" : "O. taurus whole body, mixed stage RNAseq, reduced coverage, females",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "June-16-2016",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32, normalized coverage with samtools, picard and GATK",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other tissue notes" : "Mix of late larvae, prepupae, pupae and adult RNA; pool of 12 individuals",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina HiSeq 2000m 100PE",
+            "Sex" : "Female",
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+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "user_contributed_data/ezattara/reduced_coverage_june_2016/NC_F_merged.reduced.subset.bam"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "O. taurus whole body, mixed stage RNAseq, reduced coverage, males",
+         "label" : "O. taurus whole body, mixed stage RNAseq, reduced coverage, males",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "June-16-2016",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32, normalized coverage with samtools, picard and GATK",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other tissue notes" : "Mix of late larvae, prepupae, pupae and adult RNA; pool of 12 individuals",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina HiSeq 2000m 100PE",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "Whole body"
+         },
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+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "user_contributed_data/ezattara/reduced_coverage_june_2016/NC_M_merged.reduced.subset.bam"
+      }
+   ]
+}
diff --git a/organisms/stage/stage-v2/4_-_Onthophagus_taurus_training/trackList.json b/organisms/stage/stage-v2/4_-_Onthophagus_taurus_training/trackList.json
new file mode 100644
index 0000000..3d98296
--- /dev/null
+++ b/organisms/stage/stage-v2/4_-_Onthophagus_taurus_training/trackList.json
@@ -0,0 +1,1603 @@
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+   "names" : {
+      "type" : "Hash",
+      "url" : "names/"
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+   "plugins" : [
+      {
+         "location" : "./plugins/WebApollo",
+         "name" : "WebApollo"
+      }
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+            }
+         },
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+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Placozoa/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Platyhelminthes",
+         "label" : "protein2genome_Platyhelminthes",
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+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
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+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline."
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+            "arrowheadClass" : "webapollo-arrowhead",
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+               "match_part" : "protein2genome"
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+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Platyhelminthes/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Priapulida",
+         "label" : "protein2genome_Priapulida",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
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+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Priapulida/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Tardigrada",
+         "label" : "protein2genome_Tardigrada",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
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+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Tardigrada/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Tunicata",
+         "label" : "protein2genome_Tunicata",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
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+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Tunicata/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_UNCATEGORISED",
+         "label" : "protein2genome_UNCATEGORISED",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_UNCATEGORISED/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/2. Evidence/Repeats",
+         "compress" : 0,
+         "key" : "repeatmasker",
+         "label" : "repeatmasker",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from RepeatMasker as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
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+            "subfeatureClasses" : {
+               "match_part" : "repeat"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/repeatmasker/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/2. Evidence/Repeats",
+         "compress" : 0,
+         "key" : "repeatrunner",
+         "label" : "repeatrunner",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Repeatrunner as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "repeat"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/repeatrunner/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/1. Gene Sets/Supplementary Gene Predictions",
+         "compress" : 0,
+         "key" : "snap_masked",
+         "label" : "snap_masked",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
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+               "match_part" : "snap"
+            }
+         },
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+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/snap_masked/{refseq}/trackData.json"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Reference Assembly",
+         "key" : "Gaps in assembly",
+         "label" : "Gaps in assembly",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "white",
+            "pos_color" : "black"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/onttau_genome.fa.gaps.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "0.5",
+         "category" : "Reference Assembly",
+         "key" : "GC Content",
+         "label" : "GC Content",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "rgba(255,255,0,50)",
+            "pos_color" : "rgba(0,0,255,50)"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/onttau_genome.fa.gc.bigwig"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "Onthophagus taurus early male pupa brain transcripts",
+         "label" : "Onthophagus taurus early male pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlM-BRN_S22.sorted.subset.bam"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "Onthophagus taurus early female pupa brain transcripts",
+         "label" : "Onthophagus taurus early female pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Female",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlF-BRN_S18.sorted.subset.bam"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "Onthophagus taurus early male pupa brain transcripts (Coverage Plot)",
+         "label" : "Onthophagus taurus early male pupa brain transcripts (Coverage Plot)",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlM-BRN_S22.sorted.subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "Onthophagus taurus early female pupa brain transcripts (Coverage Plot)",
+         "label" : "Onthophagus taurus early female pupa brain transcripts (Coverage Plot)",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
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+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
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+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlF-BRN_S18.sorted.subset.bigwig"
+      },
+      {
+         "category" : "Gene Silhouette Models/1. Gene Sets/Protein Coding",
+         "compress" : 0,
+         "key" : "Gene Silhouette Models v4",
+         "label" : "Gene_Silhouette_Models_v4",
+         "metadata" : {
+            "Analysis method" : "Gene Silhouette Algorithm, alpha version, unpublished",
+            "Analysis provider" : "Douglas B. Rusch, Centre for Genomics and Bioinformatics, Indiana University Bloomington",
+            "Other notes" : "Novel algorithm predicts genes based on mapped RNAseq reads; based on data from early pupae, brain, dorsal head and pronotal epidermis, and posterior abdominal epidermis only"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "container-16px",
+            "subfeatureClasses" : {
+               "CDS" : "gnomon_CDS",
+               "UTR" : "gnomon_UTR",
+               "exon" : "container-100pct",
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+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
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+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus M PD1 BRN+CHE+THE+GEN transcripts",
+         "label" : "O. taurus M PD1 BRN+CHE+THE+GEN transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "pooled brain, dorsal head epidermis, pronotum epidermis, posterior abdominal epidermis"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/mixed_transcripts_march_2016/ctrlM-ALL.merged.subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus F PD1 BRN+CHE+THE+GEN transcripts",
+         "label" : "O. taurus F PD1 BRN+CHE+THE+GEN transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Female",
+            "Strain" : "NC",
+            "Tissues included" : "pooled brain, dorsal head epidermis, pronotum epidermis, posterior abdominal epidermis"
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+         "style" : {
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+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/mixed_transcripts_march_2016/ctrlF-ALL.merged_subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus M NC L3L+PP1+PD1+AD4",
+         "label" : "O. taurus M NC L3L+PP1+PD1+AD4",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version" : "Illumina HiSeq 100PE",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "whole body, pooled late 3 larvae, prepupa 1, pupa day 1, adult day 4"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
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+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/NC-L3L_PP1_PD1_AD4/NC_M_merged.subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus F NC L3L+PP1+PD1+AD4",
+         "label" : "O. taurus F NC L3L+PP1+PD1+AD4",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version" : "Illumina HiSeq 100PE",
+            "Sex" : "Female",
+            "Strain" : "NC",
+            "Tissues included" : "whole body, pooled late 3 larvae, prepupa 1, pupa day 1, adult day 4"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/NC-L3L_PP1_PD1_AD4/NC_F_merged.subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus embryonic reads",
+         "label" : "O. taurus embryonic",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "Western Australia, Busselton",
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+}
diff --git a/organisms/stage/stage-v2/5_-_Onthophagus_taurus_training/trackList.json b/organisms/stage/stage-v2/5_-_Onthophagus_taurus_training/trackList.json
new file mode 100644
index 0000000..3d98296
--- /dev/null
+++ b/organisms/stage/stage-v2/5_-_Onthophagus_taurus_training/trackList.json
@@ -0,0 +1,1603 @@
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+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Echinodermata proteins as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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+            "arrowheadClass" : "webapollo-arrowhead",
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+               "match_part" : "protein2genome"
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+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Echinodermata/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Mollusca",
+         "label" : "protein2genome_Mollusca",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Mollusca proteins as part of the MAKER automated annotation pipeline."
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+            "arrowheadClass" : "webapollo-arrowhead",
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+         "urlTemplate" : "tracks/protein2genome_Mollusca/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+         "key" : "protein2genome_Nemata",
+         "label" : "protein2genome_Nemata",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline."
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+            "arrowheadClass" : "webapollo-arrowhead",
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+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+         "key" : "protein2genome_Nematomorpha",
+         "label" : "protein2genome_Nematomorpha",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Nematomorpha proteins as part of the MAKER automated annotation pipeline."
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+            "arrowheadClass" : "webapollo-arrowhead",
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+      {
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+         "key" : "protein2genome_Onychophora",
+         "label" : "protein2genome_Onychophora",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Onychophora proteins as part of the MAKER automated annotation pipeline."
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+            "arrowheadClass" : "webapollo-arrowhead",
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+         "urlTemplate" : "tracks/protein2genome_Onychophora/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Parazoa",
+         "label" : "protein2genome_Parazoa",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
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+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Parazoa/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Placozoa",
+         "label" : "protein2genome_Placozoa",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
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+               "match_part" : "protein2genome"
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+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Placozoa/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Platyhelminthes",
+         "label" : "protein2genome_Platyhelminthes",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Platyhelminthes/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Priapulida",
+         "label" : "protein2genome_Priapulida",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Priapulida/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Tardigrada",
+         "label" : "protein2genome_Tardigrada",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Tardigrada/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Tunicata",
+         "label" : "protein2genome_Tunicata",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Tunicata/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_UNCATEGORISED",
+         "label" : "protein2genome_UNCATEGORISED",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_UNCATEGORISED/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/2. Evidence/Repeats",
+         "compress" : 0,
+         "key" : "repeatmasker",
+         "label" : "repeatmasker",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from RepeatMasker as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "repeat"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/repeatmasker/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/2. Evidence/Repeats",
+         "compress" : 0,
+         "key" : "repeatrunner",
+         "label" : "repeatrunner",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Repeatrunner as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "repeat"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/repeatrunner/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/1. Gene Sets/Supplementary Gene Predictions",
+         "compress" : 0,
+         "key" : "snap_masked",
+         "label" : "snap_masked",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "snap"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/snap_masked/{refseq}/trackData.json"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Reference Assembly",
+         "key" : "Gaps in assembly",
+         "label" : "Gaps in assembly",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "white",
+            "pos_color" : "black"
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+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/onttau_genome.fa.gaps.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "0.5",
+         "category" : "Reference Assembly",
+         "key" : "GC Content",
+         "label" : "GC Content",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "rgba(255,255,0,50)",
+            "pos_color" : "rgba(0,0,255,50)"
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+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/onttau_genome.fa.gc.bigwig"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "Onthophagus taurus early male pupa brain transcripts",
+         "label" : "Onthophagus taurus early male pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlM-BRN_S22.sorted.subset.bam"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "Onthophagus taurus early female pupa brain transcripts",
+         "label" : "Onthophagus taurus early female pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Female",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlF-BRN_S18.sorted.subset.bam"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "Onthophagus taurus early male pupa brain transcripts (Coverage Plot)",
+         "label" : "Onthophagus taurus early male pupa brain transcripts (Coverage Plot)",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
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+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlM-BRN_S22.sorted.subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "Onthophagus taurus early female pupa brain transcripts (Coverage Plot)",
+         "label" : "Onthophagus taurus early female pupa brain transcripts (Coverage Plot)",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Female",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
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+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlF-BRN_S18.sorted.subset.bigwig"
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+}
diff --git a/organisms/stage/stage-v2/6_-_Onthophagus_taurus_training/trackList.json b/organisms/stage/stage-v2/6_-_Onthophagus_taurus_training/trackList.json
new file mode 100644
index 0000000..3d98296
--- /dev/null
+++ b/organisms/stage/stage-v2/6_-_Onthophagus_taurus_training/trackList.json
@@ -0,0 +1,1603 @@
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+         "label" : "Gaps in assembly",
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+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "white",
+            "pos_color" : "black"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/onttau_genome.fa.gaps.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "0.5",
+         "category" : "Reference Assembly",
+         "key" : "GC Content",
+         "label" : "GC Content",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "rgba(255,255,0,50)",
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+         "urlTemplate" : "bigwig/onttau_genome.fa.gc.bigwig"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "Onthophagus taurus early male pupa brain transcripts",
+         "label" : "Onthophagus taurus early male pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
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+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlM-BRN_S22.sorted.subset.bam"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "Onthophagus taurus early female pupa brain transcripts",
+         "label" : "Onthophagus taurus early female pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
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+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
+            "Strain" : "NC",
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+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
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+         "key" : "Onthophagus taurus early female pupa brain transcripts (Coverage Plot)",
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+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Female",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
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+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlF-BRN_S18.sorted.subset.bigwig"
+      },
+      {
+         "category" : "Gene Silhouette Models/1. Gene Sets/Protein Coding",
+         "compress" : 0,
+         "key" : "Gene Silhouette Models v4",
+         "label" : "Gene_Silhouette_Models_v4",
+         "metadata" : {
+            "Analysis method" : "Gene Silhouette Algorithm, alpha version, unpublished",
+            "Analysis provider" : "Douglas B. Rusch, Centre for Genomics and Bioinformatics, Indiana University Bloomington",
+            "Other notes" : "Novel algorithm predicts genes based on mapped RNAseq reads; based on data from early pupae, brain, dorsal head and pronotal epidermis, and posterior abdominal epidermis only"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "trellis-arrowhead",
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+               "CDS" : "gnomon_CDS",
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+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus M PD1 BRN+CHE+THE+GEN transcripts",
+         "label" : "O. taurus M PD1 BRN+CHE+THE+GEN transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
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+            "Tissues included" : "pooled brain, dorsal head epidermis, pronotum epidermis, posterior abdominal epidermis"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
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+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/mixed_transcripts_march_2016/ctrlM-ALL.merged.subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus F PD1 BRN+CHE+THE+GEN transcripts",
+         "label" : "O. taurus F PD1 BRN+CHE+THE+GEN transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Female",
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+            "Tissues included" : "pooled brain, dorsal head epidermis, pronotum epidermis, posterior abdominal epidermis"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
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+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/mixed_transcripts_march_2016/ctrlF-ALL.merged_subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus M NC L3L+PP1+PD1+AD4",
+         "label" : "O. taurus M NC L3L+PP1+PD1+AD4",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version" : "Illumina HiSeq 100PE",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "whole body, pooled late 3 larvae, prepupa 1, pupa day 1, adult day 4"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/NC-L3L_PP1_PD1_AD4/NC_M_merged.subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus F NC L3L+PP1+PD1+AD4",
+         "label" : "O. taurus F NC L3L+PP1+PD1+AD4",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version" : "Illumina HiSeq 100PE",
+            "Sex" : "Female",
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+            "Tissues included" : "whole body, pooled late 3 larvae, prepupa 1, pupa day 1, adult day 4"
+         },
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+      {
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+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus embryonic reads",
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+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "Western Australia, Busselton",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
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+            "Sex" : "pooled",
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+            "Analysis method" : "tophat2 v2.0.14",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
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+         "key" : "O. taurus embryonic junctions",
+         "label" : "O. taurus embryonic junctions",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "Western Australia, Busselton",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq500, 75SE",
+            "Sex" : "pooled",
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+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/O. taurus embryonic junctions/{refseq}/trackData.json"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "O. taurus whole body, mixed stage RNAseq, reduced coverage, females",
+         "label" : "O. taurus whole body, mixed stage RNAseq, reduced coverage, females",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "June-16-2016",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32, normalized coverage with samtools, picard and GATK",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other tissue notes" : "Mix of late larvae, prepupae, pupae and adult RNA; pool of 12 individuals",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina HiSeq 2000m 100PE",
+            "Sex" : "Female",
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+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "user_contributed_data/ezattara/reduced_coverage_june_2016/NC_F_merged.reduced.subset.bam"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "O. taurus whole body, mixed stage RNAseq, reduced coverage, males",
+         "label" : "O. taurus whole body, mixed stage RNAseq, reduced coverage, males",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "June-16-2016",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32, normalized coverage with samtools, picard and GATK",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other tissue notes" : "Mix of late larvae, prepupae, pupae and adult RNA; pool of 12 individuals",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina HiSeq 2000m 100PE",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "Whole body"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "user_contributed_data/ezattara/reduced_coverage_june_2016/NC_M_merged.reduced.subset.bam"
+      }
+   ]
+}
diff --git a/organisms/stage/stage-v2/7_-_Onthophagus_taurus_training/trackList.json b/organisms/stage/stage-v2/7_-_Onthophagus_taurus_training/trackList.json
new file mode 100644
index 0000000..3d98296
--- /dev/null
+++ b/organisms/stage/stage-v2/7_-_Onthophagus_taurus_training/trackList.json
@@ -0,0 +1,1603 @@
+{
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+   "names" : {
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+      "url" : "names/"
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+   "plugins" : [
+      {
+         "location" : "./plugins/WebApollo",
+         "name" : "WebApollo"
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+               "rRNA" : {
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+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Priapulida/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Tardigrada",
+         "label" : "protein2genome_Tardigrada",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
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+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Tardigrada/{refseq}/trackData.json"
+      },
+      {
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+         "key" : "protein2genome_Tunicata",
+         "label" : "protein2genome_Tunicata",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
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+         "urlTemplate" : "tracks/protein2genome_Tunicata/{refseq}/trackData.json"
+      },
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+         "compress" : 0,
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+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline."
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+         "style" : {
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+      },
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+         "label" : "repeatmasker",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from RepeatMasker as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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+            "arrowheadClass" : "webapollo-arrowhead",
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+         "urlTemplate" : "tracks/repeatmasker/{refseq}/trackData.json"
+      },
+      {
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+         "compress" : 0,
+         "key" : "repeatrunner",
+         "label" : "repeatrunner",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Repeatrunner as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
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+         },
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+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/repeatrunner/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/1. Gene Sets/Supplementary Gene Predictions",
+         "compress" : 0,
+         "key" : "snap_masked",
+         "label" : "snap_masked",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
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+               "match_part" : "snap"
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+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Reference Assembly",
+         "key" : "Gaps in assembly",
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+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
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+            "neg_color" : "white",
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+         "urlTemplate" : "bigwig/onttau_genome.fa.gaps.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "0.5",
+         "category" : "Reference Assembly",
+         "key" : "GC Content",
+         "label" : "GC Content",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "rgba(255,255,0,50)",
+            "pos_color" : "rgba(0,0,255,50)"
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+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/onttau_genome.fa.gc.bigwig"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "Onthophagus taurus early male pupa brain transcripts",
+         "label" : "Onthophagus taurus early male pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlM-BRN_S22.sorted.subset.bam"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "Onthophagus taurus early female pupa brain transcripts",
+         "label" : "Onthophagus taurus early female pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Female",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlF-BRN_S18.sorted.subset.bam"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "Onthophagus taurus early male pupa brain transcripts (Coverage Plot)",
+         "label" : "Onthophagus taurus early male pupa brain transcripts (Coverage Plot)",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
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+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
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+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlM-BRN_S22.sorted.subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
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+         "key" : "Onthophagus taurus early female pupa brain transcripts (Coverage Plot)",
+         "label" : "Onthophagus taurus early female pupa brain transcripts (Coverage Plot)",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
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+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
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+      {
+         "category" : "Gene Silhouette Models/1. Gene Sets/Protein Coding",
+         "compress" : 0,
+         "key" : "Gene Silhouette Models v4",
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+         "metadata" : {
+            "Analysis method" : "Gene Silhouette Algorithm, alpha version, unpublished",
+            "Analysis provider" : "Douglas B. Rusch, Centre for Genomics and Bioinformatics, Indiana University Bloomington",
+            "Other notes" : "Novel algorithm predicts genes based on mapped RNAseq reads; based on data from early pupae, brain, dorsal head and pronotal epidermis, and posterior abdominal epidermis only"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "container-16px",
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+               "CDS" : "gnomon_CDS",
+               "UTR" : "gnomon_UTR",
+               "exon" : "container-100pct",
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+            }
+         },
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+         "type" : "FeatureTrack",
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+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
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+         "key" : "O. taurus M PD1 BRN+CHE+THE+GEN transcripts",
+         "label" : "O. taurus M PD1 BRN+CHE+THE+GEN transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
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+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
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+            "Tissues included" : "pooled brain, dorsal head epidermis, pronotum epidermis, posterior abdominal epidermis"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
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+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/mixed_transcripts_march_2016/ctrlM-ALL.merged.subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus F PD1 BRN+CHE+THE+GEN transcripts",
+         "label" : "O. taurus F PD1 BRN+CHE+THE+GEN transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
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+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
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+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
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+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus M NC L3L+PP1+PD1+AD4",
+         "label" : "O. taurus M NC L3L+PP1+PD1+AD4",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version" : "Illumina HiSeq 100PE",
+            "Sex" : "Male",
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+            "Tissues included" : "whole body, pooled late 3 larvae, prepupa 1, pupa day 1, adult day 4"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
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+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/NC-L3L_PP1_PD1_AD4/NC_M_merged.subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
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+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus F NC L3L+PP1+PD1+AD4",
+         "label" : "O. taurus F NC L3L+PP1+PD1+AD4",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
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+            "Other organism notes" : "Large female",
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+            "Sequencing platform and version" : "Illumina HiSeq 100PE",
+            "Sex" : "Female",
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+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
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+         "urlTemplate" : "user_contributed_data/ezattara/NC-L3L_PP1_PD1_AD4/NC_F_merged.subset.bigwig"
+      },
+      {
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+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus embryonic reads",
+         "label" : "O. taurus embryonic",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "Western Australia, Busselton",
+            "NCBI TaxID" : "166361",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq500, 75SE",
+            "Sex" : "pooled",
+            "Strain" : "WA",
+            "Tissues included" : "whole embryos, pooled mixed stages"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/whole_embryos/Otau-embryos.subset.bigwig"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "O. taurus embryonic reads",
+         "label" : "O. taurus embryonic reads",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "Western Australia, Busselton",
+            "NCBI TaxID" : "166361",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq500, 75SE",
+            "Sex" : "pooled",
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+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "user_contributed_data/ezattara/whole_embryos/Otau-embryos.accepted_hits.sorted.subset.bam"
+      },
+      {
+         "category" : "Transcriptome/Splice Junctions",
+         "compress" : 0,
+         "key" : "O. taurus embryonic junctions",
+         "label" : "O. taurus embryonic junctions",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.0.14",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "Western Australia, Busselton",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
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+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
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+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32, normalized coverage with samtools, picard and GATK",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other tissue notes" : "Mix of late larvae, prepupae, pupae and adult RNA; pool of 12 individuals",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
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+}
diff --git a/organisms/stage/stage-v2/8_-_Onthophagus_taurus_training/trackList.json b/organisms/stage/stage-v2/8_-_Onthophagus_taurus_training/trackList.json
new file mode 100644
index 0000000..3d98296
--- /dev/null
+++ b/organisms/stage/stage-v2/8_-_Onthophagus_taurus_training/trackList.json
@@ -0,0 +1,1603 @@
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+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline."
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+         "urlTemplate" : "tracks/protein2genome_Nemata/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+         "key" : "protein2genome_Nematomorpha",
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+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Nematomorpha proteins as part of the MAKER automated annotation pipeline."
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+            "arrowheadClass" : "webapollo-arrowhead",
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+         "urlTemplate" : "tracks/protein2genome_Nematomorpha/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Onychophora",
+         "label" : "protein2genome_Onychophora",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Onychophora proteins as part of the MAKER automated annotation pipeline."
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+            "arrowheadClass" : "webapollo-arrowhead",
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+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Onychophora/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Parazoa",
+         "label" : "protein2genome_Parazoa",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline."
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+            "arrowheadClass" : "webapollo-arrowhead",
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+         "urlTemplate" : "tracks/protein2genome_Parazoa/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Placozoa",
+         "label" : "protein2genome_Placozoa",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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+            "arrowheadClass" : "webapollo-arrowhead",
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+               "match_part" : "protein2genome"
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+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Placozoa/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Platyhelminthes",
+         "label" : "protein2genome_Platyhelminthes",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
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+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Platyhelminthes/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Priapulida",
+         "label" : "protein2genome_Priapulida",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Priapulida/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Tardigrada",
+         "label" : "protein2genome_Tardigrada",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Tardigrada/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Tunicata",
+         "label" : "protein2genome_Tunicata",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
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+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Tunicata/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_UNCATEGORISED",
+         "label" : "protein2genome_UNCATEGORISED",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
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+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_UNCATEGORISED/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/2. Evidence/Repeats",
+         "compress" : 0,
+         "key" : "repeatmasker",
+         "label" : "repeatmasker",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from RepeatMasker as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
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+            "subfeatureClasses" : {
+               "match_part" : "repeat"
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+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/repeatmasker/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/2. Evidence/Repeats",
+         "compress" : 0,
+         "key" : "repeatrunner",
+         "label" : "repeatrunner",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Repeatrunner as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "repeat"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/repeatrunner/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/1. Gene Sets/Supplementary Gene Predictions",
+         "compress" : 0,
+         "key" : "snap_masked",
+         "label" : "snap_masked",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "snap"
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+         },
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+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/snap_masked/{refseq}/trackData.json"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Reference Assembly",
+         "key" : "Gaps in assembly",
+         "label" : "Gaps in assembly",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "white",
+            "pos_color" : "black"
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+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/onttau_genome.fa.gaps.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "0.5",
+         "category" : "Reference Assembly",
+         "key" : "GC Content",
+         "label" : "GC Content",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "rgba(255,255,0,50)",
+            "pos_color" : "rgba(0,0,255,50)"
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+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/onttau_genome.fa.gc.bigwig"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "Onthophagus taurus early male pupa brain transcripts",
+         "label" : "Onthophagus taurus early male pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlM-BRN_S22.sorted.subset.bam"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "Onthophagus taurus early female pupa brain transcripts",
+         "label" : "Onthophagus taurus early female pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Female",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlF-BRN_S18.sorted.subset.bam"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "Onthophagus taurus early male pupa brain transcripts (Coverage Plot)",
+         "label" : "Onthophagus taurus early male pupa brain transcripts (Coverage Plot)",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlM-BRN_S22.sorted.subset.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "Onthophagus taurus early female pupa brain transcripts (Coverage Plot)",
+         "label" : "Onthophagus taurus early female pupa brain transcripts (Coverage Plot)",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Female",
+            "Strain" : "NC",
+            "Tissues included" : "Brain"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlF-BRN_S18.sorted.subset.bigwig"
+      },
+      {
+         "category" : "Gene Silhouette Models/1. Gene Sets/Protein Coding",
+         "compress" : 0,
+         "key" : "Gene Silhouette Models v4",
+         "label" : "Gene_Silhouette_Models_v4",
+         "metadata" : {
+            "Analysis method" : "Gene Silhouette Algorithm, alpha version, unpublished",
+            "Analysis provider" : "Douglas B. Rusch, Centre for Genomics and Bioinformatics, Indiana University Bloomington",
+            "Other notes" : "Novel algorithm predicts genes based on mapped RNAseq reads; based on data from early pupae, brain, dorsal head and pronotal epidermis, and posterior abdominal epidermis only"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "container-16px",
+            "subfeatureClasses" : {
+               "CDS" : "gnomon_CDS",
+               "UTR" : "gnomon_UTR",
+               "exon" : "container-100pct",
+               "wholeCDS" : null
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/Gene_Silhouette_Models_v4/{refseq}/trackData.json"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Transcriptome/Coverage Plots (BigWig)",
+         "key" : "O. taurus M PD1 BRN+CHE+THE+GEN transcripts",
+         "label" : "O. taurus M PD1 BRN+CHE+THE+GEN transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large male",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Sequencing platform and version" : "Illumina NextSeq 500, High Output 75 cycles ",
+            "Sex" : "Male",
+            "Strain" : "NC",
+            "Tissues included" : "pooled brain, dorsal head epidermis, pronotum epidermis, posterior abdominal epidermis"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
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diff --git a/organisms/stage/stage-v2/9_-_Onthophagus_taurus_training/trackList.json b/organisms/stage/stage-v2/9_-_Onthophagus_taurus_training/trackList.json
new file mode 100644
index 0000000..3d98296
--- /dev/null
+++ b/organisms/stage/stage-v2/9_-_Onthophagus_taurus_training/trackList.json
@@ -0,0 +1,1603 @@
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+         "key" : "protein2genome_Chelicerata",
+         "label" : "protein2genome_Chelicerata",
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+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Chelicerata proteins as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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+            "arrowheadClass" : "webapollo-arrowhead",
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+         "urlTemplate" : "tracks/protein2genome_Chelicerata/{refseq}/trackData.json"
+      },
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+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+         "key" : "protein2genome_Cnidaria",
+         "label" : "protein2genome_Cnidaria",
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+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Cnidaria proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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+         "urlTemplate" : "tracks/protein2genome_Cnidaria/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+         "key" : "protein2genome_Craniata",
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+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Craniata proteins as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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+            "arrowheadClass" : "webapollo-arrowhead",
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+         "urlTemplate" : "tracks/protein2genome_Craniata/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+         "key" : "protein2genome_Crustacea",
+         "label" : "protein2genome_Crustacea",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Crustacea proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
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+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Crustacea/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Echinodermata",
+         "label" : "protein2genome_Echinodermata",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Echinodermata proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
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+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Echinodermata/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+         "key" : "protein2genome_Mollusca",
+         "label" : "protein2genome_Mollusca",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Mollusca proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
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+         },
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+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Nemata",
+         "label" : "protein2genome_Nemata",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline."
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+            "arrowheadClass" : "webapollo-arrowhead",
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+         },
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+         "urlTemplate" : "tracks/protein2genome_Nemata/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+         "key" : "protein2genome_Nematomorpha",
+         "label" : "protein2genome_Nematomorpha",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Nematomorpha proteins as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
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+               "match_part" : "protein2genome"
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+         },
+         "trackType" : null,
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+         "urlTemplate" : "tracks/protein2genome_Nematomorpha/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+         "key" : "protein2genome_Onychophora",
+         "label" : "protein2genome_Onychophora",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Onychophora proteins as part of the MAKER automated annotation pipeline."
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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+            "arrowheadClass" : "webapollo-arrowhead",
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+               "match_part" : "protein2genome"
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+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Onychophora/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Parazoa",
+         "label" : "protein2genome_Parazoa",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
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+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Parazoa/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Placozoa",
+         "label" : "protein2genome_Placozoa",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
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+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Placozoa/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Platyhelminthes",
+         "label" : "protein2genome_Platyhelminthes",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
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+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Platyhelminthes/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Priapulida",
+         "label" : "protein2genome_Priapulida",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
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+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Priapulida/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Tardigrada",
+         "label" : "protein2genome_Tardigrada",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Tardigrada/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_Tunicata",
+         "label" : "protein2genome_Tunicata",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
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+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_Tunicata/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+         "compress" : 0,
+         "key" : "protein2genome_UNCATEGORISED",
+         "label" : "protein2genome_UNCATEGORISED",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Protein2genome alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "protein2genome"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/protein2genome_UNCATEGORISED/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/2. Evidence/Repeats",
+         "compress" : 0,
+         "key" : "repeatmasker",
+         "label" : "repeatmasker",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from RepeatMasker as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "repeat"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/repeatmasker/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/2. Evidence/Repeats",
+         "compress" : 0,
+         "key" : "repeatrunner",
+         "label" : "repeatrunner",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from Repeatrunner as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "repeat"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/repeatrunner/{refseq}/trackData.json"
+      },
+      {
+         "category" : "BCM_v0.5.3/1. Gene Sets/Supplementary Gene Predictions",
+         "compress" : 0,
+         "key" : "snap_masked",
+         "label" : "snap_masked",
+         "metadata" : {
+            "Analysis contact" : "Daniel Hughes, Baylor College of Medicine",
+            "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+            "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+            "Track legend" : "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "webapollo-arrowhead",
+            "className" : "container-10px",
+            "subfeatureClasses" : {
+               "match_part" : "snap"
+            }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/snap_masked/{refseq}/trackData.json"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Reference Assembly",
+         "key" : "Gaps in assembly",
+         "label" : "Gaps in assembly",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "white",
+            "pos_color" : "black"
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+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/onttau_genome.fa.gaps.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "0.5",
+         "category" : "Reference Assembly",
+         "key" : "GC Content",
+         "label" : "GC Content",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "rgba(255,255,0,50)",
+            "pos_color" : "rgba(0,0,255,50)"
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+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/onttau_genome.fa.gc.bigwig"
+      },
+      {
+         "category" : "Transcriptome/Mapped Reads",
+         "key" : "Onthophagus taurus early male pupa brain transcripts",
+         "label" : "Onthophagus taurus early male pupa brain transcripts",
+         "metadata" : {
+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32",
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+            "Analysis method" : "Gene Silhouette Algorithm, alpha version, unpublished",
+            "Analysis provider" : "Douglas B. Rusch, Centre for Genomics and Bioinformatics, Indiana University Bloomington",
+            "Other notes" : "Novel algorithm predicts genes based on mapped RNAseq reads; based on data from early pupae, brain, dorsal head and pronotal epidermis, and posterior abdominal epidermis only"
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+            "Analysis method" : "tophat2 v2.1.0",
+            "Date completed" : "Nov-15",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
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+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
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+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes" : "Part of a larger project still unpublished",
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+            "Sequencing platform and version" : "Illumina HiSeq 100PE",
+            "Sex" : "Male",
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+            "Tissues included" : "whole body, pooled late 3 larvae, prepupa 1, pupa day 1, adult day 4"
+         },
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+      {
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+         "label" : "O. taurus F NC L3L+PP1+PD1+AD4",
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+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
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+            "Other methods" : "Trimmomatic 0.32",
+            "Other notes" : "Part of a larger project still unpublished",
+            "Other organism notes" : "Large female",
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+      },
+      {
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+         "label" : "O. taurus whole body, mixed stage RNAseq, reduced coverage, females",
+         "metadata" : {
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+            "Date completed" : "June-16-2016",
+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
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+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other tissue notes" : "Mix of late larvae, prepupae, pupae and adult RNA; pool of 12 individuals",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
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+            "File provider" : "Eduardo E Zattara, Indiana University Bloomington",
+            "Geographical location of specimen collection" : "United States, Mapple View Farm, NC",
+            "NCBI TaxID" : "166361",
+            "Other methods" : "Trimmomatic 0.32, normalized coverage with samtools, picard and GATK",
+            "Other notes on methods" : "Part of a larger project still unpublished",
+            "Other tissue notes" : "Mix of late larvae, prepupae, pupae and adult RNA; pool of 12 individuals",
+            "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+            "Sequencing platform and version" : "Illumina HiSeq 2000m 100PE",
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+      }
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+}
diff --git a/organisms/stage/stage-v2/Aethina_tumida/trackList.json b/organisms/stage/stage-v2/Aethina_tumida/trackList.json
new file mode 100644
index 0000000..97e119b
--- /dev/null
+++ b/organisms/stage/stage-v2/Aethina_tumida/trackList.json
@@ -0,0 +1,232 @@
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diff --git a/organisms/stage/stage-v2/Agrilus_planipennis/trackList.json b/organisms/stage/stage-v2/Agrilus_planipennis/trackList.json
new file mode 100644
index 0000000..f6521e3
--- /dev/null
+++ b/organisms/stage/stage-v2/Agrilus_planipennis/trackList.json
@@ -0,0 +1,1337 @@
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diff --git a/organisms/stage/stage-v2/Amyelois_transitella/trackList.json b/organisms/stage/stage-v2/Amyelois_transitella/trackList.json
new file mode 100644
index 0000000..626b91b
--- /dev/null
+++ b/organisms/stage/stage-v2/Amyelois_transitella/trackList.json
@@ -0,0 +1,364 @@
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diff --git a/organisms/stage/stage-v2/Anoplophora_glabripennis/trackList.json b/organisms/stage/stage-v2/Anoplophora_glabripennis/trackList.json
new file mode 100644
index 0000000..90c3098
--- /dev/null
+++ b/organisms/stage/stage-v2/Anoplophora_glabripennis/trackList.json
@@ -0,0 +1,1371 @@
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+        "Track legend": "Results from Protein2genome alignments of a set of Echinodermata proteins as part of the MAKER automated annotation pipeline."
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+      "key": "protein2genome_Nematomorpha",
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+      "urlTemplate": "tracks/protein2genome_Nematomorpha/{refseq}/trackData.json"
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+      "key": "protein2genome_Onychophora",
+      "label": "protein2genome_Onychophora",
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+      "key": "protein2genome_Placozoa",
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+      "key": "protein2genome_Platyhelminthes",
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+      "key": "protein2genome_Priapulida",
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+        "Track legend": "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline."
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+        "Track legend": "Results from Protein2genome alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline."
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+        "Track legend": "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline."
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+        "Data Source 1": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Asian_long-horned_beetle/RNA_sequence/Agla_RNA-male_ICD_AGI5DM.DDM3005-M-1_1pA_D16AUACXX-4-ID02_1_sequence.txt.bz2",
+        "Data Source 2": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Asian_long-horned_beetle/RNA_sequence/Agla_RNA-male_ICD_AGI5DM.DDM3005-M-1_1pA_D16AUACXX-4-ID02_2_sequence.txt.bz2",
+        "Read cleaning method": "None"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "clip_marker_color": "red",
+        "height": 75,
+        "neg_color": "#0086B3",
+        "pos_color": "#00BFFF"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "bigwig/Agla_RNA-male_ICD_AGI5DM.bigwig"
+    },
+    {
+      "category": "Transcriptome/Mapped Reads",
+      "key": "Scully et al. larval RNA-Seq",
+      "label": "ALBwholelarva",
+      "metadata": {
+        "Alignment method": "Remaining pairs were mapped to the ALB genome using TopHat2 with the following non-default parameters:  --library-type fr-unstranded –mate-inner-dist -30 –mate-std-dev 50 –b2-sensitive.",
+        "Bioproject accession number": "PRJNA247974",
+        "Data provider": "Erin D. Scully (USDA-ARS-Grain, Forage, and Bioenergy Research Unit, Lincoln, NE), Scott M. Geib (USDA-ARS-Pacific Basin Agricultural Research Center, Hilo, HI), and Kelli Hoover (Pennsylvania State University, University Park, PA).",
+        "Library preparation": "Four whole larvae were homogenized and pooled together for RNA isolation.  Total RNA was isolated from whole larvae using the Power Microbiome RNA isolation kit (MoBio, Carlsbad, CA) and ribosomal RNA was depleted from the sample using the Ribominus Eukaryotic Kit for RNA Seq (Life Technologies, Carlsbad, CA).  The library was prepared using the TruSeq RNA Sample Prep Kit (Illumina, San Diego, CA) and the library was enriched for 175 nt fragments so that the paired ends overlapped by 30 nt.",
+        "Read cleaning method": "Paired reads were quality filtered using ea-utils.  Pairs where one or both reads had a mean quality score less of than 30 were discarded.",
+        "Rearing conditions": "Asian longhorned beetle adults were allowed to mate and oviposit onto potted sugar maple trees maintained at a USDA-approved quarantine greenhouse located at The Pennsylvania State University, University Park, PA.  60 days after the eggs hatched (indicated by the first appearance of frass), trees were harvested and third instar larvae were collected and surface sterilized with 70% ethanol.",
+        "SRA accession number": "SRR1290861 and SRR1292125",
+        "Sequencing": "Approximately 19 million 100 nt  unstranded paired end reads were sequenced on the Illumina HiSeq 2000 platform in two separate runs.  Data for runs 1 and 2 are available under the accession numbers SRR1290861 and SRR1292125, respectively.",
+        "Track legend": "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)"
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+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "bam/escully/ALBwholelarva.bam"
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+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
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+      "label": "Gaps in assembly",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "white",
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+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "bigwig/Agla_Btl03082013.GAPS.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "0.5",
+      "category": "Reference Assembly",
+      "key": "GC Content",
+      "label": "GC Content",
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+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+      },
+      "scoreType": "avgScore",
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "rgba(255,255,0,50)",
+        "pos_color": "rgba(0,0,255,50)"
+      },
+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "bigwig/Agla_Btl03082013.genome_GC.bigwig"
+    },
+    {
+      "category": "Official Gene Set/1. Protein Coding Genes",
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+      "fmtDetailValue_Id": "function (id, feature) {  var name2 = id.replace(/-R./, '');  if(feature.get('type')=='mRNA') {    return '<a target=_blank href=https://i5k.nal.usda.gov/'+name2+'>'+id+'</a>';} else { return id;}}",
+      "key": "Official Gene Set v1.2 - protein-coding genes",
+      "label": "anogla_current_models",
+      "menuTemplate": [
+        {
+          "label": "View details"
+        },
+        {
+          "action": "newWindow",
+          "iconClass": "dijitIconDatabase",
+          "label": "function(track,feature){ return 'Open gene page for '+feature.get('id').replace(/-R./, '')}",
+          "title": "function(track,feature){ return 'Open gene page for '+feature.get('id').replace(/-R./, '')}",
+          "url": "function(track,feature){ return 'https://i5k.nal.usda.gov/'+feature.get('id').replace(/-R./, '')}"
+        }
+      ],
+      "metadata": {
+        "Data contact": "The i5k workspace@NAL; Duane McKenna (University of Memphis)",
+        "Data description": "Official Gene Set generated in collaboration with the Baylor College of Medicine, the National Agricultural Library, and the Anoplophora glabripennis manual annotation community. The OGS is a merge of a Maker2 gene set generated by Dan Hughes at BCM (AGLA_v0.5.3-Models) and manual curated genes by the Anoplophora glabripennis manual annotation community.",
+        "Publication status": "unpublished - Please follow Ft. Lauderdale and Toronto agreements"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "CDS": "ogs-cds",
+          "UTR": "ogs-utr",
+          "exon": "container-100pct",
+          "five_prime_utr": "ogs-utr",
+          "three_prime_utr": "ogs-utr",
+          "wholeCDS": null
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/anogla_current_models/{refseq}/trackData.json"
+    },
+    {
+      "category": "Official Gene Set/2. Noncoding Genes",
+      "compress": 0,
+      "key": "Official Gene Set v1.2 - pseudogenes",
+      "label": "OGS_v1.2_pseudogene",
+      "metadata": {
+        "Data contact": "The i5k workspace@NAL; Duane McKenna (University of Memphis)",
+        "Data description": "Official Gene Set generated in collaboration with the Baylor College of Medicine, the National Agricultural Library, and the Anoplophora glabripennis manual annotation community. The OGS is a merge of a Maker2 gene set generated by Dan Hughes at BCM (AGLA_v0.5.3-Models) and manual curated genes by the Anoplophora glabripennis manual annotation community.",
+        "Publication status": "unpublished - Please follow Ft. Lauderdale and Toronto agreements"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
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+        "subfeatureClasses": {
+          "CDS": "ogs-cds",
+          "UTR": "ogs-utr",
+          "pseudogenic_exon": "ogs-utr",
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+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/OGS_v1.2_pseudogene/{refseq}/trackData.json"
+    }
+  ]
+}
diff --git a/organisms/stage/stage-v2/Apis_mellifera/trackList.json b/organisms/stage/stage-v2/Apis_mellifera/trackList.json
new file mode 100644
index 0000000..c557e3d
--- /dev/null
+++ b/organisms/stage/stage-v2/Apis_mellifera/trackList.json
@@ -0,0 +1,142 @@
+{
+  "formatVersion": 1,
+  "names": {
+    "type": "Hash",
+    "url": "names/"
+  },
+  "tracks": [
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+      "faiUrlTemplate": "seq/GCF_000002195.4_Amel_4.5_genomic.fna.fai",
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+      "type": "SequenceTrack",
+      "urlTemplate": "seq/GCF_000002195.4_Amel_4.5_genomic.fna",
+      "useAsRefSeqStore": 1
+    },
+    {
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+      "fmtDetailValue_Id": "function(id, feature) { var name2 = id.replace(/-R./, ''); if(feature.get('type')=='mRNA') { return ''+id+' (Click for Gene page)';} else {return id}}",
+      "key": "apimel_OGSv3.3 Gene",
+      "label": "apimel_current_models",
+      "menuTemplate": [
+        {
+          "label": "View details"
+        },
+        {
+          "action": "newWindow",
+          "iconClass": "dijitIconDatabase",
+          "label": "function(track,feature){ return 'Search HymenopteraMine for '+feature.get('id')}",
+          "title": "function(track,feature){ return 'Search HymenopteraMine for '+feature.get('id')}",
+          "url": "function(track,feature){ return 'http://128.206.116.3:8080/hymenopteramine/keywordSearchResults.do?searchTerm='+feature.get('id')+'&searchSubmit=Search'}"
+        }
+      ],
+      "metadata": {
+        "Data description": "Honey Bee Genome Sequencing Consortium. 2014. doi: 10.1186/1471-2164-15-86; https://i5k.nal.usda.gov/node/739241",
+        "Data provider": "BeeBase, http://hymenopteragenome.org/beebase/?q=consortium_datasets",
+        "Data source": "BeeBase, http://hymenopteragenome.org/beebase/?q=consortium_datasets",
+        "Method": "Honey Bee Genome Sequencing Consortium. 2014. doi: 10.1186/1471-2164-15-86; https://i5k.nal.usda.gov/node/739241",
+        "Publication status": "Published, Honey Bee Genome Sequencing Consortium. 2014. doi: 10.1186/1471-2164-15-86"
+      },
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+      "style": {
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+      },
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+      "urlTemplate": "tracks/apimel_current_models/{refseq}/trackData.json"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
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+      "key": "Gaps in assembly",
+      "label": "Gaps in assembly",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "white",
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+      "urlTemplate": "bigwig/GCF_000002195.4_Amel_4.5_genomic.fna.gaps.bigwig"
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+      "bicolor_pivot": "0.5",
+      "category": "Reference Assembly",
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+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+      },
+      "scoreType": "avgScore",
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
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+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "bigwig/GCF_000002195.4_Amel_4.5_genomic.fna.gc.bigwig"
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+      "key": "NCBI_Annotation_Release_103_Pseudogene",
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+        "Method": "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
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+      "type": "HTMLFeatures",
+      "urlTemplate": "tracks/NCBI_Annotation_Release_103_Pseudogene/{refseq}/trackData.json"
+    },
+    {
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+      "compress": 0,
+      "key": "NCBI_Annotation_Release_103_Gene",
+      "label": "NCBI_Annotation_Release_103_Gene",
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+        "Data source": "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/002/195/GCF_000002195.4_Amel_4.5/GCF_000002195.4_Amel_4.5_genomic.gff.gz",
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+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "trackType": "HTMLFeatures",
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/NCBI_Annotation_Release_103_Gene/{refseq}/trackData.json"
+    }
+  ]
+}
diff --git a/organisms/stage/stage-v2/Athalia_rosae/trackList.json b/organisms/stage/stage-v2/Athalia_rosae/trackList.json
new file mode 100644
index 0000000..b3607cf
--- /dev/null
+++ b/organisms/stage/stage-v2/Athalia_rosae/trackList.json
@@ -0,0 +1,1815 @@
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+  "names": {
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+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
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+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
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+      "label": "blastx_Atelocerata",
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+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Blastx alignments of a set of Atelocerata proteins as part of the MAKER automated annotation pipeline."
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+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Blastx alignments of a set of Cephalochordata proteins as part of the MAKER automated annotation pipeline."
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+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Blastx alignments of a set of Chelicerata proteins as part of the MAKER automated annotation pipeline."
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+      "label": "blastx_Cnidaria",
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+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Blastx alignments of a set of Cnidaria proteins as part of the MAKER automated annotation pipeline."
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+      "label": "blastx_Craniata",
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+        "Track legend": "Results from Blastx alignments of a set of Craniata proteins as part of the MAKER automated annotation pipeline."
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+      "label": "blastx_Echinodermata",
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+        "Track legend": "Results from Blastx alignments of a set of Echinodermata proteins as part of the MAKER automated annotation pipeline."
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+    },
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+      "label": "blastx_Mollusca",
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+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Blastx alignments of a set of Mollusca proteins as part of the MAKER automated annotation pipeline."
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+    },
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+      "key": "blastx_Nemata",
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+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Blastx alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline."
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+    },
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+      "key": "blastx_Nematomorpha",
+      "label": "blastx_Nematomorpha",
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+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Blastx alignments of a set of Nematomorpha proteins as part of the MAKER automated annotation pipeline."
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+        "arrowheadClass": "webapollo-arrowhead",
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+    },
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+      "label": "blastx_Onychophora",
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+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Blastx alignments of a set of Onychophora proteins as part of the MAKER automated annotation pipeline."
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+        "arrowheadClass": "webapollo-arrowhead",
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+    },
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+      "key": "blastx_Parazoa",
+      "label": "blastx_Parazoa",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Blastx alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline."
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+    },
+    {
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+      "key": "blastx_Placozoa",
+      "label": "blastx_Placozoa",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Blastx alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline."
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+      "key": "blastx_Platyhelminthes",
+      "label": "blastx_Platyhelminthes",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Blastx alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline."
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+      "urlTemplate": "tracks/blastx_Platyhelminthes/{refseq}/trackData.json"
+    },
+    {
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+      "key": "blastx_Priapulida",
+      "label": "blastx_Priapulida",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Blastx alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline."
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+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
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+        "arrowheadClass": "webapollo-arrowhead",
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+      "urlTemplate": "tracks/blastx_Priapulida/{refseq}/trackData.json"
+    },
+    {
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+      "key": "blastx_Tardigrada",
+      "label": "blastx_Tardigrada",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Blastx alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
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+        "arrowheadClass": "webapollo-arrowhead",
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+    },
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+      "key": "blastx_Tunicata",
+      "label": "blastx_Tunicata",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Blastx alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline."
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+      "label": "blastx_UNCATEGORISED",
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+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Blastx alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline."
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from EST alignments resulting from the Cufflinks software as part of the MAKER automated annotation pipeline."
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+      "label": "protein2genome_Annelida",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Annelida proteins as part of the MAKER automated annotation pipeline."
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+        "arrowheadClass": "webapollo-arrowhead",
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+      "urlTemplate": "tracks/protein2genome_Annelida/{refseq}/trackData.json"
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+      "key": "protein2genome_Arthropoda",
+      "label": "protein2genome_Arthropoda",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Arthropoda proteins as part of the MAKER automated annotation pipeline."
+      },
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+        "arrowheadClass": "webapollo-arrowhead",
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Arthropoda/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Atelocerata",
+      "label": "protein2genome_Atelocerata",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Atelocerata proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Atelocerata/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Cephalochordata",
+      "label": "protein2genome_Cephalochordata",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Cephalochordata proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Cephalochordata/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Chelicerata",
+      "label": "protein2genome_Chelicerata",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Chelicerata proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Chelicerata/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Cnidaria",
+      "label": "protein2genome_Cnidaria",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Cnidaria proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Cnidaria/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Craniata",
+      "label": "protein2genome_Craniata",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Craniata proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
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+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Craniata/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Crustacea",
+      "label": "protein2genome_Crustacea",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Crustacea proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
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+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Crustacea/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Echinodermata",
+      "label": "protein2genome_Echinodermata",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Echinodermata proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
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+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Echinodermata/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Mollusca",
+      "label": "protein2genome_Mollusca",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Mollusca proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Mollusca/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Nemata",
+      "label": "protein2genome_Nemata",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Nemata/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Nematomorpha",
+      "label": "protein2genome_Nematomorpha",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Nematomorpha proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Nematomorpha/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Onychophora",
+      "label": "protein2genome_Onychophora",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Onychophora proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Onychophora/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Parazoa",
+      "label": "protein2genome_Parazoa",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Parazoa/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Placozoa",
+      "label": "protein2genome_Placozoa",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Placozoa/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Platyhelminthes",
+      "label": "protein2genome_Platyhelminthes",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Platyhelminthes/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Priapulida",
+      "label": "protein2genome_Priapulida",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Priapulida/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Tardigrada",
+      "label": "protein2genome_Tardigrada",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Tardigrada/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Tunicata",
+      "label": "protein2genome_Tunicata",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Tunicata/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_UNCATEGORISED",
+      "label": "protein2genome_UNCATEGORISED",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_UNCATEGORISED/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/2. Evidence/Repeats",
+      "compress": 0,
+      "key": "repeatmasker",
+      "label": "repeatmasker",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from RepeatMasker as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "repeat"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/repeatmasker/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/2. Evidence/Repeats",
+      "compress": 0,
+      "key": "repeatrunner",
+      "label": "repeatrunner",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Repeatrunner as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "repeat"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/repeatrunner/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/1. Gene Sets/Supplementary Gene Predictions",
+      "compress": 0,
+      "key": "snap_masked",
+      "label": "snap_masked",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "snap"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/snap_masked/{refseq}/trackData.json"
+    },
+    {
+      "category": "Transcriptome/Mapped Reads",
+      "key": "A. rosae female-1 raw reads",
+      "label": "Aros_ID05",
+      "metadata": {
+        "Alignment method": "TopHat 2.0, default parameters",
+        "Alignment summary": "http://de.iplantcollaborative.org/dl/d/14EEEDD5-99A7-4C0E-98F2-2AE508F0ACE3/align_summary.txt",
+        "Data Provider": "Baylor College of Medicine",
+        "Data Source 1": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.W-1544-1_2pA_D191TACXX-6-ID05_D191TACXX-6-ID05_1_sequence.txt.bz2",
+        "Data Source 2": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.W-1544-1_2pA_D191TACXX-6-ID05_D191TACXX-6-ID05_2_sequence.txt.bz2",
+        "File note": "This track replaces the previous track, 'Aros_ID05'.",
+        "Read cleaning method": "None",
+        "Track legend": "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "bam/Aros_ID05.bam"
+    },
+    {
+      "category": "Transcriptome/Mapped Reads",
+      "key": "A. rosae female-2 raw reads",
+      "label": "Aros_ID06",
+      "metadata": {
+        "Alignment method": "TopHat 2.0, default parameters",
+        "Alignment summary": "http://de.iplantcollaborative.org/dl/d/5D8FF6D9-C9E8-43AB-B492-85B96244F147/align_summary.txt",
+        "Data Provider": "Baylor College of Medicine",
+        "Data Source 1": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-66-1_2pA_D191TACXX-6-ID06_D191TACXX-6-ID06_1_sequence.txt.bz2",
+        "Data Source 2": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-66-1_2pA_D191TACXX-6-ID06_D191TACXX-6-ID06_2_sequence.txt.bz2",
+        "File note": "This track replaces the previous track, 'Aros_ID06'.",
+        "Read cleaning method": "None",
+        "Track legend": "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "bam/Aros_ID06.bam"
+    },
+    {
+      "category": "Transcriptome/Mapped Reads",
+      "key": "A. rosae male-2 raw reads",
+      "label": "Aros_ID07",
+      "metadata": {
+        "Alignment method": "TopHat 2.0, default parameters",
+        "Alignment summary": "http://de.iplantcollaborative.org/dl/d/DFED2491-A36F-41E0-BE8B-DDEDAE6050FD/align_summary.txt",
+        "Data Provider": "Baylor College of Medicine",
+        "Data Source 1": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-63-1_2pA_D191TACXX-6-ID07_D191TACXX-6-ID07_1_sequence.txt.bz2",
+        "Data Source 2": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-63-1_2pA_D191TACXX-6-ID07_D191TACXX-6-ID07_2_sequence.txt.bz2",
+        "File note": "This track replaces the previous track, 'Aros_ID07'.",
+        "Read cleaning method": "None",
+        "Track legend": "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "bam/Aros_ID07.bam"
+    },
+    {
+      "category": "Transcriptome/Mapped Reads",
+      "key": "A. rosae male-1 raw reads",
+      "label": "Aros_ID08",
+      "metadata": {
+        "Alignment method": "TopHat 2.0, default parameters",
+        "Alignment summary": "http://de.iplantcollaborative.org/dl/d/C72E8FAE-2A8F-48CC-8E81-E763757DC126/align_summary.txt",
+        "Data Provider": "Baylor College of Medicine",
+        "Data Source 1": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.sw-1228-WT-63-1_2pA_D191TACXX-6-ID08_D191TACXX-6-ID08_1_sequence.txt.bz2",
+        "Data Source 2": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.sw-1228-WT-63-1_2pA_D191TACXX-6-ID08_D191TACXX-6-ID08_2_sequence.txt.bz2",
+        "File note": "This track replaces the previous track, 'Aros_ID08'.",
+        "Read cleaning method": "None",
+        "Track legend": "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "bam/Aros_ID08.bam"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "0.5",
+      "category": "Reference Assembly",
+      "key": "GC Content",
+      "label": "GC Content",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+      },
+      "scoreType": "avgScore",
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "rgba(255,255,0,50)",
+        "pos_color": "rgba(0,0,255,50)"
+      },
+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "bigwig/Aros01112013-genome_GC.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Reference Assembly",
+      "key": "Gaps in assembly",
+      "label": "Gaps in assembly",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "white",
+        "pos_color": "black"
+      },
+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "bigwig/Aros01112013-GAPS.bigwig"
+    },
+    {
+      "category": "Transcriptome/Assembly",
+      "compress": 0,
+      "key": "A. rosae females-combined Trinity transcriptome",
+      "label": "atro-females-comb_est2genome",
+      "metadata": {
+        "Data Source 1": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.W-1544-1_2pA_D191TACXX-6-ID05_D191TACXX-6-ID05_1_sequence.txt.bz2",
+        "Data Source 2": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.W-1544-1_2pA_D191TACXX-6-ID05_D191TACXX-6-ID05_2_sequence.txt.bz2",
+        "Data Source 3": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-66-1_2pA_D191TACXX-6-ID06_D191TACXX-6-ID06_1_sequence.txt.bz2",
+        "Data Source 4": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-66-1_2pA_D191TACXX-6-ID06_D191TACXX-6-ID06_2_sequence.txt.bz2",
+        "Method": "Raw reads cleaned with Trimmomatic v0.32, using the options ILLUMINACLIP:'costumadapterlist.fa':2:30:10, SLIDINGWINDOW:4:33 and MINLEN:45. Cleaned reads from two females were concatenated and then assembled using Trinity version trinityrnaseq_r20140413p1 using default settings. Assembled transcripts were mapped to the genome using Exonerate-gff3 (https://github.com/hotdogee/exonerate-gff3) with the options: --model est2genome --showtargetgff yes --gff3 yes --showalignment no --showvulgar no --geneseed 250 --bestn 2 --percent 50 --minintron 20 --maxintron 10000. Transcripts mapping to two locations were detected and marked with a note using a custom perl script (available from JP Oeyen (Univ. Bonn/ZFMK, ZMB), janphilipoyen@gmail.com)",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "est_gff"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/atro-females-comb_est2genome/{refseq}/trackData.json"
+    },
+    {
+      "category": "Transcriptome/Assembly",
+      "compress": 0,
+      "key": "A. rosae male-1 Trinity transcriptome",
+      "label": "atro-male-1_est2genome",
+      "metadata": {
+        "Data Source 1": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.sw-1228-WT-63-1_2pA_D191TACXX-6-ID08_D191TACXX-6-ID08_1_sequence.txt.bz2",
+        "Data Source 2": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.sw-1228-WT-63-1_2pA_D191TACXX-6-ID08_D191TACXX-6-ID08_2_sequence.txt.bz2",
+        "Method": "Raw reads cleaned with Trimmomatic v0.32, using the options ILLUMINACLIP:'costumadapterlist.fa':2:30:10, SLIDINGWINDOW:4:33 and MINLEN:45. Cleaned reads were assembled using Trinity version trinityrnaseq_r20140413p1 using default settings. Assembled transcripts were mapped to the genome using Exonerate-gff3 (https://github.com/hotdogee/exonerate-gff3) with the options: --model est2genome --showtargetgff yes --gff3 yes --showalignment no --showvulgar no --geneseed 250 --bestn 2 --percent 50 --minintron 20 --maxintron 10000. Transcripts mapping to two locations were detected and marked with a note using a custom perl script (available from JP Oeyen (Univ. Bonn/ZFMK, ZMB), janphilipoyen@gmail.com)",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "est_gff"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/atro-male-1_est2genome/{refseq}/trackData.json"
+    },
+    {
+      "category": "Transcriptome/Assembly",
+      "compress": 0,
+      "key": "A. rosae male-2 Trinity transcriptome",
+      "label": "atro-male-2_est2genome",
+      "metadata": {
+        "Data Source 1": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-63-1_2pA_D191TACXX-6-ID07_D191TACXX-6-ID07_1_sequence.txt.bz2",
+        "Data Source 2": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-63-1_2pA_D191TACXX-6-ID07_D191TACXX-6-ID07_2_sequence.txt.bz2",
+        "Method": "Raw reads cleaned with Trimmomatic v0.32, using the options ILLUMINACLIP:'costumadapterlist.fa':2:30:10, SLIDINGWINDOW:4:33 and MINLEN:45. Cleaned reads were assembled using Trinity version trinityrnaseq_r20140413p1 using default settings. Assembled transcripts were mapped to the genome using Exonerate-gff3 (https://github.com/hotdogee/exonerate-gff3) with the options: --model est2genome --showtargetgff yes --gff3 yes --showalignment no --showvulgar no --geneseed 250 --bestn 2 --percent 50 --minintron 20 --maxintron 10000. Transcripts mapping to two locations were detected and marked with a note using a custom perl script (available from JP Oeyen (Univ. Bonn/ZFMK, ZMB), janphilipoyen@gmail.com)",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "est_gff"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/atro-male-2_est2genome/{refseq}/trackData.json"
+    },
+    {
+      "category": "Transcriptome/Mapped Reads",
+      "key": "A. rosae male-1 cleaned reads",
+      "label": "aros_male-1_tophat-accepted_hits",
+      "metadata": {
+        "Data Source 1": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.sw-1228-WT-63-1_2pA_D191TACXX-6-ID08_D191TACXX-6-ID08_1_sequence.txt.bz2",
+        "Data Source 2": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.sw-1228-WT-63-1_2pA_D191TACXX-6-ID08_D191TACXX-6-ID08_2_sequence.txt.bz2",
+        "Method": "Raw reads cleaned with Trimmomatic v0.32, using the options ILLUMINACLIP:'costumadapterlist.fa':2:30:10, SLIDINGWINDOW:4:33 and MINLEN:45. Cleaned reads mapped with TopHat v2.0.12 using default settings.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "bam/janphilipoeyen/Athalia_rosae/cleaned-reads-tophat/aros_male-1_tophat-accepted_hits.bam"
+    },
+    {
+      "category": "Transcriptome/Mapped Reads",
+      "key": "A. rosae male-2 cleaned reads",
+      "label": "aros_male-2_tophat-accepted_hits",
+      "metadata": {
+        "Data Source 1": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-63-1_2pA_D191TACXX-6-ID07_D191TACXX-6-ID07_1_sequence.txt.bz2",
+        "Data Source 2": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-63-1_2pA_D191TACXX-6-ID07_D191TACXX-6-ID07_2_sequence.txt.bz2",
+        "Method": "Raw reads cleaned with Trimmomatic v0.32, using the options ILLUMINACLIP:'costumadapterlist.fa':2:30:10, SLIDINGWINDOW:4:33 and MINLEN:45. Cleaned reads mapped with TopHat v2.0.12 using default settings.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "bam/janphilipoeyen/Athalia_rosae/cleaned-reads-tophat/aros_male-2_tophat-accepted_hits.bam"
+    },
+    {
+      "category": "Transcriptome/Mapped Reads",
+      "key": "A. rosae female-1 cleaned reads",
+      "label": "aros_female-1_tophat-accepted_hits",
+      "metadata": {
+        "Data Source 1": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.W-1544-1_2pA_D191TACXX-6-ID05_D191TACXX-6-ID05_1_sequence.txt.bz2",
+        "Data Source 2": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.W-1544-1_2pA_D191TACXX-6-ID05_D191TACXX-6-ID05_2_sequence.txt.bz2",
+        "Method": "Raw reads cleaned with Trimmomatic v0.32, using the options ILLUMINACLIP:'costumadapterlist.fa':2:30:10, SLIDINGWINDOW:4:33 and MINLEN:45. Cleaned reads mapped with TopHat v2.0.12 using default settings.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "bam/janphilipoeyen/Athalia_rosae/cleaned-reads-tophat/aros_female-1_tophat-accepted_hits.bam"
+    },
+    {
+      "category": "Transcriptome/Mapped Reads",
+      "key": "A. rosae female-2 cleaned reads",
+      "label": "aros_female-2_tophat-accepted_hits",
+      "metadata": {
+        "Data Source 1": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-66-1_2pA_D191TACXX-6-ID06_D191TACXX-6-ID06_1_sequence.txt.bz2",
+        "Data Source 2": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-66-1_2pA_D191TACXX-6-ID06_D191TACXX-6-ID06_2_sequence.txt.bz2 ",
+        "Method": "Raw reads cleaned with Trimmomatic v0.32, using the options ILLUMINACLIP:'costumadapterlist.fa':2:30:10, SLIDINGWINDOW:4:33 and MINLEN:45. Cleaned reads mapped with TopHat v2.0.12 using default settings.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "bam/janphilipoeyen/Athalia_rosae/cleaned-reads-tophat/aros_female-2_tophat-accepted_hits.bam"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Transcriptome/Coverage plots (BigWig)",
+      "key": " A. rosae female-1 cleaned reads, XY-plots",
+      "label": "aros_female-1_tophat-accepted_hits_bigwig",
+      "metadata": {
+        "Data Source 1": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.W-1544-1_2pA_D191TACXX-6-ID05_D191TACXX-6-ID05_1_sequence.txt.bz2",
+        "Data Source 2": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.W-1544-1_2pA_D191TACXX-6-ID05_D191TACXX-6-ID05_2_sequence.txt.bz2",
+        "Method": "Raw reads cleaned with Trimmomatic v0.32, using the options ILLUMINACLIP:'costumadapterlist.fa':2:30:10, SLIDINGWINDOW:4:33 and MINLEN:45. Cleaned reads mapped with TopHat v2.0.12 using default settings. Alignment files were converted by the NAL to bigwig format; reads that failed QC, secondary and supplementary alignments, and optical or PCR duplicates were ignored.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "This track represents an X-Y plot of RNA-Seq coverage."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "clip_marker_color": "red",
+        "height": 50,
+        "neg_color": "#005EFF",
+        "pos_color": "#FFA600"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "bigwig/janphilipoeyen/Athalia_rosae/cleaned-reads-tophat/aros_female-1_tophat-accepted_hits.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Transcriptome/Coverage plots (BigWig)",
+      "key": " A. rosae female-2 cleaned reads, XY-plots",
+      "label": "aros_female-2_tophat-accepted_hits_bigwig",
+      "metadata": {
+        "Data Source 1": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-66-1_2pA_D191TACXX-6-ID06_D191TACXX-6-ID06_1_sequence.txt.bz2",
+        "Data Source 2": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-66-1_2pA_D191TACXX-6-ID06_D191TACXX-6-ID06_2_sequence.txt.bz2 ",
+        "Method": "Raw reads cleaned with Trimmomatic v0.32, using the options ILLUMINACLIP:'costumadapterlist.fa':2:30:10, SLIDINGWINDOW:4:33 and MINLEN:45. Cleaned reads mapped with TopHat v2.0.12 using default settings. Alignment files were converted by the NAL to bigwig format; reads that failed QC, secondary and supplementary alignments, and optical or PCR duplicates were ignored.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "This track represents an X-Y plot of RNA-Seq coverage."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "clip_marker_color": "red",
+        "height": 50,
+        "neg_color": "#005EFF",
+        "pos_color": "#FFA600"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
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diff --git a/organisms/stage/stage-v2/Bactrocera_cucurbitae/trackList.json b/organisms/stage/stage-v2/Bactrocera_cucurbitae/trackList.json
new file mode 100644
index 0000000..95a3cc9
--- /dev/null
+++ b/organisms/stage/stage-v2/Bactrocera_cucurbitae/trackList.json
@@ -0,0 +1,216 @@
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diff --git a/organisms/stage/stage-v2/Bactrocera_dorsalis/trackList.json b/organisms/stage/stage-v2/Bactrocera_dorsalis/trackList.json
new file mode 100644
index 0000000..c3e40e0
--- /dev/null
+++ b/organisms/stage/stage-v2/Bactrocera_dorsalis/trackList.json
@@ -0,0 +1,576 @@
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+        "Publication Status": "Published - Geib et al.: Characterizing the developmental transcriptome of the oriental fruit fly, Bactrocera dorsalis (Diptera: Tephritidae) through comparative genomic analysis with Drosophila melanogaster utilizing modENCODE datasets. BMC Genomics 2014 15:942",
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+        "Publication Status": "Published - Geib et al.: Characterizing the developmental transcriptome of the oriental fruit fly, Bactrocera dorsalis (Diptera: Tephritidae) through comparative genomic analysis with Drosophila melanogaster utilizing modENCODE datasets. BMC Genomics 2014 15:942",
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+        "Sequencing platform and version ": "Illumina GAIIx, 2x100 bp PE",
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+        "Publication Status": "Published - Geib et al.: Characterizing the developmental transcriptome of the oriental fruit fly, Bactrocera dorsalis (Diptera: Tephritidae) through comparative genomic analysis with Drosophila melanogaster utilizing modENCODE datasets. BMC Genomics 2014 15:942",
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+      "category": "Transcriptome/Mapped Reads",
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+        "Publication Status": "Published - Geib et al.: Characterizing the developmental transcriptome of the oriental fruit fly, Bactrocera dorsalis (Diptera: Tephritidae) through comparative genomic analysis with Drosophila melanogaster utilizing modENCODE datasets. BMC Genomics 2014 15:942",
+        "Sequencing platform and version ": "Illumina GAIIx, 2x100 bp PE",
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diff --git a/organisms/stage/stage-v2/Bactrocera_oleae/trackList.json b/organisms/stage/stage-v2/Bactrocera_oleae/trackList.json
new file mode 100644
index 0000000..bdfce96
--- /dev/null
+++ b/organisms/stage/stage-v2/Bactrocera_oleae/trackList.json
@@ -0,0 +1,1252 @@
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diff --git a/organisms/stage/stage-v2/Bemisia_tabaci/trackList.json b/organisms/stage/stage-v2/Bemisia_tabaci/trackList.json
new file mode 100644
index 0000000..773af15
--- /dev/null
+++ b/organisms/stage/stage-v2/Bemisia_tabaci/trackList.json
@@ -0,0 +1,1234 @@
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+        "Publication status": "Published: Please cite https://doi.org/10.1186/s12915-016-0321-y",
+        "Tissues/Life stage included": "Eggs",
+        "Track legend": "Mapped RNA-Seq reads:<br>Aligned regions: blue<br>Spanned regions (possible splice junctions): light blue<br>Deletions in the read relative to the reference: red<br>Insertions in the read relative to the reference: green<br>Mismatch: yellow (hover over the mismatch to see what the snp is)",
+        "isolate": "MEAM19"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "user_contributed_data/ARS_11_2017/Bemisia_tabaci_Nov_29__2017/Bemisia_tabaci_Bam_Files/WF-37.bam.sorted"
+    },
+    {
+      "category": "Transcriptome/Mapped Reads",
+      "key": "TYLCV_24h_rep1",
+      "label": "TYLCV_24h_rep1",
+      "metadata": {
+        "Data description": "RNA derived from adults fed on TYLCV-infected tomato cuttings for 24 h",
+        "Data provider": "Kai-Shu Ling, USDA-ARS",
+        "Data source": "PRJNA312467",
+        "Geographic location (latitude and longitude)": "Charleston, SC, USA",
+        "Method": "Illumina HiSeq 2503",
+        "Publication status": "Published: Please cite https://doi.org/10.1186/s12915-016-0321-y",
+        "Tissues/Life stage included": "adults",
+        "Track legend": "Mapped RNA-Seq reads:<br>Aligned regions: blue<br>Spanned regions (possible splice junctions): light blue<br>Deletions in the read relative to the reference: red<br>Insertions in the read relative to the reference: green<br>Mismatch: yellow (hover over the mismatch to see what the snp is)",
+        "isolate": "MEAM4"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "user_contributed_data/ARS_11_2017/Bemisia_tabaci_Nov_29__2017/Bemisia_tabaci_Bam_Files/WF-22.bam.sorted"
+    },
+    {
+      "category": "Transcriptome/Mapped Reads",
+      "key": "healthy_24h_rep3",
+      "label": "healthy_24h_rep3",
+      "metadata": {
+        "Data description": "RNA derived from adults fed on uninfected tomato cuttings for 24 h",
+        "Data provider": "Kai-Shu Ling, USDA-ARS",
+        "Data source": "PRJNA312467",
+        "Geographic location (latitude and longitude)": "Charleston, SC, USA",
+        "Method": "Illumina HiSeq 2502",
+        "Publication status": "Published: Please cite https://doi.org/10.1186/s12915-016-0321-y",
+        "Tissues/Life stage included": "adults",
+        "Track legend": "Mapped RNA-Seq reads:<br>Aligned regions: blue<br>Spanned regions (possible splice junctions): light blue<br>Deletions in the read relative to the reference: red<br>Insertions in the read relative to the reference: green<br>Mismatch: yellow (hover over the mismatch to see what the snp is)",
+        "isolate": "MEAM3"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "user_contributed_data/ARS_11_2017/Bemisia_tabaci_Nov_29__2017/Bemisia_tabaci_Bam_Files/WF-21.bam.sorted"
+    },
+    {
+      "category": "Transcriptome/Mapped Reads",
+      "key": "healthy_72h_rep2",
+      "label": "healthy_72h_rep2",
+      "metadata": {
+        "Data description": "RNA derived from adults fed on uninfected tomato cuttings for 72 h",
+        "Data provider": "Kai-Shu Ling, USDA-ARS",
+        "Data source": "PRJNA312467",
+        "Geographic location (latitude and longitude)": "Charleston, SC, USA",
+        "Method": "Illumina HiSeq 2513",
+        "Publication status": "Published: Please cite https://doi.org/10.1186/s12915-016-0321-y",
+        "Tissues/Life stage included": "adults",
+        "Track legend": "Mapped RNA-Seq reads:<br>Aligned regions: blue<br>Spanned regions (possible splice junctions): light blue<br>Deletions in the read relative to the reference: red<br>Insertions in the read relative to the reference: green<br>Mismatch: yellow (hover over the mismatch to see what the snp is)",
+        "isolate": "MEAM14"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "user_contributed_data/ARS_11_2017/Bemisia_tabaci_Nov_29__2017/Bemisia_tabaci_Bam_Files/WF-32.bam.sorted"
+    },
+    {
+      "category": "Transcriptome/Mapped Reads",
+      "key": "TYLCV_72h_rep3",
+      "label": "TYLCV_72h_rep3",
+      "metadata": {
+        "Data description": "RNA derived from adults fed on TYLCV-infected tomato cuttings for 72 h",
+        "Data provider": "Kai-Shu Ling, USDA-ARS",
+        "Data source": "PRJNA312467",
+        "Geographic location (latitude and longitude)": "Charleston, SC, USA",
+        "Method": "Illumina HiSeq 2517",
+        "Publication status": "Published: Please cite https://doi.org/10.1186/s12915-016-0321-y",
+        "Tissues/Life stage included": "adults",
+        "Track legend": "Mapped RNA-Seq reads:<br>Aligned regions: blue<br>Spanned regions (possible splice junctions): light blue<br>Deletions in the read relative to the reference: red<br>Insertions in the read relative to the reference: green<br>Mismatch: yellow (hover over the mismatch to see what the snp is)",
+        "isolate": "MEAM18"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "user_contributed_data/ARS_11_2017/Bemisia_tabaci_Nov_29__2017/Bemisia_tabaci_Bam_Files/WF-36.bam.sorted"
+    },
+    {
+      "category": "Transcriptome/Mapped Reads",
+      "key": "TYLCV_48h_rep2",
+      "label": "TYLCV_48h_rep2",
+      "metadata": {
+        "Data description": "RNA derived from adults fed on TYLCV-infected tomato cuttings for 48 h",
+        "Data provider": "Kai-Shu Ling, USDA-ARS",
+        "Data source": "PRJNA312467",
+        "Geographic location (latitude and longitude)": "Charleston, SC, USA",
+        "Method": "Illumina HiSeq 2510",
+        "Publication status": "Published: Please cite https://doi.org/10.1186/s12915-016-0321-y",
+        "Tissues/Life stage included": "adults",
+        "Track legend": "Mapped RNA-Seq reads:<br>Aligned regions: blue<br>Spanned regions (possible splice junctions): light blue<br>Deletions in the read relative to the reference: red<br>Insertions in the read relative to the reference: green<br>Mismatch: yellow (hover over the mismatch to see what the snp is)",
+        "isolate": "MEAM11"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "user_contributed_data/ARS_11_2017/Bemisia_tabaci_Nov_29__2017/Bemisia_tabaci_Bam_Files/WF-29.bam.sorted"
+    },
+    {
+      "category": "Transcriptome/Mapped Reads",
+      "key": "TYLCV_48h_rep1",
+      "label": "TYLCV_48h_rep1",
+      "metadata": {
+        "Data description": "RNA derived from adults fed on TYLCV-infected tomato cuttings for 48 h",
+        "Data provider": "Kai-Shu Ling, USDA-ARS",
+        "Data source": "PRJNA312467",
+        "Geographic location (latitude and longitude)": "Charleston, SC, USA",
+        "Method": "Illumina HiSeq 2509",
+        "Publication status": "Published: Please cite https://doi.org/10.1186/s12915-016-0321-y",
+        "Tissues/Life stage included": "adults",
+        "Track legend": "Mapped RNA-Seq reads:<br>Aligned regions: blue<br>Spanned regions (possible splice junctions): light blue<br>Deletions in the read relative to the reference: red<br>Insertions in the read relative to the reference: green<br>Mismatch: yellow (hover over the mismatch to see what the snp is)",
+        "isolate": "MEAM10"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "user_contributed_data/ARS_11_2017/Bemisia_tabaci_Nov_29__2017/Bemisia_tabaci_Bam_Files/WF-28.bam.sorted"
+    },
+    {
+      "category": "Transcriptome/Mapped Reads",
+      "key": "TYLCV_72h_rep1",
+      "label": "TYLCV_72h_rep1",
+      "metadata": {
+        "Data description": "RNA derived from adults fed on TYLCV-infected tomato cuttings for 72 h",
+        "Data provider": "Kai-Shu Ling, USDA-ARS",
+        "Data source": "PRJNA312467",
+        "Geographic location (latitude and longitude)": "Charleston, SC, USA",
+        "Method": "Illumina HiSeq 2515",
+        "Publication status": "Published: Please cite https://doi.org/10.1186/s12915-016-0321-y",
+        "Tissues/Life stage included": "adults",
+        "Track legend": "Mapped RNA-Seq reads:<br>Aligned regions: blue<br>Spanned regions (possible splice junctions): light blue<br>Deletions in the read relative to the reference: red<br>Insertions in the read relative to the reference: green<br>Mismatch: yellow (hover over the mismatch to see what the snp is)",
+        "isolate": "MEAM16"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "user_contributed_data/ARS_11_2017/Bemisia_tabaci_Nov_29__2017/Bemisia_tabaci_Bam_Files/WF-34.bam.sorted"
+    },
+    {
+      "category": "Transcriptome/Mapped Reads",
+      "key": "healthy_48h_rep3",
+      "label": "healthy_48h_rep3",
+      "metadata": {
+        "Data description": "RNA derived from adults fed on uninfected tomato cuttings for 48 h",
+        "Data provider": "Kai-Shu Ling, USDA-ARS",
+        "Data source": "PRJNA312467",
+        "Geographic location (latitude and longitude)": "Charleston, SC, USA",
+        "Method": "Illumina HiSeq 2508",
+        "Publication status": "Published: Please cite https://doi.org/10.1186/s12915-016-0321-y",
+        "Tissues/Life stage included": "adults",
+        "Track legend": "Mapped RNA-Seq reads:<br>Aligned regions: blue<br>Spanned regions (possible splice junctions): light blue<br>Deletions in the read relative to the reference: red<br>Insertions in the read relative to the reference: green<br>Mismatch: yellow (hover over the mismatch to see what the snp is)",
+        "isolate": "MEAM9"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "user_contributed_data/ARS_11_2017/Bemisia_tabaci_Nov_29__2017/Bemisia_tabaci_Bam_Files/WF-27.bam.sorted"
+    },
+    {
+      "category": "Transcriptome/Mapped Reads",
+      "key": "TYLCV_48h_rep3",
+      "label": "TYLCV_48h_rep3",
+      "metadata": {
+        "Data description": "RNA derived from adults fed on TYLCV-infected tomato cuttings for 48 h",
+        "Data provider": "Kai-Shu Ling, USDA-ARS",
+        "Data source": "PRJNA312467",
+        "Geographic location (latitude and longitude)": "Charleston, SC, USA",
+        "Method": "Illumina HiSeq 2511",
+        "Publication status": "Published: Please cite https://doi.org/10.1186/s12915-016-0321-y",
+        "Tissues/Life stage included": "adults",
+        "Track legend": "Mapped RNA-Seq reads:<br>Aligned regions: blue<br>Spanned regions (possible splice junctions): light blue<br>Deletions in the read relative to the reference: red<br>Insertions in the read relative to the reference: green<br>Mismatch: yellow (hover over the mismatch to see what the snp is)",
+        "isolate": "MEAM12"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "user_contributed_data/ARS_11_2017/Bemisia_tabaci_Nov_29__2017/Bemisia_tabaci_Bam_Files/WF-30.bam.sorted"
+    },
+    {
+      "category": "Transcriptome/Mapped Reads",
+      "key": "healthy_24h_rep1",
+      "label": "healthy_24h_rep1",
+      "metadata": {
+        "Data description": "RNA derived from adults fed on uninfected tomato cuttings for 24 h",
+        "Data provider": "Kai-Shu Ling, USDA-ARS",
+        "Data source": "PRJNA312467",
+        "Geographic location (latitude and longitude)": "Charleston, SC, USA",
+        "Method": "Illumina HiSeq 2500",
+        "Publication status": "Published: Please cite https://doi.org/10.1186/s12915-016-0321-y",
+        "Tissues/Life stage included": "adults",
+        "Track legend": "Mapped RNA-Seq reads:<br>Aligned regions: blue<br>Spanned regions (possible splice junctions): light blue<br>Deletions in the read relative to the reference: red<br>Insertions in the read relative to the reference: green<br>Mismatch: yellow (hover over the mismatch to see what the snp is)",
+        "isolate": "MEAM1"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "user_contributed_data/ARS_11_2017/Bemisia_tabaci_Nov_29__2017/Bemisia_tabaci_Bam_Files/WF-19.bam.sorted"
+    },
+    {
+      "category": "Transcriptome/Mapped Reads",
+      "key": "TYLCV_24h_rep2",
+      "label": "TYLCV_24h_rep2",
+      "metadata": {
+        "Data description": "RNA derived from adults fed on TYLCV-infected tomato cuttings for 24 h",
+        "Data provider": "Kai-Shu Ling, USDA-ARS",
+        "Data source": "PRJNA312467",
+        "Geographic location (latitude and longitude)": "Charleston, SC, USA",
+        "Method": "Illumina HiSeq 2504",
+        "Publication status": "Published: Please cite https://doi.org/10.1186/s12915-016-0321-y",
+        "Tissues/Life stage included": "adults",
+        "Track legend": "Mapped RNA-Seq reads:<br>Aligned regions: blue<br>Spanned regions (possible splice junctions): light blue<br>Deletions in the read relative to the reference: red<br>Insertions in the read relative to the reference: green<br>Mismatch: yellow (hover over the mismatch to see what the snp is)",
+        "isolate": "MEAM5"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "user_contributed_data/ARS_11_2017/Bemisia_tabaci_Nov_29__2017/Bemisia_tabaci_Bam_Files/WF-23.bam.sorted"
+    },
+    {
+      "category": "Transcriptome/Mapped Reads",
+      "key": "healthy_72h_rep1",
+      "label": "healthy_72h_rep1",
+      "metadata": {
+        "Data description": "RNA derived from adults fed on uninfected tomato cuttings for 72 h",
+        "Data provider": "Kai-Shu Ling, USDA-ARS",
+        "Data source": "PRJNA312467",
+        "Geographic location (latitude and longitude)": "Charleston, SC, USA",
+        "Method": "Illumina HiSeq 2512",
+        "Publication status": "Published: Please cite https://doi.org/10.1186/s12915-016-0321-y",
+        "Tissues/Life stage included": "adults",
+        "Track legend": "Mapped RNA-Seq reads:<br>Aligned regions: blue<br>Spanned regions (possible splice junctions): light blue<br>Deletions in the read relative to the reference: red<br>Insertions in the read relative to the reference: green<br>Mismatch: yellow (hover over the mismatch to see what the snp is)",
+        "isolate": "MEAM13"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "user_contributed_data/ARS_11_2017/Bemisia_tabaci_Nov_29__2017/Bemisia_tabaci_Bam_Files/WF-31.bam.sorted"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Transcriptome/Coverage Plots (BigWig)",
+      "key": "TYLCV_48h_rep2 (Coverage Plots)",
+      "label": "TYLCV_48h_rep2 (Coverage Plots)",
+      "metadata": {
+        "Data description": "RNA derived from adults fed on TYLCV-infected tomato cuttings for 48 h",
+        "Data provider": "Kai-Shu Ling, USDA-ARS",
+        "Data source": "PRJNA312467",
+        "Geographic location (latitude and longitude)": "Charleston, SC, USA",
+        "Method": "Illumina HiSeq 2510",
+        "Publication status": "Published: Please cite https://doi.org/10.1186/s12915-016-0321-y",
+        "Tissues/Life stage included": "adults",
+        "Track legend": "This track represents an RNA-Seq coverage plot.",
+        "isolate": "MEAM11"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "pos_color": "#00BFFF"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "user_contributed_data/ARS_11_2017/Bemisia_tabaci_Nov_29__2017/Bemisia_tabaci_Bam_Files/WF-29.bigwig.sorted"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Transcriptome/Coverage Plots (BigWig)",
+      "key": "TYLCV_24h_rep3 (Coverage Plots)",
+      "label": "TYLCV_24h_rep3 (Coverage Plots)",
+      "metadata": {
+        "Data description": "RNA derived from adults fed on TYLCV-infected tomato cuttings for 24 h",
+        "Data provider": "Kai-Shu Ling, USDA-ARS",
+        "Data source": "PRJNA312467",
+        "Geographic location (latitude and longitude)": "Charleston, SC, USA",
+        "Method": "Illumina HiSeq 2505",
+        "Publication status": "Published: Please cite https://doi.org/10.1186/s12915-016-0321-y",
+        "Tissues/Life stage included": "adults",
+        "Track legend": "This track represents an RNA-Seq coverage plot.",
+        "isolate": "MEAM6"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "pos_color": "#00BFFF"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "user_contributed_data/ARS_11_2017/Bemisia_tabaci_Nov_29__2017/Bemisia_tabaci_Bam_Files/WF-24.bigwig.sorted"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Transcriptome/Coverage Plots (BigWig)",
+      "key": "healthy_72h_rep3 (Coverage Plots)",
+      "label": "healthy_72h_rep3 (Coverage Plots)",
+      "metadata": {
+        "Data description": "RNA derived from adults fed on uninfected tomato cuttings for 72 h",
+        "Data provider": "Kai-Shu Ling, USDA-ARS",
+        "Data source": "PRJNA312467",
+        "Geographic location (latitude and longitude)": "Charleston, SC, USA",
+        "Method": "Illumina HiSeq 2514",
+        "Publication status": "Published: Please cite https://doi.org/10.1186/s12915-016-0321-y",
+        "Tissues/Life stage included": "adults",
+        "Track legend": "This track represents an RNA-Seq coverage plot.",
+        "isolate": "MEAM15"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "pos_color": "#00BFFF"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "user_contributed_data/ARS_11_2017/Bemisia_tabaci_Nov_29__2017/Bemisia_tabaci_Bam_Files/WF-33.bigwig.sorted"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Transcriptome/Coverage Plots (BigWig)",
+      "key": "healthy_72h_rep1 (Coverage Plots)",
+      "label": "healthy_72h_rep1 (Coverage Plots)",
+      "metadata": {
+        "Data description": "RNA derived from adults fed on uninfected tomato cuttings for 72 h",
+        "Data provider": "Kai-Shu Ling, USDA-ARS",
+        "Data source": "PRJNA312467",
+        "Geographic location (latitude and longitude)": "Charleston, SC, USA",
+        "Method": "Illumina HiSeq 2512",
+        "Publication status": "Published: Please cite https://doi.org/10.1186/s12915-016-0321-y",
+        "Tissues/Life stage included": "adults",
+        "Track legend": "This track represents an RNA-Seq coverage plot.",
+        "isolate": "MEAM13"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "pos_color": "#00BFFF"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "user_contributed_data/ARS_11_2017/Bemisia_tabaci_Nov_29__2017/Bemisia_tabaci_Bam_Files/WF-31.bigwig.sorted"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Transcriptome/Coverage Plots (BigWig)",
+      "key": "healthy_48h_rep2 (Coverage Plots)",
+      "label": "healthy_48h_rep2 (Coverage Plots)",
+      "metadata": {
+        "Data description": "RNA derived from adults fed on uninfected tomato cuttings for 48 h",
+        "Data provider": "Kai-Shu Ling, USDA-ARS",
+        "Data source": "PRJNA312467",
+        "Geographic location (latitude and longitude)": "Charleston, SC, USA",
+        "Method": "Illumina HiSeq 2507",
+        "Publication status": "Published: Please cite https://doi.org/10.1186/s12915-016-0321-y",
+        "Tissues/Life stage included": "adults",
+        "Track legend": "This track represents an RNA-Seq coverage plot.",
+        "isolate": "MEAM8"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "pos_color": "#00BFFF"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "user_contributed_data/ARS_11_2017/Bemisia_tabaci_Nov_29__2017/Bemisia_tabaci_Bam_Files/WF-26.bigwig.sorted"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Transcriptome/Coverage Plots (BigWig)",
+      "key": "healthy_72h_rep2 (Coverage Plots)",
+      "label": "healthy_72h_rep2 (Coverage Plots)",
+      "metadata": {
+        "Data description": "RNA derived from adults fed on uninfected tomato cuttings for 72 h",
+        "Data provider": "Kai-Shu Ling, USDA-ARS",
+        "Data source": "PRJNA312467",
+        "Geographic location (latitude and longitude)": "Charleston, SC, USA",
+        "Method": "Illumina HiSeq 2513",
+        "Publication status": "Published: Please cite https://doi.org/10.1186/s12915-016-0321-y",
+        "Tissues/Life stage included": "adults",
+        "Track legend": "This track represents an RNA-Seq coverage plot.",
+        "isolate": "MEAM14"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "pos_color": "#00BFFF"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "user_contributed_data/ARS_11_2017/Bemisia_tabaci_Nov_29__2017/Bemisia_tabaci_Bam_Files/WF-32.bigwig.sorted"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Transcriptome/Coverage Plots (BigWig)",
+      "key": "healthy_24h_rep3 (Coverage Plots)",
+      "label": "healthy_24h_rep3 (Coverage Plots)",
+      "metadata": {
+        "Data description": "RNA derived from adults fed on uninfected tomato cuttings for 24 h",
+        "Data provider": "Kai-Shu Ling, USDA-ARS",
+        "Data source": "PRJNA312467",
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diff --git a/organisms/stage/stage-v2/Blattella_germanica/trackList.json b/organisms/stage/stage-v2/Blattella_germanica/trackList.json
new file mode 100644
index 0000000..1878a2c
--- /dev/null
+++ b/organisms/stage/stage-v2/Blattella_germanica/trackList.json
@@ -0,0 +1,1673 @@
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+        "Track legend": "Results from Protein2genome alignments of a set of Annelida proteins as part of the MAKER automated annotation pipeline."
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+    },
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+      "label": "protein2genome_Arthropoda",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Arthropoda proteins as part of the MAKER automated annotation pipeline."
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+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Atelocerata proteins as part of the MAKER automated annotation pipeline."
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+      "key": "protein2genome_Cephalochordata",
+      "label": "protein2genome_Cephalochordata",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Cephalochordata proteins as part of the MAKER automated annotation pipeline."
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+    },
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+      "key": "protein2genome_Chelicerata",
+      "label": "protein2genome_Chelicerata",
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+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Chelicerata proteins as part of the MAKER automated annotation pipeline."
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+    },
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+      "key": "protein2genome_Cnidaria",
+      "label": "protein2genome_Cnidaria",
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+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Cnidaria proteins as part of the MAKER automated annotation pipeline."
+      },
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+    },
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+      "compress": 0,
+      "key": "protein2genome_Craniata",
+      "label": "protein2genome_Craniata",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Craniata proteins as part of the MAKER automated annotation pipeline."
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+    },
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+      "compress": 0,
+      "key": "protein2genome_Crustacea",
+      "label": "protein2genome_Crustacea",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Crustacea proteins as part of the MAKER automated annotation pipeline."
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+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
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+      "type": "FeatureTrack",
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+    },
+    {
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+      "compress": 0,
+      "key": "protein2genome_Echinodermata",
+      "label": "protein2genome_Echinodermata",
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+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Echinodermata proteins as part of the MAKER automated annotation pipeline."
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+      "type": "FeatureTrack",
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+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Mollusca",
+      "label": "protein2genome_Mollusca",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Mollusca proteins as part of the MAKER automated annotation pipeline."
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+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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+          "match_part": "protein2genome"
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Mollusca/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Nemata",
+      "label": "protein2genome_Nemata",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline."
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+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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+          "match_part": "protein2genome"
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Nemata/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Nematomorpha",
+      "label": "protein2genome_Nematomorpha",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Nematomorpha proteins as part of the MAKER automated annotation pipeline."
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+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
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+          "match_part": "protein2genome"
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Nematomorpha/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Onychophora",
+      "label": "protein2genome_Onychophora",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Onychophora proteins as part of the MAKER automated annotation pipeline."
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+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Onychophora/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Parazoa",
+      "label": "protein2genome_Parazoa",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Parazoa/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Placozoa",
+      "label": "protein2genome_Placozoa",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
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+          "match_part": "protein2genome"
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+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Placozoa/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Platyhelminthes",
+      "label": "protein2genome_Platyhelminthes",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
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+      },
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Platyhelminthes/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Priapulida",
+      "label": "protein2genome_Priapulida",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Priapulida/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Tardigrada",
+      "label": "protein2genome_Tardigrada",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline."
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+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
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+      },
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Tardigrada/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Tunicata",
+      "label": "protein2genome_Tunicata",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline."
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+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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+        "subfeatureClasses": {
+          "match_part": "protein2genome"
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+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Tunicata/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_UNCATEGORISED",
+      "label": "protein2genome_UNCATEGORISED",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
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+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_UNCATEGORISED/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/2. Evidence/Repeats",
+      "compress": 0,
+      "key": "repeatmasker",
+      "label": "repeatmasker",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from RepeatMasker as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "repeat"
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+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/repeatmasker/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/2. Evidence/Repeats",
+      "compress": 0,
+      "key": "repeatrunner",
+      "label": "repeatrunner",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Repeatrunner as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "repeat"
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+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/repeatrunner/{refseq}/trackData.json"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Reference Assembly",
+      "key": "Gaps in assembly",
+      "label": "Gaps in assembly",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "white",
+        "pos_color": "black"
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+        "Data Source 4 Alignment Summary": "http://de.iplantcollaborative.org/dl/d/DAA3D4D7-4D22-451D-9914-EAD37D2E0A5B/align_summary.txt",
+        "Note": "This is merged dataset from four separate sources",
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+        "Note": "This is merged dataset from four separate sources",
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+        "Species name": "Blattella germanica"
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+        "Citation": "Recurrent loss of CenH3 is associated with independent transitions to holocentricity in insects. Drinnenberg IA, deYoung D, Henikoff S, Malik HS. Elife. 2014 Sep 23;3. doi: 10.7554/eLife.03676.PMID:25247700",
+        "Data URL": "http://www.ncbi.nlm.nih.gov/Traces/sra/?run=SRR1552487; http://www.ncbi.nlm.nih.gov/Traces/sra/?run=SRR1552488",
+        "Data provider": "Inez Anna Drinnenberg",
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+        "Citation": "Recurrent loss of CenH3 is associated with independent transitions to holocentricity in insects. Drinnenberg IA, deYoung D, Henikoff S, Malik HS. Elife. 2014 Sep 23;3. doi: 10.7554/eLife.03676.PMID:25247700",
+        "Data URL": "http://www.ncbi.nlm.nih.gov/Traces/sra/?run=SRR1552487; http://www.ncbi.nlm.nih.gov/Traces/sra/?run=SRR1552488",
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+        "File provider": "Kim Walden, University of Illinois at Urbana-Champaign",
+        "Geographical location of specimen collection": " unknown",
+        "Publication": "Dong-Juan Niu, Yan Liu, Xiao-Tong Dong, Shuang-Lin Dong. 2016. Transcriptome based identification and tissue expression profiles of chemosensory genes in Blattella germanica (Blattaria: Blattidae). http://dx.doi.org/10.1016/j.cbd.2016.03.002",
+        "Sequencing platform and version": "Illumina Hiseq 2000",
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+        "File provider": "Kim Walden, University of Illinois at Urbana-Champaign",
+        "Geographical location of specimen collection": " unknown",
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+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Manual annotations of the computationally predicted gene set BGERv0.6.2. Note that stop codon read-through features are visualized as a purple box on the CDS feature."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/BGERv0.6.2_manual_annotations_v1/{refseq}/trackData.json"
+    }
+  ]
+}
diff --git a/organisms/stage/stage-v2/Bombus_impatiens/trackList.json b/organisms/stage/stage-v2/Bombus_impatiens/trackList.json
new file mode 100644
index 0000000..16c44b3
--- /dev/null
+++ b/organisms/stage/stage-v2/Bombus_impatiens/trackList.json
@@ -0,0 +1,184 @@
+{
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+}
diff --git a/organisms/stage/stage-v2/Bombus_terrestris/trackList.json b/organisms/stage/stage-v2/Bombus_terrestris/trackList.json
new file mode 100644
index 0000000..7a82024
--- /dev/null
+++ b/organisms/stage/stage-v2/Bombus_terrestris/trackList.json
@@ -0,0 +1,152 @@
+{
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+}
diff --git a/organisms/stage/stage-v2/Bradysia_coprophila/trackList.json b/organisms/stage/stage-v2/Bradysia_coprophila/trackList.json
new file mode 100644
index 0000000..d8f9ce2
--- /dev/null
+++ b/organisms/stage/stage-v2/Bradysia_coprophila/trackList.json
@@ -0,0 +1,261 @@
+{
+  "formatVersion": 1,
+  "names": {
+    "type": "Hash",
+    "url": "names/"
+  },
+  "tracks": [
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+      "chunkSize": 20000,
+      "key": "Reference sequence",
+      "label": "DNA",
+      "refSeqOrder": "length descending",
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+      "storeClass": "JBrowse/Store/Sequence/StaticChunked",
+      "type": "SequenceTrack",
+      "urlTemplate": "seq/{refseq_dirpath}/{refseq}-"
+    },
+    {
+      "category": "NCBI Annotation Release 100",
+      "compress": 0,
+      "key": "NCBI_Annotation_Release_100_Gene",
+      "label": "bracop_current_models",
+      "menuTemplate": [
+        {
+          "label": "View details"
+        },
+        {
+          "action": "newWindow",
+          "iconClass": "dijitIconDatabase",
+          "label": "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
+          "title": "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
+          "url": "function(track,feature){ return 'https://i5k.nal.usda.gov/'+feature.get('name')}"
+        }
+      ],
+      "metadata": {
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+        "Data provider": "NCBI",
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+        "Method": "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "description": "product, note, description",
+        "subfeatureClasses": {
+          "CDS": "gnomon_CDS",
+          "UTR": "gnomon_UTR",
+          "exon": "container-100pct",
+          "wholeCDS": null
+        }
+      },
+      "trackType": "HTMLFeatures",
+      "type": "HTMLFeatures",
+      "urlTemplate": "tracks/bracop_current_models/{refseq}/trackData.json"
+    },
+    {
+      "category": "NCBI Annotation Release 100",
+      "compress": 0,
+      "key": "NCBI_Annotation_Release_100_Pseudogene",
+      "label": "NCBI_Annotation_Release_100_Pseudogene",
+      "metadata": {
+        "Data description": "ftp://ftp.ncbi.nlm.nih.gov/genomes/Bradysia_coprophila/README_CURRENT_RELEASE",
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+        "Method": "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
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+      "style": {
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+        "className": "{type}",
+        "description": "product, note, description",
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+      },
+      "trackType": "HTMLFeatures",
+      "type": "HTMLFeatures",
+      "urlTemplate": "tracks/NCBI_Annotation_Release_100_Pseudogene/{refseq}/trackData.json"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Reference Assembly",
+      "key": "Gaps in assembly",
+      "label": "Gaps in assembly",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
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+      "urlTemplate": "bigwig/GCF_014529535.1_BU_Bcop_v1_genomic.fna.gaps.bigwig"
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+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
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+      "urlTemplate": "bigwig/GCF_014529535.1_BU_Bcop_v1_genomic.fna.gc.bigwig"
+    },
+    {
+      "category": "Other Gene Sets",
+      "compress": 0,
+      "key": "Bcop_v1.0-Gene_set",
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+        "Data provider": "John Urban, Carnegie Institution for Science",
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+        "Publication status": "Published, please cite https://doi.org/10.1101/2020.02.24.963009"
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+      },
+      "trackType": "HTMLFeatures",
+      "type": "HTMLFeatures",
+      "urlTemplate": "tracks/Bcop_v1.0-Gene_set/{refseq}/trackData.json"
+    },
+    {
+      "category": "Other Gene Sets",
+      "compress": 0,
+      "key": "Bcop_v1.0-Evidence",
+      "label": "Bcop_v1.0-Evidence",
+      "metadata": {
+        "Data provider": "John Urban, Carnegie Institution for Science",
+        "Data source": "https://data.nal.usda.gov/dataset/bradysia-coprophila-genome-annotations-bcopv10",
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+          "match_part": "blast-match_part",
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+      "type": "HTMLFeatures",
+      "urlTemplate": "tracks/Bcop_v1.0-Evidence/{refseq}/trackData.json"
+    },
+    {
+      "category": "RNA-Seq/Mapped Reads",
+      "key": "Bracop_BU_Bcop_v1_RNA-Seq-alignments_2021-06-10",
+      "label": "Bracop_BU_Bcop_v1_RNA-Seq-alignments_2021-06-10",
+      "metadata": {
+        "Analysis method": "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+        "Analysis provider": "i5k Workspace@NAL",
+        "Data source": "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR9969381'>SRR9969381</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR9969372'>SRR9969372</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR9969367'>SRR9969367</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR9969378'>SRR9969378</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR9969374'>SRR9969374</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR9969368'>SRR9969368</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR9969375'>SRR9969375</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR9969373'>SRR9969373</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR9969382'>SRR9969382</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR9969369'>SRR9969369</a>",
+        "Publication status": "Analysis: NA; Source data: see individual SRA accessions",
+        "Track legend": "Dark red alignments: Mapped portion of read aligned to forward strand<br>Light red alignments: Spliced portion of read aligned to forward strand<br>Dark blue alignments: Mapped portion of read aligned to reverse strand<br>Light blue alignments: Spliced portion of read aligned to reverse strand<br>Red marking - deletion in the read relative to the reference<br>Green marking - insertion in the read relative to the reference<br>Yellow marking  - mismatch (hover over the mismatch to see what the snp is)"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "analyses/Bradysia-coprophila-RNA-Seq_2021-06-10_v1.0/Bracop_BU_Bcop_v1_RNA-Seq-alignments_2021-06-10.bam"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "RNA-Seq/Coverage Plots",
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+      "label": "Bracop_BU_Bcop_v1_RNA-Seq-alignments_2021-06-10_coverage",
+      "metadata": {
+        "Analysis method": "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+        "Analysis provider": "i5k Workspace@NAL",
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+        "Publication status": "Analysis: NA; Source data: see individual SRA accessions",
+        "Track legend": "This track represents an X-Y plot of RNA-Seq coverage."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "pos_color": "#00BFFF"
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+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "analyses/Bradysia-coprophila-RNA-Seq_2021-06-10_v1.0/Bracop_BU_Bcop_v1_RNA-Seq-alignments_2021-06-10.bigwig"
+    },
+    {
+      "category": "RNA-Seq/Splice junctions",
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+      "key": "Bracop_BU_Bcop_v1_RNA-Seq-alignments_2021-06-10_junctions",
+      "label": "Bracop_BU_Bcop_v1_RNA-Seq-alignments_2021-06-10_junctions",
+      "metadata": {
+        "Analysis method": "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+        "Analysis provider": "i5k Workspace@NAL",
+        "Data source": "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR9969381'>SRR9969381</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR9969372'>SRR9969372</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR9969367'>SRR9969367</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR9969378'>SRR9969378</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR9969374'>SRR9969374</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR9969368'>SRR9969368</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR9969375'>SRR9969375</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR9969373'>SRR9969373</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR9969382'>SRR9969382</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR9969369'>SRR9969369</a>",
+        "Publication status": "Analysis: NA; Source data: see individual SRA accessions",
+        "Track legend": "Junction reads generated by Hisat2 aligner and regtools. The number of alignments supporting the junction read is listed in blue."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "className": "feature",
+        "description": "score"
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/Bracop_BU_Bcop_v1_RNA-Seq-alignments_2021-06-10_junctions/{refseq}/trackData.json"
+    },
+    {
+      "category": "Other Gene Sets",
+      "compress": 0,
+      "key": "Bcop_v1.0-Repeats",
+      "label": "Bcop_v1.0-Repeats",
+      "metadata": {
+        "Data provider": "John Urban, Carnegie Institution for Science",
+        "Data source": "https://data.nal.usda.gov/dataset/bradysia-coprophila-genome-annotations-bcopv10",
+        "Materials and Methods": "Mapped repeat sequences, for details see https://doi.org/10.1101/2020.02.24.963009",
+        "Publication status": "Published, please cite https://doi.org/10.1101/2020.02.24.963009",
+        "Track legend": "Mapped repeat sequences from RepeatModeler, known repeat sequences from Bradysia coprophila and the RepeatMasker Combined Database: Dfam_Consensus-20181026"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "description": "name",
+        "subfeatureClasses": {
+          "match": "repeat",
+          "match_part": "repeat",
+          "wholeCDS": null
+        }
+      },
+      "trackType": "HTMLFeatures",
+      "type": "HTMLFeatures",
+      "urlTemplate": "tracks/Bcop_v1.0-Repeats/{refseq}/trackData.json"
+    }
+  ]
+}
diff --git a/organisms/stage/stage-v2/Catajapyx_aquilonaris/trackList.json b/organisms/stage/stage-v2/Catajapyx_aquilonaris/trackList.json
new file mode 100644
index 0000000..e23b689
--- /dev/null
+++ b/organisms/stage/stage-v2/Catajapyx_aquilonaris/trackList.json
@@ -0,0 +1,1228 @@
+{
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+  "css": "./plugins/NAL_CSS/css/main.css",
+  "favicon": "./plugins/WebApollo/img/webapollo_favicon.ico",
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+  "names": {
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+    "url": "names/"
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+  "share_link": 0,
+  "tracks": [
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+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
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+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
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+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
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+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Blastx alignments of a set of Arthropoda proteins as part of the MAKER automated annotation pipeline."
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+        "Track legend": "Results from Blastx alignments of a set of Mollusca proteins as part of the MAKER automated annotation pipeline."
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+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Blastx alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline."
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+      "label": "blastx_Nematomorpha",
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+      "label": "blastx_Onychophora",
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+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Blastx alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline."
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+      "label": "blastx_Placozoa",
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+        "Track legend": "Results from Blastx alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline."
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+      "label": "blastx_Platyhelminthes",
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+        "Track legend": "Results from Blastx alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline."
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+      "key": "blastx_Priapulida",
+      "label": "blastx_Priapulida",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
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+        "Track legend": "Results from Blastx alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline."
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+      "key": "blastx_Tardigrada",
+      "label": "blastx_Tardigrada",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
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+        "Track legend": "Results from Blastx alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline."
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+        "Track legend": "Results from Blastx alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline."
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+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
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+      "key": "cegma",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
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+        "Track legend": "Results from CEGMA alignments as part of the MAKER automated annotation pipeline."
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+      "key": "protein2genome_Annelida",
+      "label": "protein2genome_Annelida",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
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+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Annelida proteins as part of the MAKER automated annotation pipeline."
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+      "key": "protein2genome_Arthropoda",
+      "label": "protein2genome_Arthropoda",
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+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Arthropoda proteins as part of the MAKER automated annotation pipeline."
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+      "key": "protein2genome_Atelocerata",
+      "label": "protein2genome_Atelocerata",
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+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Atelocerata proteins as part of the MAKER automated annotation pipeline."
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+      "key": "protein2genome_Cephalochordata",
+      "label": "protein2genome_Cephalochordata",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
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+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Cephalochordata proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
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+        "arrowheadClass": "webapollo-arrowhead",
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+          "match_part": "protein2genome"
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Cephalochordata/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Chelicerata",
+      "label": "protein2genome_Chelicerata",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Chelicerata proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
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+          "match_part": "protein2genome"
+        }
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Chelicerata/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Cnidaria",
+      "label": "protein2genome_Cnidaria",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Cnidaria proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Cnidaria/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Craniata",
+      "label": "protein2genome_Craniata",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Craniata proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Craniata/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Crustacea",
+      "label": "protein2genome_Crustacea",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Crustacea proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Crustacea/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Echinodermata",
+      "label": "protein2genome_Echinodermata",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Echinodermata proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
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+          "match_part": "protein2genome"
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+      },
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Echinodermata/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Mollusca",
+      "label": "protein2genome_Mollusca",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Mollusca proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
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+      },
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Mollusca/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Nemata",
+      "label": "protein2genome_Nemata",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
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+          "match_part": "protein2genome"
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Nemata/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Nematomorpha",
+      "label": "protein2genome_Nematomorpha",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Nematomorpha proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
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+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Nematomorpha/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Onychophora",
+      "label": "protein2genome_Onychophora",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Onychophora proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
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+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Onychophora/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Parazoa",
+      "label": "protein2genome_Parazoa",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
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+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Parazoa/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Placozoa",
+      "label": "protein2genome_Placozoa",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
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+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Placozoa/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Platyhelminthes",
+      "label": "protein2genome_Platyhelminthes",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
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+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Platyhelminthes/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Priapulida",
+      "label": "protein2genome_Priapulida",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Priapulida/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Tardigrada",
+      "label": "protein2genome_Tardigrada",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
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+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Tardigrada/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Tunicata",
+      "label": "protein2genome_Tunicata",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
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+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Tunicata/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_UNCATEGORISED",
+      "label": "protein2genome_UNCATEGORISED",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
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+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_UNCATEGORISED/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/2. Evidence/Repeats",
+      "compress": 0,
+      "key": "repeatmasker",
+      "label": "repeatmasker",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from RepeatMasker as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "repeat"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/repeatmasker/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/2. Evidence/Repeats",
+      "compress": 0,
+      "key": "repeatrunner",
+      "label": "repeatrunner",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Repeatrunner as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "repeat"
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+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/repeatrunner/{refseq}/trackData.json"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Reference Assembly",
+      "key": "Gaps in assembly",
+      "label": "Gaps in assembly",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "white",
+        "pos_color": "black"
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+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "bigwig/forcepstail.scaffolds_NALmod.fa.gaps.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "0.5",
+      "category": "Reference Assembly",
+      "key": "GC Content",
+      "label": "GC Content",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+      },
+      "scoreType": "avgScore",
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "rgba(255,255,0,50)",
+        "pos_color": "rgba(0,0,255,50)"
+      },
+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "bigwig/forcepstail.scaffolds_NALmod.fa.gc.bigwig"
+    },
+    {
+      "category": "Transcriptome/Mapped Reads",
+      "key": "Catajapyx aquilonaris RNAseq reads",
+      "label": "Catajapyx aquilonaris RNAseq reads",
+      "metadata": {
+        "Data Source": "Raw data available from 1kite upon request (http://www.1kite.org/)",
+        "Data Submitter": "Jan Philip",
+        "Methods": "Raw reads cleaned with Trimmomatic v0.32. Cleaned reads mapped with TopHat v2.0.12 using default settings.",
+        "Track description": "Catajapyx aquilonaris RNAseq reads"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "bam/accepted_hits_sorted.bam"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Transcriptome/Coverage plots (BigWig)",
+      "clip_marker_color": "red",
+      "height": 50,
+      "key": "Catajapyx aquilonaris RNAseq coverage",
+      "label": "catajapyx aquilonaris RNAseq coverage",
+      "metadata": {
+        "Data Source": "Raw data available from 1kite upon request (http://www.1kite.org/)",
+        "Data Submitter": "Jan Philip",
+        "Methods": "Raw reads cleaned with Trimmomatic v0.32. Cleaned reads mapped with TopHat v2.0.12 using default settings.",
+        "Track description": "Catajapyx aquilonaris RNAseq, converted to BigWig"
+      },
+      "origin_color": "#888",
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "#0086B3",
+        "pos_color": "#00BFFF"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "bigwig/accepted_hits_sorted.bigwig",
+      "variance_band_color": "rgba(0,0,0,0.3)"
+    },
+    {
+      "category": "Transcriptome/Assembly",
+      "compress": 0,
+      "key": "Catajapyx aquilonaris 1kite transcriptome",
+      "label": "Catajapyx aquilonaris 1kite transcriptome",
+      "metadata": {
+        "Data Source": "Raw data available from 1kite upon request (http://www.1kite.org/)",
+        "Data description": "Transcripts were mapped to the genome using Exonerate-gff3 (https://github.com/hotdogee/exonerate-gff3) with the options: --model est2genome --showtargetgff yes --gff3 yes --showalignment no --showvulgar no --geneseed 250 --bestn 2 --percent 50 --minintron 20 --maxintron 10000. Transcripts mapping to multiple locations were detected and marked with a note using a custom perl script (available from JP Oeyen (Univ. Bonn/ZFMK, ZMB), janphilipoyen@gmail.com)",
+        "Data provider": "Jan Philip"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
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+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/Catajapyx aquilonaris 1kite transcriptome/{refseq}/trackData.json"
+    }
+  ]
+}
diff --git a/organisms/stage/stage-v2/Centruroides_sculpturatus/trackList.json b/organisms/stage/stage-v2/Centruroides_sculpturatus/trackList.json
new file mode 100644
index 0000000..639826b
--- /dev/null
+++ b/organisms/stage/stage-v2/Centruroides_sculpturatus/trackList.json
@@ -0,0 +1,1210 @@
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+  "favicon": "./plugins/WebApollo/img/webapollo_favicon.ico",
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+  "names": {
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+          },
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+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
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+        "Track legend": "Results from the Augustus gene prediction software as part of the MAKER automated annotation pipeline."
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+      "key": "blastx_Cephalochordata",
+      "label": "blastx_Cephalochordata",
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+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research",
+        "Track legend": "Results from Blastx alignments of a set of Cephalochordata proteins as part of the MAKER automated annotation pipeline."
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/blastx_Cephalochordata/{refseq}/trackData.json"
+    },
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+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
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+      "key": "blastx_Cnidaria",
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+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
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+      "urlTemplate": "tracks/blastx_Cnidaria/{refseq}/trackData.json"
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+      "category": "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX",
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+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
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+      "style": {
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+    },
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+      "category": "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX",
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+      "key": "blastx_Crustacea",
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+      "metadata": {
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+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research",
+        "Track legend": "Results from Blastx alignments of a set of Crustacea proteins as part of the MAKER automated annotation pipeline."
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+      "type": "FeatureTrack",
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+    },
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+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
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+      "key": "blastx_Mollusca",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
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+        "Track legend": "Results from Blastx alignments of a set of Mollusca proteins as part of the MAKER automated annotation pipeline."
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+        "arrowheadClass": "webapollo-arrowhead",
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/blastx_Mollusca/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX",
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+      "key": "blastx_Nemata",
+      "label": "blastx_Nemata",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research",
+        "Track legend": "Results from Blastx alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline."
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+      "style": {
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+      "urlTemplate": "tracks/blastx_Nemata/{refseq}/trackData.json"
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+      "category": "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX",
+      "compress": 0,
+      "key": "blastx_Nematomorpha",
+      "label": "blastx_Nematomorpha",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research",
+        "Track legend": "Results from Blastx alignments of a set of Nematomorpha proteins as part of the MAKER automated annotation pipeline."
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+      "type": "FeatureTrack",
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+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX",
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+      "key": "blastx_Onychophora",
+      "label": "blastx_Onychophora",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research",
+        "Track legend": "Results from Blastx alignments of a set of Onychophora proteins as part of the MAKER automated annotation pipeline."
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+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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+      },
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/blastx_Onychophora/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX",
+      "compress": 0,
+      "key": "blastx_Parazoa",
+      "label": "blastx_Parazoa",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research",
+        "Track legend": "Results from Blastx alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
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+        "arrowheadClass": "webapollo-arrowhead",
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+    },
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+      "compress": 0,
+      "key": "blastx_Placozoa",
+      "label": "blastx_Placozoa",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research",
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+      "label": "protein2genome_Placozoa",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
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+        "Track legend": "Results from Protein2genome alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline."
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+    },
+    {
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+      "key": "protein2genome_Platyhelminthes",
+      "label": "protein2genome_Platyhelminthes",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research",
+        "Track legend": "Results from Protein2genome alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline."
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+        "arrowheadClass": "webapollo-arrowhead",
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+      "key": "protein2genome_Priapulida",
+      "label": "protein2genome_Priapulida",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research",
+        "Track legend": "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline."
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+      "key": "protein2genome_Tardigrada",
+      "label": "protein2genome_Tardigrada",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research",
+        "Track legend": "Results from Protein2genome alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline."
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+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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+    },
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+      "key": "protein2genome_Tunicata",
+      "label": "protein2genome_Tunicata",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research",
+        "Track legend": "Results from Protein2genome alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline."
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+      "key": "protein2genome_UNCATEGORISED",
+      "label": "protein2genome_UNCATEGORISED",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research",
+        "Track legend": "Results from Protein2genome alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline."
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+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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+      "key": "repeatmasker",
+      "label": "repeatmasker",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research",
+        "Track legend": "Results from RepeatMasker as part of the MAKER automated annotation pipeline."
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+    {
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+      "compress": 0,
+      "key": "repeatrunner",
+      "label": "repeatrunner",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research",
+        "Track legend": "Results from Repeatrunner as part of the MAKER automated annotation pipeline."
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+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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+      "key": "snap_masked",
+      "label": "snap_masked",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research",
+        "Track legend": "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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+      "urlTemplate": "tracks/snap_masked/{refseq}/trackData.json"
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+    {
+      "autoscale": "local",
+      "bicolor_pivot": "0.5",
+      "category": "Reference Assembly",
+      "key": "GC Content",
+      "label": "GC Content",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+      },
+      "scoreType": "avgScore",
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
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+      "urlTemplate": "bigwig/Cscul.scaffolds.50.fa.gc.bigwig"
+    }
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+}
diff --git a/organisms/stage/stage-v2/Cephus_cinctus/trackList.json b/organisms/stage/stage-v2/Cephus_cinctus/trackList.json
new file mode 100644
index 0000000..bedc85e
--- /dev/null
+++ b/organisms/stage/stage-v2/Cephus_cinctus/trackList.json
@@ -0,0 +1,1026 @@
+{
+  "formatVersion": 1,
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+    "type": "Hash",
+    "url": "names/"
+  },
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+      "chunkSize": 20000,
+      "key": "Reference sequence",
+      "label": "DNA",
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+      "type": "SequenceTrack",
+      "urlTemplate": "seq/{refseq_dirpath}/{refseq}-"
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+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Reference Assembly",
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+      "label": "Gaps in assembly",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "white",
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+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
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+      "category": "Transposon prediction",
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+        "Data provider": "Brad Coates, USDA-ARS; Fabrice Legeai, INRA",
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+        "Publication status": "Published - please cite https://doi.org/10.1093/gbe/evy232"
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+        "Date completed": "9/16/16",
+        "File provider": "Kim Walden, University of Illinois at Urbana-Champaign",
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+        "Publication Status": "Published - please cite https://doi.org/10.1093/gbe/evy232 ",
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+      "key": "2011_adult_females",
+      "label": "2011_adult_females",
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+        "File provider": "Kim Walden, University of Illinois at Urbana-Champaign",
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+        "File provider": "Kim Walden, University of Illinois at Urbana-Champaign",
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+        "File provider": "Kim Walden, University of Illinois at Urbana-Champaign",
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+        "Sequencing platform and version": "HiSeq2000",
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+        "Strain": "Amsterdam-Churchill subculture",
+        "Tissues included": "pooled adult males"
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+        "NCBI TaxID": "211228",
+        "Other methods": "Reads were trimmed with Trimmomatic prior to mapping. ",
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diff --git a/organisms/stage/stage-v2/Ceratitis_capitata/trackList.json b/organisms/stage/stage-v2/Ceratitis_capitata/trackList.json
new file mode 100644
index 0000000..4b89da3
--- /dev/null
+++ b/organisms/stage/stage-v2/Ceratitis_capitata/trackList.json
@@ -0,0 +1,1851 @@
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+    },
+    {
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+      "key": "whole adult, female, Ispra",
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+        "File provider (name and affiliation)": "Alexie Papanicolaou, Hawkesbury Institute for the Environment",
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+        "Strain": "Ispra",
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+    },
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+      "label": "Pooled Lower Reproductive tract from Mated-adult (spermatheca, female accessory glands and uterus), Female, Egypt II wild type, sample 4",
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+      "urlTemplate": "tracks/OGSv1-1_pseudogene/{refseq}/trackData.json"
+    },
+    {
+      "category": "OGSv1.1/1. Gene Sets/Protein Coding",
+      "compress": 0,
+      "key": "Published OGS v1.1, protein-coding genes",
+      "label": "cercap_current_models",
+      "metadata": {
+        "Data description": "06 Dec 2015: This track reconciles the two OGS tracks produced by JAMg (v1) and NCBI (v2) and bring in the manual curation track. For every locus, a 2-2 comparison was made and then one gene was kept in that order: manual curation that have been approved, NCBI and JAMg. No alternative splice genes were kept.",
+        "Data provider": "Alexie Papanicolaou, Hawkesbury Institute for the Environment",
+        "Method": "reconsile_OGSs_to_master_OGS and AEGeAn parseval 64f3e0f924",
+        "Publication Status": "Published, please cite Genome Biology DOI: 10.1186/s13059-016-1049-2"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "CDS": "ogs-cds",
+          "UTR": "ogs-utr",
+          "exon": "container-100pct",
+          "five_prime_cis_splice_site": null,
+          "five_prime_utr": null,
+          "intron": null,
+          "three_prime_cis_splice_site": null,
+          "three_prime_utr": null,
+          "wholeCDS": null
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/cercap_current_models/{refseq}/trackData.json"
+    }
+  ]
+}
diff --git a/organisms/stage/stage-v2/Chelonus_insularis/trackList.json b/organisms/stage/stage-v2/Chelonus_insularis/trackList.json
new file mode 100644
index 0000000..198f56b
--- /dev/null
+++ b/organisms/stage/stage-v2/Chelonus_insularis/trackList.json
@@ -0,0 +1,564 @@
+{
+  "formatVersion": 1,
+  "names": {
+    "type": "Hash",
+    "url": "names/"
+  },
+  "tracks": [
+    {
+      "category": "Reference sequence",
+      "chunkSize": 20000,
+      "key": "Reference sequence",
+      "label": "DNA",
+      "seqType": "dna",
+      "storeClass": "JBrowse/Store/Sequence/StaticChunked",
+      "type": "SequenceTrack",
+      "urlTemplate": "seq/{refseq_dirpath}/{refseq}-"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Reference Assembly",
+      "key": "Gaps in assembly",
+      "label": "Gaps in assembly",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "white",
+        "pos_color": "black"
+      },
+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "bigwig/GCF_013357705.1_ASM1335770v1_genomic.fna.gaps.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "0.5",
+      "category": "Reference Assembly",
+      "key": "GC Content",
+      "label": "GC Content",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+      },
+      "scoreType": "avgScore",
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "rgba(255,255,0,50)",
+        "pos_color": "rgba(0,0,255,50)"
+      },
+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "bigwig/GCF_013357705.1_ASM1335770v1_genomic.fna.gc.bigwig"
+    },
+    {
+      "category": "NCBI Annotation Release 100",
+      "compress": 0,
+      "key": "NCBI_Annotation_Release_100_Gene",
+      "label": "cheins_current_models",
+      "menuTemplate": [
+        {
+          "label": "View details"
+        },
+        {
+          "action": "newWindow",
+          "iconClass": "dijitIconDatabase",
+          "label": "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
+          "title": "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
+          "url": "function(track,feature){ return 'https://i5k.nal.usda.gov/'+feature.get('name')}"
+        }
+      ],
+      "metadata": {
+        "Data description": "ftp://ftp.ncbi.nlm.nih.gov/genomes/Chelonus_insularis/README_CURRENT_RELEASE",
+        "Data provider": "NCBI",
+        "Data source": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/013/357/705/GCF_013357705.1_ASM1335770v1/GCF_013357705.1_ASM1335770v1_genomic.gff.gz",
+        "Method": "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "description": "product, note, description",
+        "subfeatureClasses": {
+          "CDS": "gnomon_CDS",
+          "UTR": "gnomon_UTR",
+          "exon": "container-100pct",
+          "wholeCDS": null
+        }
+      },
+      "trackType": "HTMLFeatures",
+      "type": "HTMLFeatures",
+      "urlTemplate": "tracks/cheins_current_models/{refseq}/trackData.json"
+    },
+    {
+      "category": "NCBI Annotation Release 100",
+      "compress": 0,
+      "key": "NCBI_Annotation_Release_100_Pseudogene",
+      "label": "NCBI_Annotation_Release_100_Pseudogene",
+      "metadata": {
+        "Data description": "ftp://ftp.ncbi.nlm.nih.gov/genomes/Chelonus_insularis/README_CURRENT_RELEASE",
+        "Data provider": "NCBI",
+        "Data source": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/013/357/705/GCF_013357705.1_ASM1335770v1/GCF_013357705.1_ASM1335770v1_genomic.gff.gz",
+        "Method": "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "description": "product, note, description",
+        "subfeatureClasses": {
+          "CDS": "gnomon_CDS",
+          "UTR": "gnomon_UTR",
+          "exon": "container-100pct",
+          "wholeCDS": null
+        }
+      },
+      "trackType": "HTMLFeatures",
+      "type": "HTMLFeatures",
+      "urlTemplate": "tracks/NCBI_Annotation_Release_100_Pseudogene/{refseq}/trackData.json"
+    },
+    {
+      "category": "RNA-Seq/Mapped Reads",
+      "key": "SRR11967921",
+      "label": "SRR11967921",
+      "metadata": {
+        "Analysis method": "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+        "Analysis provider": "i5k Workspace@NAL",
+        "Data source": "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11967921'>SRR11967921</a>",
+        "Publication status": "Analysis: NA; Source data: see individual SRA accessions",
+        "Track legend": "Dark red alignments: Mapped portion of read aligned to forward strand<br>Light red alignments: Spliced portion of read aligned to forward strand<br>Dark blue alignments: Mapped portion of read aligned to reverse strand<br>Light blue alignments: Spliced portion of read aligned to reverse strand<br>Red marking - deletion in the read relative to the reference<br>Green marking - insertion in the read relative to the reference<br>Yellow marking  - mismatch (hover over the mismatch to see what the snp is)"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "analyses/Chelonus-insularis-RNA-Seq_2020-08-02_v1.0/SRR11967921.bam"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "RNA-Seq/Coverage Plots",
+      "key": "SRR11967921_coverage",
+      "label": "SRR11967921_coverage",
+      "metadata": {
+        "Analysis method": "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+        "Analysis provider": "i5k Workspace@NAL",
+        "Data source": "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11967921'>SRR11967921</a>",
+        "Publication status": "Analysis: NA; Source data: see individual SRA accessions",
+        "Track legend": "This track represents an X-Y plot of RNA-Seq coverage."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "pos_color": "#00BFFF"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "analyses/Chelonus-insularis-RNA-Seq_2020-08-02_v1.0/SRR11967921.bigwig"
+    },
+    {
+      "category": "RNA-Seq/Splice junctions",
+      "compress": 0,
+      "key": "SRR11967921_junctions",
+      "label": "SRR11967921_junctions",
+      "metadata": {
+        "Analysis method": "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+        "Analysis provider": "i5k Workspace@NAL",
+        "Data source": "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11967921'>SRR11967921</a>",
+        "Publication status": "Analysis: NA; Source data: see individual SRA accessions",
+        "Track legend": "Junction reads generated by Hisat2 aligner and regtools"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "className": "feature"
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/SRR11967921_junctions/{refseq}/trackData.json"
+    },
+    {
+      "category": "RNA-Seq/Mapped Reads",
+      "key": "SRR11967919",
+      "label": "SRR11967919",
+      "metadata": {
+        "Analysis method": "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+        "Analysis provider": "i5k Workspace@NAL",
+        "Data source": "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11967919'>SRR11967919</a>",
+        "Publication status": "Analysis: NA; Source data: see individual SRA accessions",
+        "Track legend": "Dark red alignments: Mapped portion of read aligned to forward strand<br>Light red alignments: Spliced portion of read aligned to forward strand<br>Dark blue alignments: Mapped portion of read aligned to reverse strand<br>Light blue alignments: Spliced portion of read aligned to reverse strand<br>Red marking - deletion in the read relative to the reference<br>Green marking - insertion in the read relative to the reference<br>Yellow marking  - mismatch (hover over the mismatch to see what the snp is)"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "analyses/Chelonus-insularis-RNA-Seq_2020-08-02_v1.0/SRR11967919.bam"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "RNA-Seq/Coverage Plots",
+      "key": "SRR11967919_coverage",
+      "label": "SRR11967919_coverage",
+      "metadata": {
+        "Analysis method": "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+        "Analysis provider": "i5k Workspace@NAL",
+        "Data source": "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11967919'>SRR11967919</a>",
+        "Publication status": "Analysis: NA; Source data: see individual SRA accessions",
+        "Track legend": "This track represents an X-Y plot of RNA-Seq coverage."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "pos_color": "#00BFFF"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "analyses/Chelonus-insularis-RNA-Seq_2020-08-02_v1.0/SRR11967919.bigwig"
+    },
+    {
+      "category": "RNA-Seq/Splice junctions",
+      "compress": 0,
+      "key": "SRR11967919_junctions",
+      "label": "SRR11967919_junctions",
+      "metadata": {
+        "Analysis method": "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+        "Analysis provider": "i5k Workspace@NAL",
+        "Data source": "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11967919'>SRR11967919</a>",
+        "Publication status": "Analysis: NA; Source data: see individual SRA accessions",
+        "Track legend": "Junction reads generated by Hisat2 aligner and regtools"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "className": "feature"
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/SRR11967919_junctions/{refseq}/trackData.json"
+    },
+    {
+      "category": "RNA-Seq/Mapped Reads",
+      "key": "SRR11845184",
+      "label": "SRR11845184",
+      "metadata": {
+        "Analysis method": "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+        "Analysis provider": "i5k Workspace@NAL",
+        "Data source": "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11845184'>SRR11845184</a>",
+        "Publication status": "Analysis: NA; Source data: see individual SRA accessions",
+        "Track legend": "Dark red alignments: Mapped portion of read aligned to forward strand<br>Light red alignments: Spliced portion of read aligned to forward strand<br>Dark blue alignments: Mapped portion of read aligned to reverse strand<br>Light blue alignments: Spliced portion of read aligned to reverse strand<br>Red marking - deletion in the read relative to the reference<br>Green marking - insertion in the read relative to the reference<br>Yellow marking  - mismatch (hover over the mismatch to see what the snp is)"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "analyses/Chelonus-insularis-RNA-Seq_2020-08-02_v1.0/SRR11845184.bam"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "RNA-Seq/Coverage Plots",
+      "key": "SRR11845184_coverage",
+      "label": "SRR11845184_coverage",
+      "metadata": {
+        "Analysis method": "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+        "Analysis provider": "i5k Workspace@NAL",
+        "Data source": "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11845184'>SRR11845184</a>",
+        "Publication status": "Analysis: NA; Source data: see individual SRA accessions",
+        "Track legend": "This track represents an X-Y plot of RNA-Seq coverage."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "pos_color": "#00BFFF"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "analyses/Chelonus-insularis-RNA-Seq_2020-08-02_v1.0/SRR11845184.bigwig"
+    },
+    {
+      "category": "RNA-Seq/Splice junctions",
+      "compress": 0,
+      "key": "SRR11845184_junctions",
+      "label": "SRR11845184_junctions",
+      "metadata": {
+        "Analysis method": "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+        "Analysis provider": "i5k Workspace@NAL",
+        "Data source": "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11845184'>SRR11845184</a>",
+        "Publication status": "Analysis: NA; Source data: see individual SRA accessions",
+        "Track legend": "Junction reads generated by Hisat2 aligner and regtools"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "className": "feature"
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/SRR11845184_junctions/{refseq}/trackData.json"
+    },
+    {
+      "category": "RNA-Seq/Mapped Reads",
+      "key": "SRR11845185",
+      "label": "SRR11845185",
+      "metadata": {
+        "Analysis method": "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+        "Analysis provider": "i5k Workspace@NAL",
+        "Data source": "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11845185'>SRR11845185</a>",
+        "Publication status": "Analysis: NA; Source data: see individual SRA accessions",
+        "Track legend": "Dark red alignments: Mapped portion of read aligned to forward strand<br>Light red alignments: Spliced portion of read aligned to forward strand<br>Dark blue alignments: Mapped portion of read aligned to reverse strand<br>Light blue alignments: Spliced portion of read aligned to reverse strand<br>Red marking - deletion in the read relative to the reference<br>Green marking - insertion in the read relative to the reference<br>Yellow marking  - mismatch (hover over the mismatch to see what the snp is)"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "analyses/Chelonus-insularis-RNA-Seq_2020-08-02_v1.0/SRR11845185.bam"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "RNA-Seq/Coverage Plots",
+      "key": "SRR11845185_coverage",
+      "label": "SRR11845185_coverage",
+      "metadata": {
+        "Analysis method": "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+        "Analysis provider": "i5k Workspace@NAL",
+        "Data source": "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11845185'>SRR11845185</a>",
+        "Publication status": "Analysis: NA; Source data: see individual SRA accessions",
+        "Track legend": "This track represents an X-Y plot of RNA-Seq coverage."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "pos_color": "#00BFFF"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "analyses/Chelonus-insularis-RNA-Seq_2020-08-02_v1.0/SRR11845185.bigwig"
+    },
+    {
+      "category": "RNA-Seq/Splice junctions",
+      "compress": 0,
+      "key": "SRR11845185_junctions",
+      "label": "SRR11845185_junctions",
+      "metadata": {
+        "Analysis method": "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+        "Analysis provider": "i5k Workspace@NAL",
+        "Data source": "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11845185'>SRR11845185</a>",
+        "Publication status": "Analysis: NA; Source data: see individual SRA accessions",
+        "Track legend": "Junction reads generated by Hisat2 aligner and regtools"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "className": "feature"
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/SRR11845185_junctions/{refseq}/trackData.json"
+    },
+    {
+      "category": "RNA-Seq/Mapped Reads",
+      "key": "SRR11845186",
+      "label": "SRR11845186",
+      "metadata": {
+        "Analysis method": "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+        "Analysis provider": "i5k Workspace@NAL",
+        "Data source": "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11845186'>SRR11845186</a>",
+        "Publication status": "Analysis: NA; Source data: see individual SRA accessions",
+        "Track legend": "Dark red alignments: Mapped portion of read aligned to forward strand<br>Light red alignments: Spliced portion of read aligned to forward strand<br>Dark blue alignments: Mapped portion of read aligned to reverse strand<br>Light blue alignments: Spliced portion of read aligned to reverse strand<br>Red marking - deletion in the read relative to the reference<br>Green marking - insertion in the read relative to the reference<br>Yellow marking  - mismatch (hover over the mismatch to see what the snp is)"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "analyses/Chelonus-insularis-RNA-Seq_2020-08-02_v1.0/SRR11845186.bam"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "RNA-Seq/Coverage Plots",
+      "key": "SRR11845186_coverage",
+      "label": "SRR11845186_coverage",
+      "metadata": {
+        "Analysis method": "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+        "Analysis provider": "i5k Workspace@NAL",
+        "Data source": "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11845186'>SRR11845186</a>",
+        "Publication status": "Analysis: NA; Source data: see individual SRA accessions",
+        "Track legend": "This track represents an X-Y plot of RNA-Seq coverage."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "pos_color": "#00BFFF"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "analyses/Chelonus-insularis-RNA-Seq_2020-08-02_v1.0/SRR11845186.bigwig"
+    },
+    {
+      "category": "RNA-Seq/Splice junctions",
+      "compress": 0,
+      "key": "SRR11845186_junctions",
+      "label": "SRR11845186_junctions",
+      "metadata": {
+        "Analysis method": "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+        "Analysis provider": "i5k Workspace@NAL",
+        "Data source": "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11845186'>SRR11845186</a>",
+        "Publication status": "Analysis: NA; Source data: see individual SRA accessions",
+        "Track legend": "Junction reads generated by Hisat2 aligner and regtools"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "className": "feature"
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/SRR11845186_junctions/{refseq}/trackData.json"
+    },
+    {
+      "category": "RNA-Seq/Mapped Reads",
+      "key": "SRR11845189",
+      "label": "SRR11845189",
+      "metadata": {
+        "Analysis method": "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+        "Analysis provider": "i5k Workspace@NAL",
+        "Data source": "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11845189'>SRR11845189</a>",
+        "Publication status": "Analysis: NA; Source data: see individual SRA accessions",
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diff --git a/organisms/stage/stage-v2/Cimex_lectularius/trackList.json b/organisms/stage/stage-v2/Cimex_lectularius/trackList.json
new file mode 100644
index 0000000..4851431
--- /dev/null
+++ b/organisms/stage/stage-v2/Cimex_lectularius/trackList.json
@@ -0,0 +1,1438 @@
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+      "label": "blastx_Tardigrada",
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+      "label": "blastx_Tunicata",
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+        "Publication status": "Published, if using please cite: doi:10.1038/ncomms10165.",
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+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published, if using please cite: doi:10.1038/ncomms10165.",
+        "Track legend": "Results from EST alignments resulting from the Cufflinks software as part of the MAKER automated annotation pipeline."
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+        "Publication status": "Published, if using please cite: doi:10.1038/ncomms10165.",
+        "Track legend": "Results from Protein2genome alignments of a set of Annelida proteins as part of the MAKER automated annotation pipeline."
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+      "label": "protein2genome_Arthropoda",
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+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published, if using please cite: doi:10.1038/ncomms10165.",
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+      "label": "protein2genome_Atelocerata",
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+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published, if using please cite: doi:10.1038/ncomms10165.",
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+      "label": "protein2genome_Cephalochordata",
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+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
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+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published, if using please cite: doi:10.1038/ncomms10165.",
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+      "urlTemplate": "tracks/protein2genome_Crustacea/{refseq}/trackData.json"
+    },
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+      "key": "protein2genome_Echinodermata",
+      "label": "protein2genome_Echinodermata",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published, if using please cite: doi:10.1038/ncomms10165.",
+        "Track legend": "Results from Protein2genome alignments of a set of Echinodermata proteins as part of the MAKER automated annotation pipeline."
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+        "arrowheadClass": "webapollo-arrowhead",
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Echinodermata/{refseq}/trackData.json"
+    },
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+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+      "key": "protein2genome_Mollusca",
+      "label": "protein2genome_Mollusca",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published, if using please cite: doi:10.1038/ncomms10165.",
+        "Track legend": "Results from Protein2genome alignments of a set of Mollusca proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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+          "match_part": "protein2genome"
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+      "urlTemplate": "tracks/protein2genome_Mollusca/{refseq}/trackData.json"
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+      "key": "protein2genome_Nemata",
+      "label": "protein2genome_Nemata",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published, if using please cite: doi:10.1038/ncomms10165.",
+        "Track legend": "Results from Protein2genome alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline."
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+      "label": "protein2genome_Nematomorpha",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published, if using please cite: doi:10.1038/ncomms10165.",
+        "Track legend": "Results from Protein2genome alignments of a set of Nematomorpha proteins as part of the MAKER automated annotation pipeline."
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+        "arrowheadClass": "webapollo-arrowhead",
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+      "urlTemplate": "tracks/protein2genome_Nematomorpha/{refseq}/trackData.json"
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+      "key": "protein2genome_Onychophora",
+      "label": "protein2genome_Onychophora",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published, if using please cite: doi:10.1038/ncomms10165.",
+        "Track legend": "Results from Protein2genome alignments of a set of Onychophora proteins as part of the MAKER automated annotation pipeline."
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+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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+      "urlTemplate": "tracks/protein2genome_Onychophora/{refseq}/trackData.json"
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+      "key": "protein2genome_Parazoa",
+      "label": "protein2genome_Parazoa",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published, if using please cite: doi:10.1038/ncomms10165.",
+        "Track legend": "Results from Protein2genome alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline."
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+        "arrowheadClass": "webapollo-arrowhead",
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Parazoa/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+      "key": "protein2genome_Placozoa",
+      "label": "protein2genome_Placozoa",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published, if using please cite: doi:10.1038/ncomms10165.",
+        "Track legend": "Results from Protein2genome alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline."
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+        "arrowheadClass": "webapollo-arrowhead",
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+      "urlTemplate": "tracks/protein2genome_Placozoa/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+      "key": "protein2genome_Platyhelminthes",
+      "label": "protein2genome_Platyhelminthes",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published, if using please cite: doi:10.1038/ncomms10165.",
+        "Track legend": "Results from Protein2genome alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline."
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+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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+          "match_part": "protein2genome"
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Platyhelminthes/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Priapulida",
+      "label": "protein2genome_Priapulida",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published, if using please cite: doi:10.1038/ncomms10165.",
+        "Track legend": "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline."
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+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Priapulida/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+      "key": "protein2genome_Tardigrada",
+      "label": "protein2genome_Tardigrada",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published, if using please cite: doi:10.1038/ncomms10165.",
+        "Track legend": "Results from Protein2genome alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline."
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+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
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+        "arrowheadClass": "webapollo-arrowhead",
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+          "match_part": "protein2genome"
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Tardigrada/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+      "key": "protein2genome_Tunicata",
+      "label": "protein2genome_Tunicata",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published, if using please cite: doi:10.1038/ncomms10165.",
+        "Track legend": "Results from Protein2genome alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
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+        "arrowheadClass": "webapollo-arrowhead",
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Tunicata/{refseq}/trackData.json"
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+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+      "key": "protein2genome_UNCATEGORISED",
+      "label": "protein2genome_UNCATEGORISED",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published, if using please cite: doi:10.1038/ncomms10165.",
+        "Track legend": "Results from Protein2genome alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline."
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+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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+        "subfeatureClasses": {
+          "match_part": "protein2genome"
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+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_UNCATEGORISED/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/2. Evidence/Repeats",
+      "compress": 0,
+      "key": "repeatmasker",
+      "label": "repeatmasker",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published, if using please cite: doi:10.1038/ncomms10165.",
+        "Track legend": "Results from RepeatMasker as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
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+        "arrowheadClass": "webapollo-arrowhead",
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+        "subfeatureClasses": {
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/repeatmasker/{refseq}/trackData.json"
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+    {
+      "category": "BCM_v0.5.3/2. Evidence/Repeats",
+      "compress": 0,
+      "key": "repeatrunner",
+      "label": "repeatrunner",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published, if using please cite: doi:10.1038/ncomms10165.",
+        "Track legend": "Results from Repeatrunner as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
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+        "arrowheadClass": "webapollo-arrowhead",
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+        "subfeatureClasses": {
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/repeatrunner/{refseq}/trackData.json"
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+    {
+      "category": "BCM_v0.5.3/1. Gene Sets/Supplementary Gene Predictions",
+      "compress": 0,
+      "key": "snap_masked",
+      "label": "snap_masked",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published, if using please cite: doi:10.1038/ncomms10165.",
+        "Track legend": "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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+        "subfeatureClasses": {
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+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/snap_masked/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/1. Gene Sets/Primary Gene Sets: Protein Coding",
+      "compress": 0,
+      "key": "CLEC_v0.5.2-Models-DEPRECATED",
+      "label": "cimlec_deprecated_models",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published, if using please cite: doi:10.1038/ncomms10165.",
+        "Track legend": "Consensus gene models from the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
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+        "arrowheadClass": "trellis-arrowhead",
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/CLEC_v0.5.2-Models/{refseq}/trackData.json"
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+    {
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+      "key": "female RNA-Seq",
+      "label": "cimlec_RNA_female",
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+        "Alignment summary": "http://de.iplantcollaborative.org/dl/d/D0300D5C-7D1B-4208-890D-67C1A90B2F23/align_summary.txt",
+        "Data Provider": "Baylor College of Medicine",
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+        "Read cleaning method": "None"
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+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "bam/Clec_RNA-Adult-Female_300Bp_ICD_CLI5RP.bam"
+    },
+    {
+      "category": "Transcriptome/Mapped Reads",
+      "key": "male RNA-Seq",
+      "label": "cimlec_RNA_male",
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+        "Alignment summary": "http://de.iplantcollaborative.org/dl/d/48B9A48D-1A7D-4314-9F00-0B8FC73485DB/align_summary.txt",
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+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "bam/Clec_RNA-Adult-Male_300Bp_ICD_CLI5RP.bam"
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+    {
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+      "key": "Koganemaru et al. 2013 transcriptome assembly",
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/Transcriptome models/{refseq}/trackData.json"
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+    {
+      "category": "Transcriptome/Mapped Reads",
+      "key": "3-day-old embryo RNA-Seq, combined",
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+        "Mapping program": "Tophat v2.0.10",
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+        "Source of materials": "3 day old embryos (both male and female) from Harlan strain bed bugs",
+        "Status": "unpublished - please follow Ft. Lauderdale and Toronto agreements",
+        "Track legend": "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)"
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+      "type": "WebApollo/View/Track/DraggableAlignments",
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+    {
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+      "bicolor_pivot": "zero",
+      "category": "Transcriptome/Coverage plots (BigWig)",
+      "key": "3-day-old embryo RNA-Seq, combined-density plots",
+      "label": "Harlan_RNASeq_combined-density",
+      "metadata": {
+        "Data Source": "Zach Adelman, Brittany Delong, Dini Miller (Virginia Tech)",
+        "Mapping parameters": "tophat -a 20 -i 30 -p 8 --no-discordant --no-mixed --microexon-search",
+        "Mapping program": "Tophat v2.0.10",
+        "Sequencing platform": "Illumina Hi-Seq 200 bp PE",
+        "Sex": "Mixed",
+        "Source of materials": "3 day old embryos (both male and female) from Harlan strain bed bugs",
+        "Status": "unpublished - please follow Ft. Lauderdale and Toronto agreements",
+        "Track legend": "This track represents a density plot of RNA-Seq coverage. Darker blue represents higher coverage, and lighter blue lower coverage."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "user_files/zadel/Harlan_combined_NALmod.bam.sorted_2.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "category": "Transcriptome/Coverage plots (BigWig)",
+      "key": "3-day-old embryo RNA-Seq, combined-XYplots",
+      "label": "Harlan_RNASeq_combined-XYplots",
+      "metadata": {
+        "Data Source": "Zach Adelman, Brittany Delong, Dini Miller (Virginia Tech)",
+        "Mapping parameters": "tophat -a 20 -i 30 -p 8 --no-discordant --no-mixed --microexon-search",
+        "Mapping program": "Tophat v2.0.10",
+        "Sequencing platform": "Illumina Hi-Seq 200 bp PE",
+        "Sex": "Mixed",
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+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
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+      "urlTemplate": "bigwig/Clec_Bbug02212013.GAPS.bigwig"
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+    },
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+}
diff --git a/organisms/stage/stage-v2/Clitarchus_hookeri/trackList.json b/organisms/stage/stage-v2/Clitarchus_hookeri/trackList.json
new file mode 100644
index 0000000..dde4e31
--- /dev/null
+++ b/organisms/stage/stage-v2/Clitarchus_hookeri/trackList.json
@@ -0,0 +1,46 @@
+{
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/OvaryAndTestis_Cufflinks_Cufflinks/{refseq}/trackData.json"
+    }
+  ]
+}
diff --git a/organisms/stage/stage-v2/Contarinia_nasturtii/trackList.json b/organisms/stage/stage-v2/Contarinia_nasturtii/trackList.json
new file mode 100644
index 0000000..51d3362
--- /dev/null
+++ b/organisms/stage/stage-v2/Contarinia_nasturtii/trackList.json
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+{
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diff --git a/organisms/stage/stage-v2/Copidosoma_floridanum/trackList.json b/organisms/stage/stage-v2/Copidosoma_floridanum/trackList.json
new file mode 100644
index 0000000..a5808d2
--- /dev/null
+++ b/organisms/stage/stage-v2/Copidosoma_floridanum/trackList.json
@@ -0,0 +1,1210 @@
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+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
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+        "Track legend": "Results from Blastx alignments of a set of Echinodermata proteins as part of the MAKER automated annotation pipeline."
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+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Blastx alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline."
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+      "key": "blastx_Nematomorpha",
+      "label": "blastx_Nematomorpha",
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+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Blastx alignments of a set of Nematomorpha proteins as part of the MAKER automated annotation pipeline."
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+      "label": "blastx_Onychophora",
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+      "key": "blastx_Parazoa",
+      "label": "blastx_Parazoa",
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+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Blastx alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline."
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+      "label": "blastx_Placozoa",
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+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Blastx alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline."
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+      "key": "blastx_Platyhelminthes",
+      "label": "blastx_Platyhelminthes",
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+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Blastx alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline."
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+    },
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+      "key": "blastx_Priapulida",
+      "label": "blastx_Priapulida",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
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+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Blastx alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline."
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+        "arrowheadClass": "webapollo-arrowhead",
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+      "key": "blastx_Tardigrada",
+      "label": "blastx_Tardigrada",
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+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Blastx alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline."
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+        "arrowheadClass": "webapollo-arrowhead",
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+      "label": "blastx_Tunicata",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
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+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Blastx alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline."
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+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
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+      "key": "cegma",
+      "label": "cegma",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
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+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from CEGMA alignments as part of the MAKER automated annotation pipeline."
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+      "key": "est_gff:cufflinks_i5k",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
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+      "label": "protein2genome_Annelida",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Annelida proteins as part of the MAKER automated annotation pipeline."
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+        "arrowheadClass": "webapollo-arrowhead",
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+      "key": "protein2genome_Arthropoda",
+      "label": "protein2genome_Arthropoda",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Arthropoda proteins as part of the MAKER automated annotation pipeline."
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+        "arrowheadClass": "webapollo-arrowhead",
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+      "key": "protein2genome_Atelocerata",
+      "label": "protein2genome_Atelocerata",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Atelocerata proteins as part of the MAKER automated annotation pipeline."
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+    {
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+      "key": "protein2genome_Cephalochordata",
+      "label": "protein2genome_Cephalochordata",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
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+      "label": "protein2genome_Mollusca",
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+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
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+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
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+      "urlTemplate": "tracks/protein2genome_Nematomorpha/{refseq}/trackData.json"
+    },
+    {
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+      "label": "protein2genome_Onychophora",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
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+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
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+        "arrowheadClass": "webapollo-arrowhead",
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+      "key": "protein2genome_Parazoa",
+      "label": "protein2genome_Parazoa",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
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+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
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+        "arrowheadClass": "webapollo-arrowhead",
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+          "match_part": "protein2genome"
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+      "urlTemplate": "tracks/protein2genome_Parazoa/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+      "key": "protein2genome_Placozoa",
+      "label": "protein2genome_Placozoa",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
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+        "arrowheadClass": "webapollo-arrowhead",
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Placozoa/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+      "key": "protein2genome_Platyhelminthes",
+      "label": "protein2genome_Platyhelminthes",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline."
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+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
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+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
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+      "urlTemplate": "tracks/protein2genome_Platyhelminthes/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+      "key": "protein2genome_Priapulida",
+      "label": "protein2genome_Priapulida",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline."
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+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Priapulida/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+      "key": "protein2genome_Tardigrada",
+      "label": "protein2genome_Tardigrada",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline."
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+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Tardigrada/{refseq}/trackData.json"
+    },
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+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+      "key": "protein2genome_Tunicata",
+      "label": "protein2genome_Tunicata",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline."
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+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
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+        "Track legend": "Results from Protein2genome alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline."
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+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
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+        "arrowheadClass": "webapollo-arrowhead",
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+      "key": "repeatmasker",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from RepeatMasker as part of the MAKER automated annotation pipeline."
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+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "repeat"
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+      "urlTemplate": "tracks/repeatmasker/{refseq}/trackData.json"
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+    {
+      "category": "BCM_v0.5.3/2. Evidence/Repeats",
+      "compress": 0,
+      "key": "repeatrunner",
+      "label": "repeatrunner",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Repeatrunner as part of the MAKER automated annotation pipeline."
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+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
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+        "arrowheadClass": "webapollo-arrowhead",
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/repeatrunner/{refseq}/trackData.json"
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+      "key": "snap_masked",
+      "label": "snap_masked",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
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+      },
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/snap_masked/{refseq}/trackData.json"
+    },
+    {
+      "autoscale": "local",
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+      "label": "Gaps in assembly",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "white",
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+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "bigwig/Cflo.scaffolds.fa.gaps.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "0.5",
+      "category": "Reference Assembly",
+      "key": "GC Content",
+      "label": "GC Content",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+      },
+      "scoreType": "avgScore",
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "rgba(255,255,0,50)",
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+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "bigwig/Cflo.scaffolds.fa.gc.bigwig"
+    }
+  ]
+}
diff --git a/organisms/stage/stage-v2/Culex_quinquefasciatus/trackList.json b/organisms/stage/stage-v2/Culex_quinquefasciatus/trackList.json
new file mode 100644
index 0000000..b9308b5
--- /dev/null
+++ b/organisms/stage/stage-v2/Culex_quinquefasciatus/trackList.json
@@ -0,0 +1,149 @@
+{
+   "formatVersion" : 1,
+   "names" : {
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+      "url" : "names/"
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+         "type" : "SequenceTrack",
+         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-"
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+      {
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+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+	    "Track legend":"This track represents an X-Y plot of RNA-Seq coverage."
+         },
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+         },
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+      }
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+}
diff --git a/organisms/stage/stage-v2/Diabrotica_virgifera_training/trackList.json b/organisms/stage/stage-v2/Diabrotica_virgifera_training/trackList.json
new file mode 100644
index 0000000..16e4899
--- /dev/null
+++ b/organisms/stage/stage-v2/Diabrotica_virgifera_training/trackList.json
@@ -0,0 +1,224 @@
+{
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diff --git a/organisms/stage/stage-v2/Diachasma_alloeum/trackList.json b/organisms/stage/stage-v2/Diachasma_alloeum/trackList.json
new file mode 100644
index 0000000..3a78aa4
--- /dev/null
+++ b/organisms/stage/stage-v2/Diachasma_alloeum/trackList.json
@@ -0,0 +1,124 @@
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diff --git a/organisms/stage/stage-v2/Diaphorina_citri/trackList.json b/organisms/stage/stage-v2/Diaphorina_citri/trackList.json
new file mode 100644
index 0000000..e3bd600
--- /dev/null
+++ b/organisms/stage/stage-v2/Diaphorina_citri/trackList.json
@@ -0,0 +1,956 @@
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+        "Legend": "Mapped reads are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)",
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+        "Other notes": "Parameters used for alignment: –min-intron-length 4 --max-intron-length 136000",
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+        "Data source URL": "http://www.ncbi.nlm.nih.gov/sra/SRR1259429",
+        "Date completed": "12/08/15",
+        "Description": "2x54bp paired-end RNAseq reads were mapped to NCBI-diaci1.1 genome from the control adult and nymph psyllids. See Vyas 2015",
+        "File provider (name and affiliation)": "Prashant Hosmani and Surya Saha, Boyce Thompson Institute",
+        "Geographical location of specimen collection (Country, Site, Latitude, Longitude)": "US, Florida",
+        "Legend": "Mapped reads are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)",
+        "NCBI SRA accession #": "SRR1259429, SRR1259461",
+        "Other notes": "Parameters used for alignment: –min-intron-length 4 --max-intron-length 136000",
+        "Publication status": "Published: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0130328",
+        "Sequencing platform and version (Illumina Hi-Seq 200 bp)": "Illumina GA II paired end",
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+      "label": "RNAseq reads from egg tissue",
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+        "Data source URL": "http://www.ncbi.nlm.nih.gov/sra/SRX199348[accn]",
+        "Date completed": "12/16/15",
+        "Description": "RNAseq reads from egg tissue were mapped to maker predicted genes on NCBI-diaci1.1",
+        "File provider (name and affiliation)": "Surya Saha, Boyce Thompson Institute",
+        "Geographical location of specimen collection (Country, Site, Latitude, Longitude)": "US, Florida",
+        "Legend": "Mapped reads are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)",
+        "NCBI SRA accession #": "SRX199348",
+        "Other notes": "Parameters used for alignment: –min-intron-length 4 --max-intron-length 136000",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Sequencing platform and version (Illumina Hi-Seq 200 bp)": "Illumina Hiseq paired end",
+        "TaxID": "121845"
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+      "urlTemplate": "user_contributed_data/ssaha/12-15-2015/rnaseq_egg.bam"
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+      "category": "Transcriptome/Coverage Plots (BigWig)",
+      "key": "RNAseq reads from nymph tissue (Coverage Plot)",
+      "label": "RNAseq reads from nymph tissue (Coverage Plot)",
+      "metadata": {
+        "Analysis method (program and version)": "Tophat2 v2.1.0 and bedtools v2.16.1",
+        "Data source URL": "http://www.ncbi.nlm.nih.gov/sra/SRX199348[accn]",
+        "Date completed": "12/17/15",
+        "Description": "Summary plot for RNAseq reads from nymph tissue mapped to NCBI-diaci1.1",
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+        "Legend": "This track represents an X-Y plot of RNA-Seq coverage.",
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+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
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+      "urlTemplate": "user_contributed_data/ssaha/12-15-2015/rnaseq_nymph.bw"
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+      "category": "Transcriptome/Coverage Plots (BigWig)",
+      "key": "RNAseq reads from egg tissue (Coverage Plot)",
+      "label": "RNAseq reads from egg tissue (Coverage Plot)",
+      "metadata": {
+        "Analysis method (program and version)": "Tophat2 v2.1.0 and bedtools v2.16.1",
+        "Data source URL": "http://www.ncbi.nlm.nih.gov/sra/SRX199348[accn]",
+        "Date completed": "12/17/15",
+        "Description": "Summary plot for RNAseq reads from egg tissue mapped to NCBI-diaci1.1",
+        "File provider (name and affiliation)": "Prashant Hosmani and Surya Saha, Boyce Thompson Institute",
+        "Geographical location of specimen collection (Country, Site, Latitude, Longitude)": "US, Florida",
+        "Legend": "This track represents an X-Y plot of RNA-Seq coverage.",
+        "NCBI SRA accession #": "SRX199348",
+        "Other notes": "Parameters used for tophat alignment: –min-intron-length 4 --max-intron-length 136000. bedtools used to create bigwig file from tophat BAM file. bedtools genomecov -split -ibam accepted_hits.bam -bga > accepted_hits.coverage.bedgraph. bedGraphToBigWig accepted_hits.sorted.coverage.bedgraph diaci1.chrom.sizes accepted_hits.bw",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Sequencing platform and version (Illumina Hi-Seq 200 bp)": "Illumina Hiseq paired end",
+        "TaxID": "121845"
+      },
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+      "urlTemplate": "user_contributed_data/ssaha/12-15-2015/rnaseq_egg.bw"
+    },
+    {
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+      "category": "Transcriptome/Coverage Plots (BigWig)",
+      "key": "Control adult and nymph psyllids (Vyas 2015; Coverage Plot)",
+      "label": "Control adult and nymph psyllids (Vyas 2015; Coverage Plot)",
+      "metadata": {
+        "Analysis method (program and version)": "Tophat2 v2.1.0 and bedtools v2.16.1",
+        "Data source URL": "http://www.ncbi.nlm.nih.gov/sra/SRR1259429",
+        "Date completed": "12/17/15",
+        "Description": "Summary plot for 2x54bp paired-end RNAseq reads mapped to NCBI-diaci1.1 genome from the control adult and nymph psyllid samples. See Vyas 2015 for more details.",
+        "File provider (name and affiliation)": "Prashant Hosmani and Surya Saha, Boyce Thompson Institute",
+        "Geographical location of specimen collection (Country, Site, Latitude, Longitude)": "US, Florida",
+        "Legend": "This track represents an X-Y plot of RNA-Seq coverage.",
+        "NCBI SRA accession #": "SRR1259429, SRR1259461",
+        "Other notes": "Parameters used for tophat alignment: –min-intron-length 4 --max-intron-length 136000. bedtools used to create bigwig file from tophat BAM file. bedtools genomecov -split -ibam accepted_hits.bam -bga > accepted_hits.coverage.bedgraph. bedGraphToBigWig accepted_hits.sorted.coverage.bedgraph diaci1.chrom.sizes accepted_hits.bw",
+        "Publication status": "Published: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0130328",
+        "Sequencing platform and version (Illumina Hi-Seq 200 bp)": "Illumina GA II paired end",
+        "TaxID": "121845"
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+      "urlTemplate": "user_contributed_data/ssaha/12-15-2015/AdultNymph_uninfected.bw"
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+      "category": "Transcriptome/Coverage Plots (BigWig)",
+      "key": "RNAseq reads from adult tissue (Coverage Plot)",
+      "label": "RNAseq reads from adult tissue (Coverage Plot)",
+      "metadata": {
+        "Analysis method (program and version)": "Tophat2 v2.1.0 and bedtools v2.16.1",
+        "Data source URL": "http://www.ncbi.nlm.nih.gov/sra/SRX199348[accn]",
+        "Date completed": "12/17/15",
+        "Description": "Summary plot for RNAseq reads from adult tissue mapped to NCBI-diaci1.1",
+        "File provider (name and affiliation)": "Prashant Hosmani and Surya Saha, Boyce Thompson Institute",
+        "Geographical location of specimen collection (Country, Site, Latitude, Longitude)": "US, Florida",
+        "Legend": "This track represents an X-Y plot of RNA-Seq coverage.",
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+        "Other notes": "Parameters used for tophat alignment: –min-intron-length 4 --max-intron-length 136000. bedtools used to create bigwig file from tophat BAM file. bedtools genomecov -split -ibam accepted_hits.bam -bga > accepted_hits.coverage.bedgraph. bedGraphToBigWig accepted_hits.sorted.coverage.bedgraph diaci1.chrom.sizes accepted_hits.bw",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Sequencing platform and version (Illumina Hi-Seq 200 bp)": "Illumina Hiseq paired end",
+        "TaxID": "121845"
+      },
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+      "urlTemplate": "user_contributed_data/ssaha/12-15-2015/rnaseq_adult.bw"
+    },
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+      "autoscale": "local",
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+      "category": "Transcriptome/Coverage Plots (BigWig)",
+      "key": "Infected adult and nymph psyllids (Vyas 2015; Coverage Plot)",
+      "label": "Infected adult and nymph psyllids (Vyas 2015; Coverage Plot)",
+      "metadata": {
+        "Analysis method (program and version)": "Tophat2 v2.1.0 and bedtools v2.16.1",
+        "Data source URL": "http://www.ncbi.nlm.nih.gov/sra/SRR1259432",
+        "Date completed": "12/17/15",
+        "Description": "Summary plot for 2x54bp paired-end RNAseq reads mapped to NCBI-diaci1.1 genome from the experimental adult and nymph psyllid samples. See Vyas 2015 for more details.",
+        "File provider (name and affiliation)": "Prashant Hosmani and Surya Saha, Boyce Thompson Institute",
+        "Geographical location of specimen collection (Country, Site, Latitude, Longitude)": "US, Florida",
+        "Legend": "This track represents an X-Y plot of RNA-Seq coverage.",
+        "NCBI SRA accession #": "SRR1259432, SRR1259434",
+        "Other notes": "Parameters used for tophat alignment: –min-intron-length 4 --max-intron-length 136000. bedtools used to create bigwig file from tophat BAM file. bedtools genomecov -split -ibam accepted_hits.bam -bga > accepted_hits.coverage.bedgraph. bedGraphToBigWig accepted_hits.sorted.coverage.bedgraph diaci1.chrom.sizes accepted_hits.bw",
+        "Publication status": "Published: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0130328",
+        "Sequencing platform and version (Illumina Hi-Seq 200 bp)": "Illumina GA II paired end",
+        "TaxID": "121845"
+      },
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+      "urlTemplate": "user_contributed_data/ssaha/12-15-2015/AdultNymph_Clas_infected.bw"
+    },
+    {
+      "category": "DNAseq/Mapped Reads",
+      "key": "Alignment plot for DNAseq paired-end reads",
+      "label": "Alignment plot for DNAseq paired-end reads",
+      "metadata": {
+        "Analysis method (program and version)": "Bowtie v2-2.2.6 and samtools",
+        "Assembly name": "NCBI-diaci",
+        "Assembly version": "1.1",
+        "Data source URL": "http://www.ncbi.nlm.nih.gov/sra/SRX057205[accn]",
+        "Date completed": "03/30/16",
+        "Descriptive track name": "Alignment plot for DNAseq paired-end reads mapped to NCBI-diaci1.1",
+        "File provider (name and affiliation)": "Surya Saha, Boyce Thompson Institute",
+        "File type (e.g. bam, bigwig, gff3)": "BAM",
+        "Geographical location of specimen collection": "US, Florida",
+        "Legend": "Mapped reads are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)",
+        "NCBI SRA accession #": "SRX057205",
+        "Organism common name": "Asian citrus psyllid",
+        "Organism scientific name": "Diaphorina citri",
+        "Other notes": "Parameters used for bowtie alignment: --very-fast-local --threads 30 --mm -x ncbi-diaci1.1 --rf --maxins 11000",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Sequencing platform and version": "Illumina Hiseq paired end",
+        "TaxID": "121845"
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+      "key": "Summary plot for DNAseq paired-end reads",
+      "label": "Summary plot for DNAseq paired-end reads",
+      "metadata": {
+        "Analysis method (program and version)": "Bowtie v2-2.2.6 and bedtools v2.16.1",
+        "Assembly name": "NCBI-diacil",
+        "Assembly version": "1.1",
+        "Data source URL": "http://www.ncbi.nlm.nih.gov/sra/SRX057205[accn]",
+        "Date completed": "03/30/16",
+        "Descriptive track name": "Summary plot for DNAseq paired-end reads mapped to NCBI-diaci1.1",
+        "File provider (name and affiliation)": "Prashant Hosmani and Surya Saha, Boyce Thompson Institute",
+        "Geographical location of specimen collection (Country, Site, Latitude, Longitude)": "US, Florida",
+        "Legend": "This track represents an X-Y plot of RNA-Seq coverage.",
+        "NCBI SRA accession #": "SRX057205",
+        "Organism common name": "Asian citrus psyllid",
+        "Organism scientific name": "Diaphorina citri",
+        "Other notes": "Parameters used for bowtie alignment: --very-fast-local --threads 30 --mm -x ncbi-diaci1.1 --rf --maxins 11000. bedtools used to create bigwig file from bowtie BAM file. bedtools genomecov -split -ibam all_PE.bam -bga > all_PE.coverage.bedgraph. bedGraphToBigWig all_PE.sorted.coverage.bedgraph diaci1.chrom.sizes all_PE.bw",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Sequencing platform and version (Illumina Hi-Seq 200 bp)": "Illumina Hiseq paired end",
+        "TaxID": "121845"
+      },
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+      "urlTemplate": "user_contributed_data/ssaha/04-11-2016/all_PE.bam.bedgraph.sorted.bw"
+    }
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+}
diff --git a/organisms/stage/stage-v2/Diaphorina_citri_legacy/trackList.json b/organisms/stage/stage-v2/Diaphorina_citri_legacy/trackList.json
new file mode 100644
index 0000000..39aaf53
--- /dev/null
+++ b/organisms/stage/stage-v2/Diaphorina_citri_legacy/trackList.json
@@ -0,0 +1,280 @@
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+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome/{refseq}/trackData.json"
+    },
+    {
+      "category": "DIACIT_v1/2. Evidence/Repeats",
+      "compress": 0,
+      "key": "repeatmasker",
+      "label": "repeatmasker",
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+    },
+    {
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+      "key": "repeatrunner",
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+    },
+    {
+      "category": "DIACIT_v1/1. Gene Sets/Supplementary Gene Predictions",
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+      "key": "snap_masked",
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+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Reference Assembly",
+      "key": "Gaps in assembly",
+      "label": "Gaps in assembly",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "white",
+        "pos_color": "black"
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+      "urlTemplate": "bigwig/diaci1.1_annotated_contigs.GAPS.bigwig"
+    },
+    {
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+      "bicolor_pivot": "0.5",
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+      "key": "GC Content",
+      "label": "GC Content",
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+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+      },
+      "scoreType": "avgScore",
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "rgba(255,255,0,50)",
+        "pos_color": "rgba(0,0,255,50)"
+      },
+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "bigwig/diaci1.1_annotated_contigs_GC.bigwig"
+    }
+  ]
+}
diff --git a/organisms/stage/stage-v2/Drosophila_biarmipes/trackList.json b/organisms/stage/stage-v2/Drosophila_biarmipes/trackList.json
new file mode 100644
index 0000000..e34ad5d
--- /dev/null
+++ b/organisms/stage/stage-v2/Drosophila_biarmipes/trackList.json
@@ -0,0 +1,188 @@
+{
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+  "names": {
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+    "url": "names/"
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+        "Note": "Some genes may have non-coding transcripts"
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+      "urlTemplate": "tracks/drobia_current_models/{refseq}/trackData.json"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
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+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+      },
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+        "neg_color": "white",
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+      "urlTemplate": "bigwig/GCF_000233415.1_Dbia_2.0_genomic.fna.gaps.bigwig"
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+    {
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+      "label": "GC Content",
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+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
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+        "Method": "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
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+        "arrowheadClass": "webapollo-arrowhead",
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+    },
+    {
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+      "key": "NCBI Predicted lncRNA, Annotation Release 101",
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+        "Method": "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
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+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/NCBI_Annotation_Release_101_lncRNA/{refseq}/trackData.json"
+    },
+    {
+      "category": "NCBI Annotation Release 101/1. Gene Sets/Pseudogenes",
+      "compress": 0,
+      "key": "NCBI Predicted pseudogenes, Annotation Release 101",
+      "label": "NCBI_Annotation_Release_101_Pseudogene",
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+        "Data description": "ftp://ftp.ncbi.nlm.nih.gov/genomes/Drosophila_biarmipes/README_CURRENT_RELEASE",
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+        "Method": "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/NCBI_Annotation_Release_101_Pseudogene/{refseq}/trackData.json"
+    },
+    {
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+      "compress": 0,
+      "key": "NCBI Predicted tRNAs, Annotation Release 101",
+      "label": "NCBI_Annotation_Release_101_tRNA",
+      "metadata": {
+        "Data description": "ftp://ftp.ncbi.nlm.nih.gov/genomes/Drosophila_biarmipes/README_CURRENT_RELEASE",
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+        "Method": "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
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+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "description": "product, note, description",
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+          "exon": "container-100pct",
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+      },
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/NCBI_Annotation_Release_101_tRNA/{refseq}/trackData.json"
+    }
+  ]
+}
diff --git a/organisms/stage/stage-v2/Drosophila_bipectinata/trackList.json b/organisms/stage/stage-v2/Drosophila_bipectinata/trackList.json
new file mode 100644
index 0000000..bf33697
--- /dev/null
+++ b/organisms/stage/stage-v2/Drosophila_bipectinata/trackList.json
@@ -0,0 +1,164 @@
+{
+   "formatVersion" : 1,
+   "names" : {
+      "type" : "Hash",
+      "url" : "names/"
+   },
+   "tracks" : [
+      {
+         "category" : "Reference sequence",
+         "chunkSize" : 20000,
+         "key" : "Reference sequence",
+         "label" : "DNA",
+         "seqType" : "dna",
+         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
+         "type" : "SequenceTrack",
+         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-"
+      },
+      {
+         "category" : "NCBI Annotation Release 102",
+         "compress" : 0,
+         "key" : "NCBI_Annotation_Release_102_Gene",
+         "label" : "drobip_current_models",
+         "menuTemplate" : [
+            {
+               "label" : "View details"
+            },
+            {
+               "action" : "newWindow",
+               "iconClass" : "dijitIconDatabase",
+               "label" : "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
+               "title" : "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
+               "url" : "function(track,feature){ return 'https://i5k.nal.usda.gov/'+feature.get('name')}"
+            }
+         ],
+         "metadata" : {
+            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Drosophila_bipectinata/README_CURRENT_RELEASE",
+            "Data provider" : "NCBI",
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+            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
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+               "exon" : "container-100pct",
+               "wholeCDS" : null
+            }
+         },
+         "trackType" : "HTMLFeatures",
+         "type" : "HTMLFeatures",
+         "urlTemplate" : "tracks/drobip_current_models/{refseq}/trackData.json"
+      },
+      {
+         "category" : "NCBI Annotation Release 102",
+         "compress" : 0,
+         "key" : "NCBI_Annotation_Release_102_Pseudogene",
+         "label" : "NCBI_Annotation_Release_102_Pseudogene",
+         "metadata" : {
+            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Drosophila_bipectinata/README_CURRENT_RELEASE",
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+            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "container-16px",
+            "description" : "product, note, description",
+            "subfeatureClasses" : {
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+               "UTR" : "gnomon_UTR",
+               "exon" : "container-100pct",
+               "wholeCDS" : null
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+         },
+         "trackType" : "HTMLFeatures",
+         "type" : "HTMLFeatures",
+         "urlTemplate" : "tracks/NCBI_Annotation_Release_102_Pseudogene/{refseq}/trackData.json"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "0.5",
+         "category" : "Reference Assembly",
+         "key" : "GC Content",
+         "label" : "GC Content",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+         },
+         "scoreType" : "avgScore",
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "rgba(255,255,0,50)",
+            "pos_color" : "rgba(0,0,255,50)"
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+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/GCF_018153845.1_ASM1815384v1_genomic.fna.gc.bigwig"
+      },
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+         "category" : "RNA-Seq/Mapped Reads",
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+         "label" : "Drobip_ASM1815384v1_RNA-Seq-alignments_2021-10-12",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346722'>SRR346722</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346721'>SRR346721</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346723'>SRR346723</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR15048520'>SRR15048520</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR6161778'>SRR6161778</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Dark red alignments: Mapped portion of read aligned to forward strand<br>Light red alignments: Spliced portion of read aligned to forward strand<br>Dark blue alignments: Mapped portion of read aligned to reverse strand<br>Light blue alignments: Spliced portion of read aligned to reverse strand<br>Red marking - deletion in the read relative to the reference<br>Green marking - insertion in the read relative to the reference<br>Yellow marking  - mismatch (hover over the mismatch to see what the snp is)"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+	"unsafePopup":true,
+         "urlTemplate" : "analyses/Drosophila-bipectinata-RNA-Seq_2021-10-12_v1.0/Drobip_ASM1815384v1_RNA-Seq-alignments_2021-10-12.bam"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "RNA-Seq/Coverage Plots",
+         "key" : "Drobip_ASM1815384v1_RNA-Seq-alignments_2021-10-12_coverage",
+         "label" : "Drobip_ASM1815384v1_RNA-Seq-alignments_2021-10-12_coverage",
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346722'>SRR346722</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346721'>SRR346721</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346723'>SRR346723</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR15048520'>SRR15048520</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR6161778'>SRR6161778</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage."
+         },
+         "style" : {
+            "pos_color" : "#00BFFF"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+	"unsafePopup":true,
+         "urlTemplate" : "analyses/Drosophila-bipectinata-RNA-Seq_2021-10-12_v1.0/Drobip_ASM1815384v1_RNA-Seq-alignments_2021-10-12.bigwig"
+      },
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+         "category" : "RNA-Seq/Splice junctions",
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+         "key" : "Drobip_ASM1815384v1_RNA-Seq-alignments_2021-10-12_junctions",
+         "label" : "Drobip_ASM1815384v1_RNA-Seq-alignments_2021-10-12_junctions",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346722'>SRR346722</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346721'>SRR346721</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346723'>SRR346723</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR15048520'>SRR15048520</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR6161778'>SRR6161778</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Junction reads generated by Hisat2 aligner and regtools. The number of alignments supporting the junction read is listed in blue."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+	     "description":"score",
+            "className" : "feature"
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+	"unsafePopup":true,
+         "urlTemplate" : "tracks/Drobip_ASM1815384v1_RNA-Seq-alignments_2021-10-12_junctions/{refseq}/trackData.json"
+      }
+   ]
+}
diff --git a/organisms/stage/stage-v2/Drosophila_elegans/trackList.json b/organisms/stage/stage-v2/Drosophila_elegans/trackList.json
new file mode 100644
index 0000000..b675904
--- /dev/null
+++ b/organisms/stage/stage-v2/Drosophila_elegans/trackList.json
@@ -0,0 +1,171 @@
+{
+   "formatVersion" : 1,
+   "names" : {
+      "type" : "Hash",
+      "url" : "names/"
+   },
+   "tracks" : [
+      {
+         "category" : "Reference sequence",
+         "chunkSize" : 20000,
+         "key" : "Reference sequence",
+         "label" : "DNA",
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+         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
+         "type" : "SequenceTrack",
+         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-"
+      },
+      {
+         "category" : "NCBI Annotation Release 102",
+         "compress" : 0,
+         "key" : "NCBI_Annotation_Release_102_Gene",
+         "label" : "droele_current_models",
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+            {
+               "label" : "View details"
+            },
+            {
+               "action" : "newWindow",
+               "iconClass" : "dijitIconDatabase",
+               "label" : "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
+               "title" : "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
+               "url" : "function(track,feature){ return 'https://i5k.nal.usda.gov/'+feature.get('name')}"
+            }
+         ],
+         "metadata" : {
+            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Drosophila_elegans/README_CURRENT_RELEASE",
+            "Data provider" : "NCBI",
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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+               "exon" : "container-100pct",
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+         },
+         "trackType" : "HTMLFeatures",
+         "type" : "HTMLFeatures",
+         "urlTemplate" : "tracks/droele_current_models/{refseq}/trackData.json"
+      },
+      {
+         "category" : "NCBI Annotation Release 102",
+         "compress" : 0,
+         "key" : "NCBI_Annotation_Release_102_Pseudogene",
+         "label" : "NCBI_Annotation_Release_102_Pseudogene",
+         "metadata" : {
+            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Drosophila_elegans/README_CURRENT_RELEASE",
+            "Data provider" : "NCBI",
+            "Data source" : "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/018/152/505/GCF_018152505.1_ASM1815250v1/GCF_018152505.1_ASM1815250v1_genomic.gff.gz",
+            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "container-16px",
+            "description" : "product, note, description",
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+               "exon" : "container-100pct",
+               "wholeCDS" : null
+            }
+         },
+         "trackType" : "HTMLFeatures",
+         "type" : "HTMLFeatures",
+         "urlTemplate" : "tracks/NCBI_Annotation_Release_102_Pseudogene/{refseq}/trackData.json"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "0.5",
+         "category" : "Reference Assembly",
+         "key" : "GC Content",
+         "label" : "GC Content",
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+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
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+         },
+         "scoreType" : "avgScore",
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "rgba(255,255,0,50)",
+            "pos_color" : "rgba(0,0,255,50)"
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+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/GCF_018152505.1_ASM1815250v1_genomic.fna.gc.bigwig"
+      },
+      {
+         "category" : "RNA-Seq/Mapped Reads",
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+         "label" : "Droele_ASM1815250v1_RNA-Seq-alignments_2021-09-28",
+         "metadata" : {
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+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Dark red alignments: Mapped portion of read aligned to forward strand<br>Light red alignments: Spliced portion of read aligned to forward strand<br>Dark blue alignments: Mapped portion of read aligned to reverse strand<br>Light blue alignments: Spliced portion of read aligned to reverse strand<br>Red marking - deletion in the read relative to the reference<br>Green marking - insertion in the read relative to the reference<br>Yellow marking  - mismatch (hover over the mismatch to see what the snp is)"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "analyses/Drosophila-elegans-RNA-Seq_2021-09-28_v1.0/Droele_ASM1815250v1_RNA-Seq-alignments_2021-09-28.bam"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "RNA-Seq/Coverage Plots",
+         "key" : "Droele_ASM1815250v1_RNA-Seq-alignments_2021-09-28_coverage",
+         "label" : "Droele_ASM1815250v1_RNA-Seq-alignments_2021-09-28_coverage",
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346725'>SRR346725</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346724'>SRR346724</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346726'>SRR346726</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage."
+         },
+         "style" : {
+            "pos_color" : "#00BFFF"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "analyses/Drosophila-elegans-RNA-Seq_2021-09-28_v1.0/Droele_ASM1815250v1_RNA-Seq-alignments_2021-09-28.bigwig"
+      },
+      {
+         "category" : "RNA-Seq/Splice junctions",
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+         "key" : "Droele_ASM1815250v1_RNA-Seq-alignments_2021-09-28_junctions",
+         "label" : "Droele_ASM1815250v1_RNA-Seq-alignments_2021-09-28_junctions",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346725'>SRR346725</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346724'>SRR346724</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346726'>SRR346726</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Junction reads generated by Hisat2 aligner and regtools. The number of alignments supporting the junction read is listed in blue."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+	     "description" : "score",
+            "className" : "feature",
+    "subfeatureClasses": {
+      "UTR": "webapollo-UTR",
+      "CDS": "junction-cds",
+      "exon": "container-100pct",
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+      "start_codon": null,
+      "stop_codon": null,
+      "match_part": "darkblue-80pct"
+    }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/Droele_ASM1815250v1_RNA-Seq-alignments_2021-09-28_junctions/{refseq}/trackData.json"
+      }
+   ]
+}
diff --git a/organisms/stage/stage-v2/Drosophila_eugracilis/trackList.json b/organisms/stage/stage-v2/Drosophila_eugracilis/trackList.json
new file mode 100644
index 0000000..4e3c297
--- /dev/null
+++ b/organisms/stage/stage-v2/Drosophila_eugracilis/trackList.json
@@ -0,0 +1,171 @@
+{
+   "formatVersion" : 1,
+   "names" : {
+      "type" : "Hash",
+      "url" : "names/"
+   },
+   "tracks" : [
+      {
+         "category" : "Reference sequence",
+         "chunkSize" : 20000,
+         "key" : "Reference sequence",
+         "label" : "DNA",
+         "seqType" : "dna",
+         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
+         "type" : "SequenceTrack",
+         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-"
+      },
+      {
+         "category" : "NCBI Annotation Release 102",
+         "compress" : 0,
+         "key" : "NCBI_Annotation_Release_102_Gene",
+         "label" : "droeug_current_models",
+         "menuTemplate" : [
+            {
+               "label" : "View details"
+            },
+            {
+               "action" : "newWindow",
+               "iconClass" : "dijitIconDatabase",
+               "label" : "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
+               "title" : "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
+               "url" : "function(track,feature){ return 'https://i5k.nal.usda.gov/'+feature.get('name')}"
+            }
+         ],
+         "metadata" : {
+            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Drosophila_eugracilis/README_CURRENT_RELEASE",
+            "Data provider" : "NCBI",
+            "Data source" : "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/018/153/835/GCF_018153835.1_ASM1815383v1/GCF_018153835.1_ASM1815383v1_genomic.gff.gz",
+            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "container-16px",
+            "description" : "product, note, description",
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+               "UTR" : "gnomon_UTR",
+               "exon" : "container-100pct",
+               "wholeCDS" : null
+            }
+         },
+         "trackType" : "HTMLFeatures",
+         "type" : "HTMLFeatures",
+         "urlTemplate" : "tracks/droeug_current_models/{refseq}/trackData.json"
+      },
+      {
+         "category" : "NCBI Annotation Release 102",
+         "compress" : 0,
+         "key" : "NCBI_Annotation_Release_102_Pseudogene",
+         "label" : "NCBI_Annotation_Release_102_Pseudogene",
+         "metadata" : {
+            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Drosophila_eugracilis/README_CURRENT_RELEASE",
+            "Data provider" : "NCBI",
+            "Data source" : "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/018/153/835/GCF_018153835.1_ASM1815383v1/GCF_018153835.1_ASM1815383v1_genomic.gff.gz",
+            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "container-16px",
+            "description" : "product, note, description",
+            "subfeatureClasses" : {
+               "CDS" : "gnomon_CDS",
+               "UTR" : "gnomon_UTR",
+               "exon" : "container-100pct",
+               "wholeCDS" : null
+            }
+         },
+         "trackType" : "HTMLFeatures",
+         "type" : "HTMLFeatures",
+         "urlTemplate" : "tracks/NCBI_Annotation_Release_102_Pseudogene/{refseq}/trackData.json"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "0.5",
+         "category" : "Reference Assembly",
+         "key" : "GC Content",
+         "label" : "GC Content",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+         },
+         "scoreType" : "avgScore",
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "rgba(255,255,0,50)",
+            "pos_color" : "rgba(0,0,255,50)"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/GCF_018153835.1_ASM1815383v1_genomic.fna.gc.bigwig"
+      },
+      {
+         "category" : "RNA-Seq/Mapped Reads",
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+         "label" : "Droeug_ASM1815383v1_RNA-Seq-alignments_2021-08-20",
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+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
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+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346729'>SRR346729</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346727'>SRR346727</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346728'>SRR346728</a>",
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+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "analyses/Drosophila-eugracilis-RNA-Seq_2021-08-20_v1.0/Droeug_ASM1815383v1_RNA-Seq-alignments_2021-08-20.bam"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "RNA-Seq/Coverage Plots",
+         "key" : "Droeug_ASM1815383v1_RNA-Seq-alignments_2021-08-20_coverage",
+         "label" : "Droeug_ASM1815383v1_RNA-Seq-alignments_2021-08-20_coverage",
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346729'>SRR346729</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346727'>SRR346727</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346728'>SRR346728</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage."
+         },
+         "style" : {
+            "pos_color" : "#00BFFF"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "analyses/Drosophila-eugracilis-RNA-Seq_2021-08-20_v1.0/Droeug_ASM1815383v1_RNA-Seq-alignments_2021-08-20.bigwig"
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+         "label" : "Droeug_ASM1815383v1_RNA-Seq-alignments_2021-08-20_junctions",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346729'>SRR346729</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346727'>SRR346727</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346728'>SRR346728</a>",
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+            "Track legend" : "Junction reads generated by Hisat2 aligner and regtools. The number of alignments supporting the junction read is listed in blue."
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+         "style" : {
+    "subfeatureClasses": {
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+      "start_codon": null,
+      "stop_codon": null,
+      "match_part": "darkblue-80pct"
+    },
+	     "description" : "score",
+            "className" : "feature"
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/Droeug_ASM1815383v1_RNA-Seq-alignments_2021-08-20_junctions/{refseq}/trackData.json"
+      }
+   ]
+}
diff --git a/organisms/stage/stage-v2/Drosophila_ficusphila/trackList.json b/organisms/stage/stage-v2/Drosophila_ficusphila/trackList.json
new file mode 100644
index 0000000..660cdc9
--- /dev/null
+++ b/organisms/stage/stage-v2/Drosophila_ficusphila/trackList.json
@@ -0,0 +1,164 @@
+{
+   "formatVersion" : 1,
+   "names" : {
+      "type" : "Hash",
+      "url" : "names/"
+   },
+   "tracks" : [
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+         "chunkSize" : 20000,
+         "key" : "Reference sequence",
+         "label" : "DNA",
+         "seqType" : "dna",
+         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
+         "type" : "SequenceTrack",
+         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-"
+      },
+      {
+         "category" : "NCBI Annotation Release 102",
+         "compress" : 0,
+         "key" : "NCBI_Annotation_Release_102_Gene",
+         "label" : "drofic_current_models",
+         "menuTemplate" : [
+            {
+               "label" : "View details"
+            },
+            {
+               "action" : "newWindow",
+               "iconClass" : "dijitIconDatabase",
+               "label" : "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
+               "title" : "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
+               "url" : "function(track,feature){ return 'https://i5k.nal.usda.gov/'+feature.get('name')}"
+            }
+         ],
+         "metadata" : {
+            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Drosophila_ficusphila/README_CURRENT_RELEASE",
+            "Data provider" : "NCBI",
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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+            "className" : "container-16px",
+            "description" : "product, note, description",
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+               "exon" : "container-100pct",
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+         "trackType" : "HTMLFeatures",
+         "type" : "HTMLFeatures",
+         "urlTemplate" : "tracks/drofic_current_models/{refseq}/trackData.json"
+      },
+      {
+         "category" : "NCBI Annotation Release 102",
+         "compress" : 0,
+         "key" : "NCBI_Annotation_Release_102_Pseudogene",
+         "label" : "NCBI_Annotation_Release_102_Pseudogene",
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+            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Drosophila_ficusphila/README_CURRENT_RELEASE",
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
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+         "urlTemplate" : "tracks/NCBI_Annotation_Release_102_Pseudogene/{refseq}/trackData.json"
+      },
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+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
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+         "metadata" : {
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+         },
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+         "type" : "WebApollo/View/Track/DraggableAlignments",
+	"unsafePopup":true,
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+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
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+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346750'>SRR346750</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346751'>SRR346751</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346748'>SRR346748</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346749'>SRR346749</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR346752'>SRR346752</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage."
+         },
+         "style" : {
+            "pos_color" : "#00BFFF"
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+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
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+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
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+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+	     "description":"score",
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+         "type" : "FeatureTrack",
+	"unsafePopup":true,
+         "urlTemplate" : "tracks/Drofic_ASM1815226v1_RNA-Seq-alignments_2021-10-08_junctions/{refseq}/trackData.json"
+      }
+   ]
+}
diff --git a/organisms/stage/stage-v2/Drosophila_kikkawai/trackList.json b/organisms/stage/stage-v2/Drosophila_kikkawai/trackList.json
new file mode 100644
index 0000000..967353f
--- /dev/null
+++ b/organisms/stage/stage-v2/Drosophila_kikkawai/trackList.json
@@ -0,0 +1,172 @@
+{
+   "formatVersion" : 1,
+   "names" : {
+      "type" : "Hash",
+      "url" : "names/"
+   },
+   "tracks" : [
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+         "category" : "Reference sequence",
+         "chunkSize" : 20000,
+         "key" : "Reference sequence",
+         "label" : "DNA",
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+         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
+         "type" : "SequenceTrack",
+         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-"
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+      {
+         "category" : "NCBI Annotation Release 102",
+         "compress" : 0,
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+         "label" : "drokik_current_models",
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+            {
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+            {
+               "action" : "newWindow",
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+               "label" : "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
+               "title" : "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
+               "url" : "function(track,feature){ return 'https://i5k.nal.usda.gov/'+feature.get('name')}"
+            }
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+         "type" : "HTMLFeatures",
+         "urlTemplate" : "tracks/drokik_current_models/{refseq}/trackData.json"
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+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
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+      "wholeCDS": null,
+      "start_codon": null,
+      "stop_codon": null,
+      "match_part": "darkblue-80pct"
+    },
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+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/Drokik_ASM1815253v1_RNA-Seq-alignments_2021-08-20_junctions/{refseq}/trackData.json"
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+}
diff --git a/organisms/stage/stage-v2/Drosophila_rhopaloa/trackList.json b/organisms/stage/stage-v2/Drosophila_rhopaloa/trackList.json
new file mode 100644
index 0000000..b9cb586
--- /dev/null
+++ b/organisms/stage/stage-v2/Drosophila_rhopaloa/trackList.json
@@ -0,0 +1,188 @@
+{
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diff --git a/organisms/stage/stage-v2/Drosophila_takahashii/trackList.json b/organisms/stage/stage-v2/Drosophila_takahashii/trackList.json
new file mode 100644
index 0000000..39e9d4b
--- /dev/null
+++ b/organisms/stage/stage-v2/Drosophila_takahashii/trackList.json
@@ -0,0 +1,188 @@
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diff --git a/organisms/stage/stage-v2/Dufourea_novaeangliae/trackList.json b/organisms/stage/stage-v2/Dufourea_novaeangliae/trackList.json
new file mode 100644
index 0000000..eeacef6
--- /dev/null
+++ b/organisms/stage/stage-v2/Dufourea_novaeangliae/trackList.json
@@ -0,0 +1,388 @@
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+    },
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+}
diff --git a/organisms/stage/stage-v2/Ephemera_danica/trackList.json b/organisms/stage/stage-v2/Ephemera_danica/trackList.json
new file mode 100644
index 0000000..e92628c
--- /dev/null
+++ b/organisms/stage/stage-v2/Ephemera_danica/trackList.json
@@ -0,0 +1,99 @@
+{
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diff --git a/organisms/stage/stage-v2/Eufriesea_mexicana/trackList.json b/organisms/stage/stage-v2/Eufriesea_mexicana/trackList.json
new file mode 100644
index 0000000..a2aa8ef
--- /dev/null
+++ b/organisms/stage/stage-v2/Eufriesea_mexicana/trackList.json
@@ -0,0 +1,153 @@
+{
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diff --git a/organisms/stage/stage-v2/Euglossa_dilemma/trackList.json b/organisms/stage/stage-v2/Euglossa_dilemma/trackList.json
new file mode 100644
index 0000000..d36dc77
--- /dev/null
+++ b/organisms/stage/stage-v2/Euglossa_dilemma/trackList.json
@@ -0,0 +1,155 @@
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diff --git a/organisms/stage/stage-v2/Eurytemora_affinis/trackList.json b/organisms/stage/stage-v2/Eurytemora_affinis/trackList.json
new file mode 100644
index 0000000..16316c2
--- /dev/null
+++ b/organisms/stage/stage-v2/Eurytemora_affinis/trackList.json
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diff --git a/organisms/stage/stage-v2/Eurytemora_affinis_-_training/trackList.json b/organisms/stage/stage-v2/Eurytemora_affinis_-_training/trackList.json
new file mode 100644
index 0000000..16316c2
--- /dev/null
+++ b/organisms/stage/stage-v2/Eurytemora_affinis_-_training/trackList.json
@@ -0,0 +1,1795 @@
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+      "label": "blastx_Platyhelminthes",
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+      "label": "blastx_Priapulida",
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+        "Publication status": "Published - please cite doi: 10.1093/molbev/msx147",
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+      "label": "blastx_Tardigrada",
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+      "key": "cegma",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
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+      "label": "protein2genome_Arthropoda",
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+      "label": "protein2genome_Chelicerata",
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+      "label": "protein2genome_Parazoa",
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+      "key": "protein2genome_Placozoa",
+      "label": "protein2genome_Placozoa",
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+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
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+      "key": "protein2genome_Platyhelminthes",
+      "label": "protein2genome_Platyhelminthes",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published - please cite doi: 10.1093/molbev/msx147",
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+      "urlTemplate": "tracks/protein2genome_Platyhelminthes/{refseq}/trackData.json"
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+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+      "key": "protein2genome_Priapulida",
+      "label": "protein2genome_Priapulida",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
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+        "Track legend": "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline."
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+      "key": "protein2genome_Tardigrada",
+      "label": "protein2genome_Tardigrada",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published - please cite doi: 10.1093/molbev/msx147",
+        "Track legend": "Results from Protein2genome alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline."
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+        "arrowheadClass": "webapollo-arrowhead",
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+      "key": "protein2genome_Tunicata",
+      "label": "protein2genome_Tunicata",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
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+        "Track legend": "Results from Protein2genome alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline."
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+        "arrowheadClass": "webapollo-arrowhead",
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+      "label": "protein2genome_UNCATEGORISED",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
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+      "key": "repeatmasker",
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+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
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+        "Track legend": "Results from RepeatMasker as part of the MAKER automated annotation pipeline."
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+        "arrowheadClass": "webapollo-arrowhead",
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+      "key": "repeatrunner",
+      "label": "repeatrunner",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published - please cite doi: 10.1093/molbev/msx147",
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+      "label": "TF1_accepted_hits (Coverage Plot)",
+      "metadata": {
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+        "File provider": "Joana C. Silva , Institute for Genome Sciences, University of Maryland School of Medicine",
+        "Publication status": "Published - please cite doi: 10.1093/molbev/msx147",
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+        "Sex": "female",
+        "Tissues included": "whole animal homogenate"
+      },
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+      "urlTemplate": "user_contributed_data/jmunro/april_2016/TF_1-accepted_hits.bigwig"
+    },
+    {
+      "category": "Transcriptome/Splice Junctions",
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+      "key": "TF1_tophat_junctions",
+      "label": "TF1_tophat_junctions",
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+        "File provider": "Joana C. Silva , Institute for Genome Sciences, University of Maryland School of Medicine",
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+        "Sex": "female",
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+      "style": {
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+      "urlTemplate": "tracks/TF1_tophat_junctions/{refseq}/trackData.json"
+    }
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+}
diff --git a/organisms/stage/stage-v2/Fopius_arisanus/trackList.json b/organisms/stage/stage-v2/Fopius_arisanus/trackList.json
new file mode 100644
index 0000000..cf86bd5
--- /dev/null
+++ b/organisms/stage/stage-v2/Fopius_arisanus/trackList.json
@@ -0,0 +1,422 @@
+{
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+  "css": "./plugins/NAL_CSS/css/main.css",
+  "favicon": "./plugins/WebApollo/img/webapollo_favicon.ico",
+  "formatVersion": 1,
+  "share_link": 0,
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+            "renderClassName": "gray-center-30pct"
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+            "className": "light-purple-80pct",
+            "renderClassName": "gray-center-30pct"
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+      "label": "RefSeq_Psuedogene",
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+        "File provider": "Scott Geib, USDA-ARS-PBARC",
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+        "Data source URL": "http://www.ncbi.nlm.nih.gov/bioproject/259573",
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+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "user_contributed_data/sgeib/Fari_i5k/female_accepted_hits_refSeq_IDs.bam"
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+    {
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+      "label": "Fari_RNAseq_pupae",
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+        "Analysis method": "TopHat v2.0.13",
+        "Data source URL": "http://www.ncbi.nlm.nih.gov/bioproject/259571",
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+      "urlTemplate": "user_contributed_data/sgeib/Fari_i5k/larvae_accepted_hits_refSeq_IDs.bigwig"
+    },
+    {
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+      "label": "Fari_RNAseq_pupae (Coverage Plot)",
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+        "Date completed": "12/2/15",
+        "File provider": "Scott Geib, USDA-ARS-PBARC",
+        "Geographical location of specimen collection": "Fari Lab colony Bdor adapted, USDA-ARS Pacific Basin Agricultural Research Center, Hilo, HI",
+        "NCBI SRA accession #": "SRA: SRX689038",
+        "Other notes": "See publication and NCBI Bioproject for sample details",
+        "Publication status": "Published. Calla et al. Transcriptome of the egg parasitoid Fopius arisanus: an important biocontrol tool for Tephritid fruit fly suppression, Gigascience,  2015, 4:36   doi:10.1186/s13742-015-0075-4 (http://www.gigasciencejournal.com/content/4/1/36)",
+        "Sequencing platform and version": "Illumina HiSeq2000, 2x100 bp PE",
+        "Sex ": "Pool",
+        "Strain": "Fari_Bdor",
+        "Tissues included": "Pooled Pupae"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "pos_color": "#00BFFF"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "user_contributed_data/sgeib/Fari_i5k/pupae_accepted_hits_refSeq_IDs.bigwig"
+    }
+  ]
+}
diff --git a/organisms/stage/stage-v2/Frankliniella_occidentalis/trackList.json b/organisms/stage/stage-v2/Frankliniella_occidentalis/trackList.json
new file mode 100644
index 0000000..8a7bedf
--- /dev/null
+++ b/organisms/stage/stage-v2/Frankliniella_occidentalis/trackList.json
@@ -0,0 +1,233 @@
+{
+  "formatVersion": 1,
+  "names": {
+    "type": "Hash",
+    "url": "names/"
+  },
+  "tracks": [
+    {
+      "category": "Reference sequence",
+      "chunkSize": 20000,
+      "key": "Reference sequence",
+      "label": "DNA",
+      "seqType": "dna",
+      "storeClass": "JBrowse/Store/Sequence/StaticChunked",
+      "type": "SequenceTrack",
+      "urlTemplate": "seq/{refseq_dirpath}/{refseq}-"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Reference Assembly",
+      "key": "Gaps in assembly",
+      "label": "Gaps in assembly",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "white",
+        "pos_color": "black"
+      },
+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "bigwig/GCA_000697945.4_Focc_3.0_genomic.fna.gaps.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "0.5",
+      "category": "Reference Assembly",
+      "key": "GC Content",
+      "label": "GC Content",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+      },
+      "scoreType": "avgScore",
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "rgba(255,255,0,50)",
+        "pos_color": "rgba(0,0,255,50)"
+      },
+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "bigwig/GCA_000697945.4_Focc_3.0_genomic.fna.gc.bigwig"
+    },
+    {
+      "category": "Official Gene Set",
+      "compress": 0,
+      "fmtDetailValue_Id": "function (id, feature) {  var name2 = id.replace(/-R./, '');  if(feature.get('type')=='mRNA') {    return '<a target=_blank href=https://i5k.nal.usda.gov/'+name2+'>'+id+'</a>';} else { return id;}}",
+      "key": "OGSv1.1 Gene",
+      "label": "fraocc_current_models",
+      "menuTemplate": [
+        {
+          "label": "View details"
+        },
+        {
+          "action": "newWindow",
+          "iconClass": "dijitIconDatabase",
+          "label": "function(track,feature){ return 'Open gene page for '+feature.get('id').replace(/-R./, '')}",
+          "title": "function(track,feature){ return 'Open gene page for '+feature.get('id').replace(/-R./, '')}",
+          "url": "function(track,feature){ return 'https://i5k.nal.usda.gov/'+feature.get('id').replace(/-R./, '')}"
+        }
+      ],
+      "metadata": {
+        "Data provider": "Dorith Rotenberg, NC State University",
+        "Data source": "https://data.nal.usda.gov/dataset/frankliniella-occidentalis-official-gene-set-ogsv11",
+        "Materials and Methods": "The Frankliniella occidentalis Official Gene Set fraocc_OGSv1.1 is an update of OGSv1.0 (https://doi.org/10.15482/USDA.ADC/1504029). OGSv1.0 is an integration of automatic gene predictions from the Baylor College of Medicine's i5k pilot project, with manual annotations by the research community (performed via the Apollo manual curation software, http://genomearchitect.org/). OGSv1.1 was updated from OGSv1.0 (https://doi.org/10.15482/USDA.ADC/1504029) to the coordinates of genome assembly GCA_000697945.4 (https://www.ncbi.nlm.nih.gov/assembly/GCA_000697945.4) using https://github.com/NAL-i5K/coordinates_conversion/.",
+        "Publication status": "In review"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "description": "product, note, description",
+        "subfeatureClasses": {
+          "CDS": "gnomon_CDS",
+          "UTR": "gnomon_UTR",
+          "exon": "container-100pct",
+          "wholeCDS": null
+        }
+      },
+      "trackType": "HTMLFeatures",
+      "type": "HTMLFeatures",
+      "urlTemplate": "tracks/fraocc_current_models/{refseq}/trackData.json"
+    },
+    {
+      "category": "Transcriptome",
+      "key": "FO_Salivary_CS_Ullman",
+      "label": "FO_Salivary_CS_Ullman",
+      "metadata": {
+        "Analysis method": "GMAP 2015-06-23",
+        "Citation": "Stafford-Banks CA, Rotenberg D, Johnson BR, Whitfield AE, Ullman DE (2014) Analysis of the Salivary Gland Transcriptome of Frankliniella occidentalis. PLoS ONE 9(4): e94447. doi:10.1371/journal.pone.0094447",
+        "Data provider": "Diane Ullman, Univ. of CA-Davis",
+        "Publication status": "published",
+        "Track legend": "These mapping results are displayed so that the contigs are light blue. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "user_contributed_data/drotenberg/sal_gland_sorted_updated.bam"
+    },
+    {
+      "category": "Transcriptome",
+      "key": "Transcriptome: 454 contigs assembled by Newbler",
+      "label": "Transcriptome: 454 contigs assembled by Newbler",
+      "metadata": {
+        "Analysis method": "GMAP v2014-5-15",
+        "Analysis provider": "Dorith Rotenberg, Kansas State University",
+        "Publication status": "unpublished - No usage restrictions",
+        "Track legend": "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark red or blue while the introns spanning the predicted splicing sites are light red or blue. Reads mapped to the forward strand are red; reads mapped to the reverse strand are blue. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "user_contributed_data/drotenberg/FO_454AllContigs_30793seqs.parse_updated.bam"
+    },
+    {
+      "category": "RNA-Seq/Mapped Reads",
+      "key": "FO_RNAseq_females",
+      "label": "FO_RNAseq_females",
+      "metadata": {
+        "Alignment method": "TopHat",
+        "Alignment summary": "http://de.iplantcollaborative.org/dl/d/42FD83E1-1694-4394-A50A-53C7E049C905/align_summary.txt",
+        "Analysis provider": "Dorith Rotenberg, Kansas State University",
+        "Data Source": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Western_flower_thrips/RNA_sequence/",
+        "Materials Source": "Groups of whole bodies of females from a laboratory colony of Frankliniella occidentalis originating from the Kamilo Iki valley on the island of Oahu, Hawaii",
+        "Read cleaning method": "Prior to tophatPE alignment, reads were trimmed and cleaned with Prinseq-lite",
+        "Track legend": "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark red or blue while the introns spanning the predicted splicing sites are light red or blue. Reads mapped to the forward strand are red; reads mapped to the reverse strand are blue. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "user_contributed_data/drotenberg/Female_Focc_ICD_FOi5DR_updated.bam"
+    },
+    {
+      "category": "RNA-Seq/Mapped Reads",
+      "key": "FO_RNAseq_larval&pupal",
+      "label": "FO_RNAseq_larval&pupal",
+      "metadata": {
+        "Alignment method": "TopHat",
+        "Alignment summary": "http://de.iplantcollaborative.org/dl/d/6FF6BC2D-3AE9-4682-9983-E0787A3056D0/align_summary.txt",
+        "Analysis provider": "Dorith Rotenberg, Kansas State University",
+        "Data Source": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Western_flower_thrips/RNA_sequence/",
+        "Materials Source": "Groups of whole bodies of a mixture of pre-adult stages (first and second instar larva & pre-pupae and pupae) from a laboratory colony of Frankliniella occidentalis originating from the Kamilo Iki valley on the island of Oahu, Hawaii",
+        "Read cleaning method": "Prior to tophatPE alignment, reads were trimmed and cleaned with Prinseq-lite",
+        "Track legend": "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark red or blue while the introns spanning the predicted splicing sites are light red or blue. Reads mapped to the forward strand are red; reads mapped to the reverse strand are blue. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "user_contributed_data/drotenberg/Larva_Pupa_Focc_ICD_FOi5DR_updated.bam"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "RNA-Seq/Coverage Plots",
+      "key": "FO_RNAseq_larval&pupal (Coverage Plots)",
+      "label": "FO_RNAseq_larval&pupal (Coverage Plots)",
+      "metadata": {
+        "Alignment method": "TopHat",
+        "Alignment summary": "http://de.iplantcollaborative.org/dl/d/6FF6BC2D-3AE9-4682-9983-E0787A3056D0/align_summary.txt",
+        "Analysis provider": "Dorith Rotenberg, Kansas State University",
+        "Data Source": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Western_flower_thrips/RNA_sequence/",
+        "Materials Source": "Groups of whole bodies of a mixture of pre-adult stages (first and second instar larva & pre-pupae and pupae) from a laboratory colony of Frankliniella occidentalis originating from the Kamilo Iki valley on the island of Oahu, Hawaii",
+        "Read cleaning method": "Prior to tophatPE alignment, reads were trimmed and cleaned with Prinseq-lite",
+        "Track legend": "This track represents a density plot of RNA-Seq coverage. Darker blue represents higher coverage, and lighter blue lower coverage."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "pos_color": "#00BFFF"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "user_contributed_data/drotenberg/Larva_Pupa_Focc_ICD_FOi5DR_updated.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "RNA-Seq/Coverage Plots",
+      "key": "FO_RNAseq_females (Coverage Plots)",
+      "label": "FO_RNAseq_females (Coverage Plots)",
+      "metadata": {
+        "Alignment method": "TopHat",
+        "Alignment summary": "http://de.iplantcollaborative.org/dl/d/42FD83E1-1694-4394-A50A-53C7E049C905/align_summary.txt",
+        "Analysis provider": "Dorith Rotenberg, Kansas State University",
+        "Data Source": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Western_flower_thrips/RNA_sequence/",
+        "Materials Source": "Groups of whole bodies of females from a laboratory colony of Frankliniella occidentalis originating from the Kamilo Iki valley on the island of Oahu, Hawaii",
+        "Read cleaning method": "Prior to tophatPE alignment, reads were trimmed and cleaned with Prinseq-lite",
+        "Track legend": "This track represents a density plot of RNA-Seq coverage. Darker blue represents higher coverage, and lighter blue lower coverage."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "pos_color": "#00BFFF"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "user_contributed_data/drotenberg/Female_Focc_ICD_FOi5DR_updated.bigwig"
+    },
+    {
+      "category": "Transcriptome",
+      "compress": 0,
+      "key": "KSU_Cufflinks",
+      "label": "KSU_Cufflinks",
+      "metadata": {
+        "Analysis Method": "Illumina Hi-Seq 200 bp; Cufflinks 2.1.1",
+        "Data submitter": "Derek Schneweis (Kansas State University)",
+        "Description": "KSU_Cufflinks",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Sex": "Pooled",
+        "Tissue": "Whole Body Group"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "CDS": "transcriptome-cds",
+          "UTR": "transcriptome-utr",
+          "exon": "container-100pct",
+          "wholeCDS": null
+        }
+      },
+      "trackType": "null",
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/KSU_Cufflinks/{refseq}/trackData.json"
+    }
+  ]
+}
diff --git a/organisms/stage/stage-v2/Galleria_mellonella/trackList.json b/organisms/stage/stage-v2/Galleria_mellonella/trackList.json
new file mode 100644
index 0000000..65778e0
--- /dev/null
+++ b/organisms/stage/stage-v2/Galleria_mellonella/trackList.json
@@ -0,0 +1,131 @@
+{
+  "formatVersion": 1,
+  "names": {
+    "type": "Hash",
+    "url": "names/"
+  },
+  "tracks": [
+    {
+      "category": "Reference sequence",
+      "chunkSize": 20000,
+      "key": "Reference sequence",
+      "label": "DNA",
+      "seqType": "dna",
+      "storeClass": "JBrowse/Store/Sequence/StaticChunked",
+      "type": "SequenceTrack",
+      "urlTemplate": "seq/{refseq_dirpath}/{refseq}-"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Reference Assembly",
+      "key": "Gaps in assembly",
+      "label": "Gaps in assembly",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "white",
+        "pos_color": "black"
+      },
+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "bigwig/GCF_003640425.2_ASM364042v2_genomic.fna.gaps.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "0.5",
+      "category": "Reference Assembly",
+      "key": "GC Content",
+      "label": "GC Content",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+      },
+      "scoreType": "avgScore",
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "rgba(255,255,0,50)",
+        "pos_color": "rgba(0,0,255,50)"
+      },
+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "bigwig/GCF_003640425.2_ASM364042v2_genomic.fna.gc.bigwig"
+    },
+    {
+      "category": "NCBI Annotation Release 101",
+      "compress": 0,
+      "key": "NCBI_Annotation_Release_101_Gene",
+      "label": "galmel_current_models",
+      "menuTemplate": [
+        {
+          "label": "View details"
+        },
+        {
+          "action": "newWindow",
+          "iconClass": "dijitIconDatabase",
+          "label": "function(track,feature){ return 'Find i5k Workspace gene page for '+feature.get('name')}",
+          "title": "function(track,feature){ return 'Find i5k Workspace gene page for '+feature.get('name')}",
+          "url": "function(track,feature){ return 'https://i5k.nal.usda.gov/'+feature.get('name')}"
+        },
+        {
+          "action": "newWindow",
+          "iconClass": "dijitIconDatabase",
+          "label": "function(track,feature){ return 'Go to NCBI gene page for '+feature.get('name')}",
+          "title": "function(track,feature){ return 'Go to NCBI gene page for '+feature.get('name')}",
+          "url": "function(track,feature){ return 'https://www.ncbi.nlm.nih.gov/nuccore/'+feature.get('name')}"
+        }
+      ],
+      "metadata": {
+        "Data description": "ftp://ftp.ncbi.nlm.nih.gov/genomes/Galleria_mellonella/README_CURRENT_RELEASE",
+        "Data provider": "NCBI",
+        "Data source": "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/640/425/GCF_003640425.2_ASM364042v2/GCF_003640425.2_ASM364042v2_genomic.gff.gz",
+        "Method": "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "description": "product, note, description",
+        "subfeatureClasses": {
+          "CDS": "gnomon_CDS",
+          "UTR": "gnomon_UTR",
+          "exon": "container-100pct",
+          "wholeCDS": null
+        }
+      },
+      "trackType": "HTMLFeatures",
+      "type": "HTMLFeatures",
+      "urlTemplate": "tracks/galmel_current_models/{refseq}/trackData.json"
+    },
+    {
+      "category": "NCBI Annotation Release 101",
+      "compress": 0,
+      "key": "NCBI_Annotation_Release_101_Pseudogene",
+      "label": "NCBI_Annotation_Release_101_Pseudogene",
+      "metadata": {
+        "Data description": "ftp://ftp.ncbi.nlm.nih.gov/genomes/Galleria_mellonella/README_CURRENT_RELEASE",
+        "Data provider": "NCBI",
+        "Data source": "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/640/425/GCF_003640425.2_ASM364042v2/GCF_003640425.2_ASM364042v2_genomic.gff.gz",
+        "Method": "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "description": "product, note, description",
+        "subfeatureClasses": {
+          "CDS": "gnomon_CDS",
+          "UTR": "gnomon_UTR",
+          "exon": "container-100pct",
+          "wholeCDS": null
+        }
+      },
+      "trackType": "HTMLFeatures",
+      "type": "HTMLFeatures",
+      "urlTemplate": "tracks/NCBI_Annotation_Release_101_Pseudogene/{refseq}/trackData.json"
+    }
+  ]
+}
diff --git a/organisms/stage/stage-v2/Gerris_buenoi/trackList.json b/organisms/stage/stage-v2/Gerris_buenoi/trackList.json
new file mode 100644
index 0000000..ffb36c7
--- /dev/null
+++ b/organisms/stage/stage-v2/Gerris_buenoi/trackList.json
@@ -0,0 +1,1311 @@
+{
+  "alwaysOnTracks": "DNA,Annotations",
+  "css": "./plugins/NAL_CSS/css/main.css",
+  "favicon": "./plugins/WebApollo/img/webapollo_favicon.ico",
+  "formatVersion": 1,
+  "names": {
+    "type": "Hash",
+    "url": "names/"
+  },
+  "share_link": 0,
+  "tracks": [
+    {
+      "category": "Reference sequence",
+      "chunkSize": 20000,
+      "key": "Reference sequence",
+      "label": "DNA",
+      "storeClass": "JBrowse/Store/Sequence/StaticChunked",
+      "type": "SequenceTrack",
+      "urlTemplate": "seq/{refseq_dirpath}/{refseq}-"
+    },
+    {
+      "autocomplete": "none",
+      "compress": 0,
+      "key": "User-created Annotations",
+      "label": "Annotations",
+      "phase": 0,
+      "storeClass": "WebApollo/Store/SeqFeature/ScratchPad",
+      "style": {
+        "alternateClasses": {
+          "miRNA": {
+            "className": "brightgreen-80pct",
+            "renderClassName": "gray-center-30pct"
+          },
+          "ncRNA": {
+            "className": "brightgreen-80pct",
+            "renderClassName": "gray-center-30pct"
+          },
+          "pseudogene": {
+            "className": "light-purple-80pct",
+            "renderClassName": "gray-center-30pct"
+          },
+          "rRNA": {
+            "className": "brightgreen-80pct",
+            "renderClassName": "gray-center-30pct"
+          },
+          "repeat_region": {
+            "className": "magenta-80pct"
+          },
+          "snRNA": {
+            "className": "brightgreen-80pct",
+            "renderClassName": "gray-center-30pct"
+          },
+          "snoRNA": {
+            "className": "brightgreen-80pct",
+            "renderClassName": "gray-center-30pct"
+          },
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+      "key": "protein2genome_Nematomorpha",
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+      "key": "protein2genome_Platyhelminthes",
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+      "key": "protein2genome_Priapulida",
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+        "Track legend": "Results from Protein2genome alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline."
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+        "Track legend": "Results from Protein2genome alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline."
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+        "Track legend": "Results from Protein2genome alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
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+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_UNCATEGORISED/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/2. Evidence/Repeats",
+      "compress": 0,
+      "key": "repeatmasker",
+      "label": "repeatmasker",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from RepeatMasker as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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+      "urlTemplate": "tracks/repeatmasker/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/2. Evidence/Repeats",
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+      "key": "repeatrunner",
+      "label": "repeatrunner",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
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+      "urlTemplate": "tracks/repeatrunner/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/1. Gene Sets/Supplementary Gene Predictions",
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+      "key": "snap_masked",
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+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline."
+      },
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+        "arrowheadClass": "webapollo-arrowhead",
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+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
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+        "neg_color": "white",
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+      "urlTemplate": "bigwig/Gbue.scaffolds.50.fa.gaps.bigwig"
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+        "File provider": "David Armisen, Institut de genomique fonctionelle de Lyon",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)"
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+      "urlTemplate": "bam/darmisen/Gbue_ICD_GBi5AK.bam"
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+      "label": "PE reads i5k - RNA-Seq coverage",
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+        "Track legend": "This track represents an X-Y plot plot of RNA-Seq coverage. Secondary and supplementary alignments, as well as optical PCR duplicates and alignments failing QC are not included in the coverage calculations."
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+      "style": {
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+      "urlTemplate": "bigwig/darmisen/Gbue_ICD_GBi5AK.bigwig"
+    },
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+      "category": "Official Gene Set v1.0/1. Gene Sets/Protein Coding",
+      "compress": 0,
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+      "label": "gerbue_current_models",
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+        "Data provider": "The i5k Workspace@NAL",
+        "Data source": "https://doi.org/10.15482/USDA.ADC/1423873",
+        "Method": "https://github.com/NAL-i5K/GFF3toolkit",
+        "publication status": "Published, please cite https://doi.org/10.1101/242230 or https://doi.org/10.15482/USDA.ADC/1423873"
+      },
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+          "three_prime_utr": "ogs-utr",
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+        }
+      },
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+      "urlTemplate": "tracks/gerbue_current_models/{refseq}/trackData.json"
+    },
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+      "compress": 0,
+      "key": "Gerris buenoi Official Gene Set v1.0, pseudogenes",
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+      },
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+          "three_prime_utr": "ogs-utr",
+          "wholeCDS": null
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/GBUE_OGSv10_pseudogenes/{refseq}/trackData.json"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "0.5",
+      "category": "Reference Assembly",
+      "key": "GC Content",
+      "label": "GC Content",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+      },
+      "scoreType": "avgScore",
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "rgba(255,255,0,50)",
+        "pos_color": "rgba(0,0,255,50)"
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+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "bigwig/Gbue.scaffolds.50.fa.gc.bigwig"
+    }
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+}
diff --git a/organisms/stage/stage-v2/Habropoda_laboriosa/trackList.json b/organisms/stage/stage-v2/Habropoda_laboriosa/trackList.json
new file mode 100644
index 0000000..954d1c2
--- /dev/null
+++ b/organisms/stage/stage-v2/Habropoda_laboriosa/trackList.json
@@ -0,0 +1,170 @@
+{
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+  "css": "./plugins/NAL_CSS/css/main.css",
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+  "names": {
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+      "label": "Annotations",
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+      "storeClass": "WebApollo/Store/SeqFeature/ScratchPad",
+      "style": {
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+            "renderClassName": "gray-center-30pct"
+          },
+          "ncRNA": {
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+            "renderClassName": "gray-center-30pct"
+          },
+          "pseudogene": {
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+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
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+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+      },
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+      "key": "GenBank Annotations, pseudogenes",
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+        "Data provider": "NCBI/GenBank",
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/GenBank_Annotations_Pseudogene/{refseq}/trackData.json"
+    }
+  ]
+}
diff --git a/organisms/stage/stage-v2/Halyomorpha_halys/trackList.json b/organisms/stage/stage-v2/Halyomorpha_halys/trackList.json
new file mode 100644
index 0000000..37ce487
--- /dev/null
+++ b/organisms/stage/stage-v2/Halyomorpha_halys/trackList.json
@@ -0,0 +1,441 @@
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+      "type": "SequenceTrack",
+      "urlTemplate": "seq/{refseq_dirpath}/{refseq}-"
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+      "bicolor_pivot": "zero",
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+      "key": "Gaps in assembly",
+      "label": "Gaps in assembly",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
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+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+      },
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+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
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+    }
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+}
diff --git a/organisms/stage/stage-v2/Heliothis_virescens/trackList.json b/organisms/stage/stage-v2/Heliothis_virescens/trackList.json
new file mode 100644
index 0000000..5b89fd0
--- /dev/null
+++ b/organisms/stage/stage-v2/Heliothis_virescens/trackList.json
@@ -0,0 +1,626 @@
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+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "white",
+        "pos_color": "black"
+      },
+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "bigwig/GCA_002382865.1_K63_refined_pacbio_genomic.fna.gaps.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "0.5",
+      "category": "Reference Assembly",
+      "key": "GC Content",
+      "label": "GC Content",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+      },
+      "scoreType": "avgScore",
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "rgba(255,255,0,50)",
+        "pos_color": "rgba(0,0,255,50)"
+      },
+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "bigwig/GCA_002382865.1_K63_refined_pacbio_genomic.fna.gc.bigwig"
+    },
+    {
+      "category": "Transcriptome/Mapped Reads",
+      "key": "Heliothis virescens RNA-Seq HVI-HP_GKW-20, Hairpencils/adult",
+      "label": "Heliothis virescens RNA-Seq HVI-HP_GKW-20, Hairpencils/adult",
+      "metadata": {
+        "Analysis method": "Tophat v2.1.0",
+        "Data description": "https://i5k.nal.usda.gov/node/739292",
+        "Data provider": "Megan Fritz, UMD",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Tissues/life history stage": "Hairpencils/adult",
+        "Track legend": "Mapped RNA-Seq reads:<br>Aligned regions: blue<br>Spanned regions (possible splice junctions): light blue<br>Deletions in the read relative to the reference: red<br>Insertions in the read relative to the reference: green<br>Mismatch: yellow (hover over the mismatch to see what the snp is)"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "user_contributed_data/HVI-HP_GKW-20/accepted_hits.bam"
+    },
+    {
+      "category": "Transcriptome/Mapped Reads",
+      "key": "Heliothis virescens RNA-Seq HVI-CY_GKW-25, hemocytes",
+      "label": "Heliothis virescens RNA-Seq HVI-CY_GKW-25, hemocytes",
+      "metadata": {
+        "Analysis method": "Tophat v2.1.0",
+        "Data description": "https://i5k.nal.usda.gov/node/739292",
+        "Data provider": "Megan Fritz, UMD",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Tissues/life history stage": "hemocytes",
+        "Track legend": "Mapped RNA-Seq reads:<br>Aligned regions: blue<br>Spanned regions (possible splice junctions): light blue<br>Deletions in the read relative to the reference: red<br>Insertions in the read relative to the reference: green<br>Mismatch: yellow (hover over the mismatch to see what the snp is)"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "user_contributed_data/HVI-CY_GKW-25/accepted_hits.bam"
+    },
+    {
+      "category": "Transcriptome/Mapped Reads",
+      "key": "Heliothis virescens RNA-Seq HVI-FB_GKW-24, fat body",
+      "label": "Heliothis virescens RNA-Seq HVI-FB_GKW-24, fat body",
+      "metadata": {
+        "Analysis method": "Tophat v2.1.0",
+        "Data description": "https://i5k.nal.usda.gov/node/739292",
+        "Data provider": "Megan Fritz, UMD",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Tissues/life history stage": "fat body",
+        "Track legend": "Mapped RNA-Seq reads:<br>Aligned regions: blue<br>Spanned regions (possible splice junctions): light blue<br>Deletions in the read relative to the reference: red<br>Insertions in the read relative to the reference: green<br>Mismatch: yellow (hover over the mismatch to see what the snp is)"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "user_contributed_data/HVI-FB_GKW-24/accepted_hits.bam"
+    },
+    {
+      "category": "Transcriptome/Mapped Reads",
+      "key": "Heliothis virescens RNA-Seq HVI-GL_GKW-23, pheromone gland/adult",
+      "label": "Heliothis virescens RNA-Seq HVI-GL_GKW-23, pheromone gland/adult",
+      "metadata": {
+        "Analysis method": "Tophat v2.1.0",
+        "Data description": "https://i5k.nal.usda.gov/node/739292",
+        "Data provider": "Megan Fritz, UMD",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Tissues/life history stage": "pheromone gland/adult",
+        "Track legend": "Mapped RNA-Seq reads:<br>Aligned regions: blue<br>Spanned regions (possible splice junctions): light blue<br>Deletions in the read relative to the reference: red<br>Insertions in the read relative to the reference: green<br>Mismatch: yellow (hover over the mismatch to see what the snp is)"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "user_contributed_data/HVI-GL_GKW-23/accepted_hits.bam"
+    },
+    {
+      "category": "Transcriptome/Mapped Reads",
+      "key": "Heliothis virescens RNA-Seq HVI-NE_GKW-26, neonates",
+      "label": "Heliothis virescens RNA-Seq HVI-NE_GKW-26, neonates",
+      "metadata": {
+        "Analysis method": "Tophat v2.1.0",
+        "Data description": "https://i5k.nal.usda.gov/node/739292",
+        "Data provider": "Megan Fritz, UMD",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Tissues/life history stage": "neonates",
+        "Track legend": "Mapped RNA-Seq reads:<br>Aligned regions: blue<br>Spanned regions (possible splice junctions): light blue<br>Deletions in the read relative to the reference: red<br>Insertions in the read relative to the reference: green<br>Mismatch: yellow (hover over the mismatch to see what the snp is)"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "user_contributed_data/HVI-NE_GKW-26/accepted_hits.bam"
+    },
+    {
+      "category": "Transcriptome/Mapped Reads",
+      "key": "Heliothis virescens RNA-Seq HVI-AM_GKW-19, Antenna/adult",
+      "label": "Heliothis virescens RNA-Seq HVI-AM_GKW-19, Antenna/adult",
+      "metadata": {
+        "Analysis method": "Tophat v2.1.0",
+        "Data description": "https://i5k.nal.usda.gov/node/739292",
+        "Data provider": "Megan Fritz, UMD",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Tissues/life history stage": "Antenna/adult",
+        "Track legend": "Mapped RNA-Seq reads:<br>Aligned regions: blue<br>Spanned regions (possible splice junctions): light blue<br>Deletions in the read relative to the reference: red<br>Insertions in the read relative to the reference: green<br>Mismatch: yellow (hover over the mismatch to see what the snp is)"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "user_contributed_data/HVI-AM_GKW-19/accepted_hits.bam"
+    },
+    {
+      "category": "Transcriptome/Mapped Reads",
+      "key": "Heliothis virescens RNA-Seq HVI-OV_GKW-22, ovipositor/adult",
+      "label": "Heliothis virescens RNA-Seq HVI-OV_GKW-22, ovipositor/adult",
+      "metadata": {
+        "Analysis method": "Tophat v2.1.0",
+        "Data description": "https://i5k.nal.usda.gov/node/739292",
+        "Data provider": "Megan Fritz, UMD",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Tissues/life history stage": "ovipositor/adult",
+        "Track legend": "Mapped RNA-Seq reads:<br>Aligned regions: blue<br>Spanned regions (possible splice junctions): light blue<br>Deletions in the read relative to the reference: red<br>Insertions in the read relative to the reference: green<br>Mismatch: yellow (hover over the mismatch to see what the snp is)"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "user_contributed_data/HVI-OV_GKW-22/accepted_hits.bam"
+    },
+    {
+      "category": "Transcriptome/Mapped Reads",
+      "key": "Heliothis virescens RNA-Seq HVI-AF_GKW-21, Antenna/adult",
+      "label": "Heliothis virescens RNA-Seq HVI-AF_GKW-21, Antenna/adult",
+      "metadata": {
+        "Analysis method": "Tophat v2.1.0",
+        "Data description": "https://i5k.nal.usda.gov/node/739292",
+        "Data provider": "Megan Fritz, UMD",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Tissues/life history stage": "Antenna/adult",
+        "Track legend": "Mapped RNA-Seq reads:<br>Aligned regions: blue<br>Spanned regions (possible splice junctions): light blue<br>Deletions in the read relative to the reference: red<br>Insertions in the read relative to the reference: green<br>Mismatch: yellow (hover over the mismatch to see what the snp is)"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "user_contributed_data/HVI-AF_GKW-21/accepted_hits.bam"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Transcriptome/Coverage Plots (BigWig)",
+      "key": "Heliothis virescens RNA-Seq HVI-FB_GKW-24, fat body (Coverage Plot)",
+      "label": "Heliothis virescens RNA-Seq HVI-FB_GKW-24, fat body (Coverage Plot)",
+      "metadata": {
+        "Analysis method": "Tophat v2.1.0",
+        "Data description": "https://i5k.nal.usda.gov/node/739292",
+        "Data provider": "Megan Fritz, UMD",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Tissues/life history stage": "fat body",
+        "Track legend": "This track represents an RNA-Seq coverage plot."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "pos_color": "#00BFFF"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "user_contributed_data/HVI-FB_GKW-24/accepted_hits.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Transcriptome/Coverage Plots (BigWig)",
+      "key": "Heliothis virescens RNA-Seq HVI-CY_GKW-25, hemocytes (Coverage Plot)",
+      "label": "Heliothis virescens RNA-Seq HVI-CY_GKW-25, hemocytes (Coverage Plot)",
+      "metadata": {
+        "Analysis method": "Tophat v2.1.0",
+        "Data description": "https://i5k.nal.usda.gov/node/739292",
+        "Data provider": "Megan Fritz, UMD",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Tissues/life history stage": "hemocytes",
+        "Track legend": "This track represents an RNA-Seq coverage plot."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "pos_color": "#00BFFF"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "user_contributed_data/HVI-CY_GKW-25/accepted_hits.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Transcriptome/Coverage Plots (BigWig)",
+      "key": "Heliothis virescens RNA-Seq HVI-NE_GKW-26, neonates (Coverage Plot)",
+      "label": "Heliothis virescens RNA-Seq HVI-NE_GKW-26, neonates (Coverage Plot)",
+      "metadata": {
+        "Analysis method": "Tophat v2.1.0",
+        "Data description": "https://i5k.nal.usda.gov/node/739292",
+        "Data provider": "Megan Fritz, UMD",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Tissues/life history stage": "neonates",
+        "Track legend": "This track represents an RNA-Seq coverage plot."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "pos_color": "#00BFFF"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "user_contributed_data/HVI-NE_GKW-26/accepted_hits.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Transcriptome/Coverage Plots (BigWig)",
+      "key": "Heliothis virescens RNA-Seq HVI-GL_GKW-23, pheromone gland/adult (Coverage Plot)",
+      "label": "Heliothis virescens RNA-Seq HVI-GL_GKW-23, pheromone gland/adult (Coverage Plot)",
+      "metadata": {
+        "Analysis method": "Tophat v2.1.0",
+        "Data description": "https://i5k.nal.usda.gov/node/739292",
+        "Data provider": "Megan Fritz, UMD",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Tissues/life history stage": "pheromone gland/adult",
+        "Track legend": "This track represents an RNA-Seq coverage plot."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "pos_color": "#00BFFF"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "user_contributed_data/HVI-GL_GKW-23/accepted_hits.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Transcriptome/Coverage Plots (BigWig)",
+      "key": "Heliothis virescens RNA-Seq HVI-AM_GKW-19, Antenna/adult (Coverage Plot)",
+      "label": "Heliothis virescens RNA-Seq HVI-AM_GKW-19, Antenna/adult (Coverage Plot)",
+      "metadata": {
+        "Analysis method": "Tophat v2.1.0",
+        "Data description": "https://i5k.nal.usda.gov/node/739292",
+        "Data provider": "Megan Fritz, UMD",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Tissues/life history stage": "Antenna/adult",
+        "Track legend": "This track represents an RNA-Seq coverage plot."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "pos_color": "#00BFFF"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "user_contributed_data/HVI-AM_GKW-19/accepted_hits.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Transcriptome/Coverage Plots (BigWig)",
+      "key": "Heliothis virescens RNA-Seq HVI-OV_GKW-22, ovipositor/adult (Coverage Plot)",
+      "label": "Heliothis virescens RNA-Seq HVI-OV_GKW-22, ovipositor/adult (Coverage Plot)",
+      "metadata": {
+        "Analysis method": "Tophat v2.1.0",
+        "Data description": "https://i5k.nal.usda.gov/node/739292",
+        "Data provider": "Megan Fritz, UMD",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Tissues/life history stage": "ovipositor/adult",
+        "Track legend": "This track represents an RNA-Seq coverage plot."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "pos_color": "#00BFFF"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "user_contributed_data/HVI-OV_GKW-22/accepted_hits.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Transcriptome/Coverage Plots (BigWig)",
+      "key": "Heliothis virescens RNA-Seq HVI-AF_GKW-21, Antenna/adult (Coverage Plot)",
+      "label": "Heliothis virescens RNA-Seq HVI-AF_GKW-21, Antenna/adult (Coverage Plot)",
+      "metadata": {
+        "Analysis method": "Tophat v2.1.0",
+        "Data description": "https://i5k.nal.usda.gov/node/739292",
+        "Data provider": "Megan Fritz, UMD",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Tissues/life history stage": "Antenna/adult",
+        "Track legend": "This track represents an RNA-Seq coverage plot."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "pos_color": "#00BFFF"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "user_contributed_data/HVI-AF_GKW-21/accepted_hits.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Transcriptome/Coverage Plots (BigWig)",
+      "key": "Heliothis virescens RNA-Seq HVI-HP_GKW-20, Hairpencils/adult (Coverage Plot)",
+      "label": "Heliothis virescens RNA-Seq HVI-HP_GKW-20, Hairpencils/adult (Coverage Plot)",
+      "metadata": {
+        "Analysis method": "Tophat v2.1.0",
+        "Data description": "https://i5k.nal.usda.gov/node/739292",
+        "Data provider": "Megan Fritz, UMD",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Tissues/life history stage": "Hairpencils/adult",
+        "Track legend": "This track represents an RNA-Seq coverage plot."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "pos_color": "#00BFFF"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "user_contributed_data/HVI-HP_GKW-20/accepted_hits.bigwig"
+    },
+    {
+      "category": "Transcriptome/Splice Junctions",
+      "compress": 0,
+      "key": "Heliothis virescens RNA-Seq HVI-OV_GKW-22, ovipositor/adult, Tophat junctions",
+      "label": "HVI-OV_GKW-22",
+      "metadata": {
+        "Analysis method": "Tophat v2.1.0",
+        "Data description": "https://i5k.nal.usda.gov/node/739292",
+        "Data provider": "Megan Fritz, UMD",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Tissues/life history stage": "ovipositor/adult",
+        "Track legend": "Splice junction information from TopHat v2.1.0."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}"
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/HVI-OV_GKW-22/{refseq}/trackData.json"
+    },
+    {
+      "category": "Transcriptome/Splice Junctions",
+      "compress": 0,
+      "key": "Heliothis virescens RNA-Seq HVI-FB_GKW-24, fat body, Tophat junctions",
+      "label": "HVI-FB_GKW-24",
+      "metadata": {
+        "Analysis method": "Tophat v2.1.0",
+        "Data description": "https://i5k.nal.usda.gov/node/739292",
+        "Data provider": "Megan Fritz, UMD",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Tissues/life history stage": "fat body",
+        "Track legend": "Splice junction information from TopHat v2.1.0."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}"
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/HVI-FB_GKW-24/{refseq}/trackData.json"
+    },
+    {
+      "category": "Transcriptome/Splice Junctions",
+      "compress": 0,
+      "key": "Heliothis virescens RNA-Seq HVI-HP_GKW-20, Hairpencils/adult, Tophat junctions",
+      "label": "HVI-HP_GKW-20",
+      "metadata": {
+        "Analysis method": "Tophat v2.1.0",
+        "Data description": "https://i5k.nal.usda.gov/node/739292",
+        "Data provider": "Megan Fritz, UMD",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Tissues/life history stage": "Hairpencils/adult",
+        "Track legend": "Splice junction information from TopHat v2.1.0."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}"
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/HVI-HP_GKW-20/{refseq}/trackData.json"
+    },
+    {
+      "category": "Transcriptome/Splice Junctions",
+      "compress": 0,
+      "key": "Heliothis virescens RNA-Seq HVI-CY_GKW-25, hemocytes, Tophat junctions",
+      "label": "HVI-CY_GKW-25",
+      "metadata": {
+        "Analysis method": "Tophat v2.1.0",
+        "Data description": "https://i5k.nal.usda.gov/node/739292",
+        "Data provider": "Megan Fritz, UMD",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Tissues/life history stage": "hemocytes",
+        "Track legend": "Splice junction information from TopHat v2.1.0."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}"
+      },
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diff --git a/organisms/stage/stage-v2/Holacanthella_duospinosa/trackList.json b/organisms/stage/stage-v2/Holacanthella_duospinosa/trackList.json
new file mode 100644
index 0000000..e04f087
--- /dev/null
+++ b/organisms/stage/stage-v2/Holacanthella_duospinosa/trackList.json
@@ -0,0 +1,85 @@
+{
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diff --git a/organisms/stage/stage-v2/Homalodisca_vitripennis/trackList.json b/organisms/stage/stage-v2/Homalodisca_vitripennis/trackList.json
new file mode 100644
index 0000000..6e20893
--- /dev/null
+++ b/organisms/stage/stage-v2/Homalodisca_vitripennis/trackList.json
@@ -0,0 +1,1335 @@
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+        "File provider": "Stephen Richards, Baylor College of Medicine",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Sex": "male"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "user_contributed_data/srichards/male-female/male_Nvit_RNAseq_alignments_accepted_hits_GCA_000696855.1.bam"
+    }
+  ]
+}
diff --git a/organisms/stage/stage-v2/Hyalella_azteca/trackList.json b/organisms/stage/stage-v2/Hyalella_azteca/trackList.json
new file mode 100644
index 0000000..f830f72
--- /dev/null
+++ b/organisms/stage/stage-v2/Hyalella_azteca/trackList.json
@@ -0,0 +1,98 @@
+{
+  "formatVersion": 1,
+  "names": {
+    "type": "Hash",
+    "url": "names/"
+  },
+  "tracks": [
+    {
+      "category": "Reference sequence",
+      "chunkSize": 20000,
+      "key": "Reference sequence",
+      "label": "DNA",
+      "seqType": "dna",
+      "storeClass": "JBrowse/Store/Sequence/StaticChunked",
+      "type": "SequenceTrack",
+      "urlTemplate": "seq/{refseq_dirpath}/{refseq}-"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Reference Assembly",
+      "key": "Gaps in assembly",
+      "label": "Gaps in assembly",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "white",
+        "pos_color": "black"
+      },
+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "bigwig/JQDR03.fsa.gaps.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "0.5",
+      "category": "Reference Assembly",
+      "key": "GC Content",
+      "label": "GC Content",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+      },
+      "scoreType": "avgScore",
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "rgba(255,255,0,50)",
+        "pos_color": "rgba(0,0,255,50)"
+      },
+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "bigwig/JQDR03.fsa.gc.bigwig"
+    },
+    {
+      "category": "Official Gene Set",
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+      "fmtDetailValue_Id": "function (id, feature) {  var name2 = id.replace(/-R./, '');  if(feature.get('type')=='mRNA') {    return '<a target=_blank href=https://i5k.nal.usda.gov/'+name2+'>'+id+'</a>';} else { return id;}}",
+      "key": "OGSv1.2 Gene",
+      "label": "hyaazt_current_models",
+      "menuTemplate": [
+        {
+          "label": "View details"
+        },
+        {
+          "action": "newWindow",
+          "iconClass": "dijitIconDatabase",
+          "label": "function(track,feature){ return 'Open gene page for '+feature.get('id').replace(/-R./, '')}",
+          "title": "function(track,feature){ return 'Open gene page for '+feature.get('id').replace(/-R./, '')}",
+          "url": "function(track,feature){ return 'https://i5k.nal.usda.gov/'+feature.get('id').replace(/-R./, '')}"
+        }
+      ],
+      "metadata": {
+        "Data provider": "Helen Poynton; Li-Mei Chiang; Monica Poelchau",
+        "Data source": "https://data.nal.usda.gov/dataset/hyalella-azteca-official-gene-set-v12",
+        "Materials and Methods": "The Hyalella azteca Official Gene Set v1.0, originally generated from assembly Hyalella azteca Genome Assembly 1.0 (10.15482/USDA.ADC/1415994) was lifted over to Hazt_2.0 using the NCBI's remap service, the CrossMap software (http://crossmap.sourceforge.net/), and remap_gff3 (https://github.com/NAL-i5K/remap-gff3). This resulted in the unreleased OGSv1.1. OGSv1.1 received additional QA/QC during NCBI submission, generating Hyalella azteca OGSv1.2.",
+        "Publication status": "Published, please cite https://doi.org/10.1021/acs.est.8b00837"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "description": "product, note, description",
+        "subfeatureClasses": {
+          "CDS": "gnomon_CDS",
+          "UTR": "gnomon_UTR",
+          "exon": "container-100pct",
+          "wholeCDS": null
+        }
+      },
+      "trackType": "HTMLFeatures",
+      "type": "HTMLFeatures",
+      "urlTemplate": "tracks/hyaazt_current_models/{refseq}/trackData.json"
+    }
+  ]
+}
diff --git a/organisms/stage/stage-v2/Ladona_fulva/trackList.json b/organisms/stage/stage-v2/Ladona_fulva/trackList.json
new file mode 100644
index 0000000..5002248
--- /dev/null
+++ b/organisms/stage/stage-v2/Ladona_fulva/trackList.json
@@ -0,0 +1,153 @@
+{
+   "formatVersion" : 1,
+   "names" : {
+      "type" : "Hash",
+      "url" : "names/"
+   },
+   "tracks" : [
+      {
+         "category" : "Reference sequence",
+         "chunkSize" : 20000,
+         "key" : "Reference sequence",
+         "label" : "DNA",
+         "seqType" : "dna",
+         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
+         "type" : "SequenceTrack",
+         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-"
+      },
+      {
+         "category" : "Official Gene Set",
+         "compress" : 0,
+         "key" : "Ladona fulva ladful_OGSv1.0 Gene",
+         "label" : "ladful_current_models",
+         "metadata" : {
+            "Data description" : "https://doi.org/10.15482/USDA.ADC/1520869",
+            "Data provider" : "National Agricultural Library",
+            "Data source" : "https://doi.org/10.15482/USDA.ADC/1520869",
+            "Method" : "https://doi.org/10.15482/USDA.ADC/1520869"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "menuTemplate" : [
+             {
+                "label" : "View details"
+             },
+             {
+              "label": "function(track,feature){ return 'Find gene page for '+feature.get('id')}",
+              "title": "function(track,feature){ return 'Find gene page for '+feature.get('id')}",
+              "iconClass" : "dijitIconDatabase",
+              "action": "newWindow",
+              "url" : "function(track,feature){ return 'https://i5k.nal.usda.gov/'+feature.get('id')}"
+              }
+        ],
+         "style" : {
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "container-16px",
+            "description" : "product, note, description",
+            "subfeatureClasses" : {
+               "CDS" : "gnomon_CDS",
+               "UTR" : "gnomon_UTR",
+               "exon" : "container-100pct",
+               "wholeCDS" : null
+            }
+         },
+         "trackType" : "HTMLFeatures",
+         "type" : "HTMLFeatures",
+         "urlTemplate" : "tracks/ladful_current_models/{refseq}/trackData.json"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Reference Assembly",
+         "key" : "Gaps in assembly",
+         "label" : "Gaps in assembly",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "white",
+            "pos_color" : "black"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/GCA_000376725.2_Lful_2.0_genomic.fna.gaps.bigwig"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "0.5",
+         "category" : "Reference Assembly",
+         "key" : "GC Content",
+         "label" : "GC Content",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+         },
+         "scoreType" : "avgScore",
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "rgba(255,255,0,50)",
+            "pos_color" : "rgba(0,0,255,50)"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/GCA_000376725.2_Lful_2.0_genomic.fna.gc.bigwig"
+      },
+      {
+         "category" : "RNA-Seq/Mapped Reads",
+         "key" : "Ladful_Lful_2.0_RNA-Seq-alignments_2021-10-05",
+         "label" : "Ladful_Lful_2.0_RNA-Seq-alignments_2021-10-05",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR1850403'>SRR1850403</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Dark red alignments: Mapped portion of read aligned to forward strand<br>Light red alignments: Spliced portion of read aligned to forward strand<br>Dark blue alignments: Mapped portion of read aligned to reverse strand<br>Light blue alignments: Spliced portion of read aligned to reverse strand<br>Red marking - deletion in the read relative to the reference<br>Green marking - insertion in the read relative to the reference<br>Yellow marking  - mismatch (hover over the mismatch to see what the snp is)"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "analyses/Ladona-fulva-RNA-Seq_2021-10-05_v1.0/Ladful_Lful_2.0_RNA-Seq-alignments_2021-10-05.bam"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "RNA-Seq/Coverage Plots",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR1850403'>SRR1850403</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage."
+         },
+         "key" : "Ladful_Lful_2.0_RNA-Seq-alignments_2021-10-05_coverage",
+         "label" : "Ladful_Lful_2.0_RNA-Seq-alignments_2021-10-05_coverage",
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "analyses/Ladona-fulva-RNA-Seq_2021-10-05_v1.0/Ladful_Lful_2.0_RNA-Seq-alignments_2021-10-05.bigwig"
+      },
+      {
+         "category" : "RNA-Seq/Splice junctions",
+         "compress" : 0,
+         "key" : "Ladful_Lful_2.0_RNA-Seq-alignments_2021-10-05_junctions",
+         "label" : "Ladful_Lful_2.0_RNA-Seq-alignments_2021-10-05_junctions",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR1850403'>SRR1850403</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Junction reads generated by Hisat2 aligner and regtools. The number of alignments supporting the junction read is listed in blue."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+	     "description":"score",
+            "className" : "feature"
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/Ladful_Lful_2.0_RNA-Seq-alignments_2021-10-05_junctions/{refseq}/trackData.json"
+      }
+   ]
+}
diff --git a/organisms/stage/stage-v2/Laodelphax_striatellus/trackList.json b/organisms/stage/stage-v2/Laodelphax_striatellus/trackList.json
new file mode 100755
index 0000000..a8a124e
--- /dev/null
+++ b/organisms/stage/stage-v2/Laodelphax_striatellus/trackList.json
@@ -0,0 +1,162 @@
+{
+  "formatVersion": 1,
+  "names": {
+    "type": "Hash",
+    "url": "names/"
+  },
+  "refSeqs": "seq/GCA_003335185.2_ASM333518v2_genomic.fna.fai",
+  "tracks": [
+    {
+      "category": "Reference sequence",
+      "chunkSize": 20000,
+      "key": "Reference sequence",
+      "label": "DNA",
+      "seqType": "dna",
+      "storeClass": "JBrowse/Store/Sequence/StaticChunked",
+      "type": "SequenceTrack",
+      "urlTemplate": "seq/{refseq_dirpath}/{refseq}-"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Reference Assembly",
+      "key": "Gaps in assembly",
+      "label": "Gaps in assembly",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "white",
+        "pos_color": "black"
+      },
+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "bigwig/GCA_003335185.2_ASM333518v2_genomic.fna.gaps.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "0.5",
+      "category": "Reference Assembly",
+      "key": "GC Content",
+      "label": "GC Content",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+      },
+      "scoreType": "avgScore",
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "rgba(255,255,0,50)",
+        "pos_color": "rgba(0,0,255,50)"
+      },
+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "bigwig/GCA_003335185.2_ASM333518v2_genomic.fna.gc.bigwig"
+    },
+    {
+      "category": "DNA-Seq/Variant Information",
+      "key": "ASM333518v2-variant-alignment_v1.1_4-5-2019",
+      "label": "ASM333518v2-variant-alignment_v1.1_4-5-2019",
+      "metadata": {
+        "Data provider": "Junjie Zhu, Chinese Academy of Sciences",
+        "Data source": "http://dx.doi.org/10.5524/100361",
+        "Materials and Methods": "http://dx.doi.org/10.5524/100361",
+        "Publication status": "Published, please cite http://dx.doi.org/10.5524/100361 and https://doi:10.1093/gigascience/gix109"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/VCFTabix",
+      "type": "JBrowse/View/Track/HTMLVariants",
+      "urlTemplate": "ASM333518v2-variant-alignment_v1.1_4-5-2019/ASM333518v2-variant-alignment_v1.1_4-5-2019.vcf.gz"
+    },
+    {
+      "category": "Official Gene Set",
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+      "fmtDetailValue_Id": "function (id, feature) {  var name2 = id.replace(/-R./, '');  if(feature.get('type')=='mRNA') {    return '<a target=_blank href=https://i5k.nal.usda.gov/'+name2+'>'+id+'</a>';} else { return id;}}",
+      "key": "laostr_OGSv1.2 gene",
+      "label": "laostr_current_models",
+      "menuTemplate": [
+        {
+          "label": "View details"
+        },
+        {
+          "action": "newWindow",
+          "iconClass": "dijitIconDatabase",
+          "label": "function(track,feature){ return 'Open gene page for '+feature.get('id').replace(/-R./, '')}",
+          "title": "function(track,feature){ return 'Open gene page for '+feature.get('id').replace(/-R./, '')}",
+          "url": "function(track,feature){ return 'https://i5k.nal.usda.gov/'+feature.get('id').replace(/-R./, '')}"
+        }
+      ],
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+        "Data provider": "Junjie Zhu, Chinese Academy of Sciences",
+        "Data source": "http://dx.doi.org/10.5524/100361",
+        "Materials and Methods": "http://dx.doi.org/10.5524/100361",
+        "Publication status": "Published, please cite http://dx.doi.org/10.5524/100361 and https://doi:10.1093/gigascience/gix109"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "description": "product, note, description",
+        "subfeatureClasses": {
+          "CDS": "gnomon_CDS",
+          "UTR": "gnomon_UTR",
+          "exon": "container-100pct",
+          "wholeCDS": null
+        }
+      },
+      "trackType": "HTMLFeatures",
+      "type": "HTMLFeatures",
+      "urlTemplate": "tracks/laostr_current_models/{refseq}/trackData.json"
+    },
+    {
+      "category": "Official Gene Set",
+      "compress": 0,
+      "key": "laostr_OGS_v1.2 pseudogene",
+      "label": "laostr_OGS_v1.2_pseudogene",
+      "metadata": {
+        "Data provider": "Junjie Zhu, Chinese Academy of Sciences",
+        "Data source": "http://dx.doi.org/10.5524/100361",
+        "Materials and Methods": "http://dx.doi.org/10.5524/100361",
+        "Publication status": "Published, please cite http://dx.doi.org/10.5524/100361 and https://doi:10.1093/gigascience/gix109"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "description": "product, note, description",
+        "subfeatureClasses": {
+          "CDS": "gnomon_CDS",
+          "UTR": "gnomon_UTR",
+          "exon": "container-100pct",
+          "wholeCDS": null
+        }
+      },
+      "trackType": "HTMLFeatures",
+      "type": "HTMLFeatures",
+      "urlTemplate": "tracks/laostr_OGS_v1.2_pseudogene/{refseq}/trackData.json"
+    },
+    {
+      "category": "Sequence composition calculation/RepeatMasker",
+      "compress": 0,
+      "key": "ASM333518v2_Laodelphax_striatellus.RepeatMasker_v1.1_4-5-2019",
+      "label": "ASM333518v2_Laodelphax_striatellus.RepeatMasker_v1.1_4-5-2019",
+      "metadata": {
+        "Data provider": "Junjie Zhu, Chinese Academy of Sciences",
+        "Data source": "http://dx.doi.org/10.5524/100361",
+        "Materials and Methods": "http://dx.doi.org/10.5524/100361",
+        "Publication status": "Published, please cite http://dx.doi.org/10.5524/100361 and https://doi:10.1093/gigascience/gix109"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "feature",
+        "description": "target",
+        "renderClassName": "repeat"
+      },
+      "trackType": "HTMLFeatures",
+      "type": "HTMLFeatures",
+      "urlTemplate": "tracks/ASM333518v2_Laodelphax_striatellus.RepeatMasker_v1.1_4-5-2019/{refseq}/trackData.json"
+    }
+  ]
+}
diff --git a/organisms/stage/stage-v2/Lasioglossum_albipes/trackList.json b/organisms/stage/stage-v2/Lasioglossum_albipes/trackList.json
new file mode 100644
index 0000000..ec5c3db
--- /dev/null
+++ b/organisms/stage/stage-v2/Lasioglossum_albipes/trackList.json
@@ -0,0 +1,164 @@
+{
+  "alwaysOnTracks": "DNA,Annotations",
+  "css": "./plugins/NAL_CSS/css/main.css",
+  "favicon": "./plugins/WebApollo/img/webapollo_favicon.ico",
+  "formatVersion": 1,
+  "names": {
+    "type": "Hash",
+    "url": "names/"
+  },
+  "share_link": 0,
+  "tracks": [
+    {
+      "category": "Reference sequence",
+      "chunkSize": 20000,
+      "key": "Reference sequence",
+      "label": "DNA",
+      "storeClass": "JBrowse/Store/Sequence/StaticChunked",
+      "type": "SequenceTrack",
+      "urlTemplate": "seq/{refseq_dirpath}/{refseq}-"
+    },
+    {
+      "autocomplete": "none",
+      "compress": 0,
+      "key": "User-created Annotations",
+      "label": "Annotations",
+      "phase": 0,
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+        {
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+          "iconClass": "dijitIconDatabase",
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+          "title": "function(track,feature){ return 'Search HymenopteraMine for '+feature.get('id')}",
+          "url": "function(track,feature){ return 'http://128.206.116.3:8080/hymenopteramine/keywordSearchResults.do?searchTerm='+feature.get('id')+'&searchSubmit=Search'}"
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+      ],
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+        "Method": "For full methods, see the associated publication, PMID 24359881",
+        "Other notes": "The original file was transformed to GenBank coordinates by the NAL. Several gene models predicted on the original assembly were lost during the coordinate transformation due to changes in the assembly."
+      },
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+}
diff --git a/organisms/stage/stage-v2/Latrodectus_hesperus/trackList.json b/organisms/stage/stage-v2/Latrodectus_hesperus/trackList.json
new file mode 100755
index 0000000..b72b172
--- /dev/null
+++ b/organisms/stage/stage-v2/Latrodectus_hesperus/trackList.json
@@ -0,0 +1,1211 @@
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diff --git a/organisms/stage/stage-v2/Leptinotarsa_decemlineata/trackList.json b/organisms/stage/stage-v2/Leptinotarsa_decemlineata/trackList.json
new file mode 100644
index 0000000..cc7fc2c
--- /dev/null
+++ b/organisms/stage/stage-v2/Leptinotarsa_decemlineata/trackList.json
@@ -0,0 +1,512 @@
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diff --git a/organisms/stage/stage-v2/Leptinotarsa_decemlineata_training/trackList.json b/organisms/stage/stage-v2/Leptinotarsa_decemlineata_training/trackList.json
new file mode 100644
index 0000000..9edadf2
--- /dev/null
+++ b/organisms/stage/stage-v2/Leptinotarsa_decemlineata_training/trackList.json
@@ -0,0 +1,1715 @@
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+        "Track legend": "Results from Protein2genome alignments of a set of Cephalochordata proteins as part of the MAKER automated annotation pipeline."
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+        "Track legend": "Results from Protein2genome alignments of a set of Chelicerata proteins as part of the MAKER automated annotation pipeline."
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+        "Track legend": "Results from Protein2genome alignments of a set of Cnidaria proteins as part of the MAKER automated annotation pipeline."
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+        "Track legend": "Results from Protein2genome alignments of a set of Crustacea proteins as part of the MAKER automated annotation pipeline."
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+        "Track legend": "Results from Protein2genome alignments of a set of Echinodermata proteins as part of the MAKER automated annotation pipeline."
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+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
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+      "label": "protein2genome_Nemata",
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+      "key": "protein2genome_Nematomorpha",
+      "label": "protein2genome_Nematomorpha",
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+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
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+        "Track legend": "Results from Protein2genome alignments of a set of Nematomorpha proteins as part of the MAKER automated annotation pipeline."
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+        "arrowheadClass": "webapollo-arrowhead",
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+          "match_part": "protein2genome"
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+      "urlTemplate": "tracks/protein2genome_Nematomorpha/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+      "key": "protein2genome_Onychophora",
+      "label": "protein2genome_Onychophora",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
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+        "arrowheadClass": "webapollo-arrowhead",
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+    },
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+      "key": "protein2genome_Parazoa",
+      "label": "protein2genome_Parazoa",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
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+        "Track legend": "Results from Protein2genome alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline."
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+      "key": "protein2genome_Placozoa",
+      "label": "protein2genome_Placozoa",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline."
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+        "arrowheadClass": "webapollo-arrowhead",
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+      "urlTemplate": "tracks/protein2genome_Placozoa/{refseq}/trackData.json"
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+      "key": "protein2genome_Platyhelminthes",
+      "label": "protein2genome_Platyhelminthes",
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+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline."
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+    },
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+      "key": "protein2genome_Priapulida",
+      "label": "protein2genome_Priapulida",
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+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline."
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+      "key": "protein2genome_Tardigrada",
+      "label": "protein2genome_Tardigrada",
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+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline."
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+      "key": "protein2genome_Tunicata",
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+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline."
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+      "key": "protein2genome_UNCATEGORISED",
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+        "Track legend": "Results from Protein2genome alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline."
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+      "key": "repeatmasker",
+      "label": "repeatmasker",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from RepeatMasker as part of the MAKER automated annotation pipeline."
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+      "key": "repeatrunner",
+      "label": "repeatrunner",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Repeatrunner as part of the MAKER automated annotation pipeline."
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+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
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+        "arrowheadClass": "webapollo-arrowhead",
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+      "key": "snap_masked",
+      "label": "snap_masked",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
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diff --git a/organisms/stage/stage-v2/Limnephilus_lunatus/trackList.json b/organisms/stage/stage-v2/Limnephilus_lunatus/trackList.json
new file mode 100644
index 0000000..3c75026
--- /dev/null
+++ b/organisms/stage/stage-v2/Limnephilus_lunatus/trackList.json
@@ -0,0 +1,1244 @@
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diff --git a/organisms/stage/stage-v2/Locusta_migratoria/trackList.json b/organisms/stage/stage-v2/Locusta_migratoria/trackList.json
new file mode 100644
index 0000000..d54fd3c
--- /dev/null
+++ b/organisms/stage/stage-v2/Locusta_migratoria/trackList.json
@@ -0,0 +1,199 @@
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new file mode 100644
index 0000000..5d4419d
--- /dev/null
+++ b/organisms/stage/stage-v2/Loxosceles_reclusa/trackList.json
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+    {
+      "category": "BCM_v0.5.3/2. Evidence/Repeats",
+      "compress": 0,
+      "key": "repeatrunner",
+      "label": "repeatrunner",
+      "metadata": {
+        "Data description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Data provider": "Daniel Hughes, Baylor College of Medicine",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Repeatrunner as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "repeat"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/repeatrunner/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/1. Gene Sets/Supplementary Gene Predictions",
+      "compress": 0,
+      "key": "SNAP gene predictions",
+      "label": "snap_masked",
+      "metadata": {
+        "Data description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Data provider": "Daniel Hughes, Baylor College of Medicine",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "snap"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/snap_masked/{refseq}/trackData.json"
+    },
+    {
+      "autocomplete": "none",
+      "compress": 0,
+      "key": "User-created Annotations",
+      "label": "Annotations",
+      "phase": 0,
+      "storeClass": "WebApollo/Store/SeqFeature/ScratchPad",
+      "style": {
+        "alternateClasses": {
+          "miRNA": {
+            "className": "brightgreen-80pct",
+            "renderClassName": "gray-center-30pct"
+          },
+          "ncRNA": {
+            "className": "brightgreen-80pct",
+            "renderClassName": "gray-center-30pct"
+          },
+          "pseudogene": {
+            "className": "light-purple-80pct",
+            "renderClassName": "gray-center-30pct"
+          },
+          "rRNA": {
+            "className": "brightgreen-80pct",
+            "renderClassName": "gray-center-30pct"
+          },
+          "repeat_region": {
+            "className": "magenta-80pct"
+          },
+          "snRNA": {
+            "className": "brightgreen-80pct",
+            "renderClassName": "gray-center-30pct"
+          },
+          "snoRNA": {
+            "className": "brightgreen-80pct",
+            "renderClassName": "gray-center-30pct"
+          },
+          "tRNA": {
+            "className": "brightgreen-80pct",
+            "renderClassName": "gray-center-30pct"
+          },
+          "transposable_element": {
+            "className": "blue-ibeam",
+            "renderClassName": "blue-ibeam-render"
+          }
+        },
+        "arrowheadClass": "annot-arrowhead",
+        "centerSubFeature": {
+          "non_canonical_five_prime_splice_site": false,
+          "non_canonical_three_prime_splice_site": false
+        },
+        "className": "annot",
+        "renderClassName": "annot-render",
+        "subfeatureClasses": {
+          "CDS": "annot-CDS",
+          "UTR": "annot-UTR",
+          "exon": "container-100pct",
+          "non_canonical_five_prime_splice_site": "noncanonical-splice-site",
+          "non_canonical_three_prime_splice_site": "noncanonical-splice-site",
+          "wholeCDS": null
+        },
+        "uniqueIdField": "id"
+      },
+      "subfeatures": 1,
+      "type": "WebApollo/View/Track/AnnotTrack"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Reference Assembly",
+      "key": "Gaps in assembly",
+      "label": "Gaps in assembly",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "white",
+        "pos_color": "black"
+      },
+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "bigwig/GCA_001188405.1_Lrec_1.0_genomic.fna.gaps.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "0.5",
+      "category": "Reference Assembly",
+      "key": "GC Content",
+      "label": "GC Content",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+      },
+      "scoreType": "avgScore",
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "rgba(255,255,0,50)",
+        "pos_color": "rgba(0,0,255,50)"
+      },
+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "bigwig/GCA_001188405.1_Lrec_1.0_genomic.fna.gc.bigwig"
+    }
+  ]
+}
diff --git a/organisms/stage/stage-v2/Lucilia_sericata/trackList.json b/organisms/stage/stage-v2/Lucilia_sericata/trackList.json
new file mode 100644
index 0000000..c60ddee
--- /dev/null
+++ b/organisms/stage/stage-v2/Lucilia_sericata/trackList.json
@@ -0,0 +1,154 @@
+{
+   "formatVersion" : 1,
+   "names" : {
+      "type" : "Hash",
+      "url" : "names/"
+   },
+   "tracks" : [
+      {
+         "category" : "Reference sequence",
+         "chunkSize" : 20000,
+         "key" : "Reference sequence",
+         "label" : "DNA",
+         "seqType" : "dna",
+         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
+         "type" : "SequenceTrack",
+         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-"
+      },
+      {
+         "category" : "NCBI Annotation Release 100",
+         "compress" : 0,
+         "key" : "NCBI_Annotation_Release_100_Gene",
+         "label" : "lucser_current_models",
+         "menuTemplate" : [
+            {
+               "label" : "View details"
+            },
+            {
+               "action" : "newWindow",
+               "iconClass" : "dijitIconDatabase",
+               "label" : "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
+               "title" : "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
+               "url" : "function(track,feature){ return 'https://i5k.nal.usda.gov/'+feature.get('name')}"
+            }
+         ],
+         "metadata" : {
+            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Lucilia_sericata/README_CURRENT_RELEASE",
+            "Data provider" : "NCBI",
+            "Data source" : "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/015/586/225/GCF_015586225.1_ASM1558622v1/GCF_015586225.1_ASM1558622v1_genomic.gff.gz",
+            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "container-16px",
+            "description" : "product, note, description",
+            "subfeatureClasses" : {
+               "CDS" : "gnomon_CDS",
+               "UTR" : "gnomon_UTR",
+               "exon" : "container-100pct",
+               "wholeCDS" : null
+            }
+         },
+         "trackType" : "HTMLFeatures",
+         "type" : "HTMLFeatures",
+         "urlTemplate" : "tracks/lucser_current_models/{refseq}/trackData.json"
+      },
+      {
+         "category" : "NCBI Annotation Release 100",
+         "compress" : 0,
+         "key" : "NCBI_Annotation_Release_100_Pseudogene",
+         "label" : "NCBI_Annotation_Release_100_Pseudogene",
+         "metadata" : {
+            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Lucilia_sericata/README_CURRENT_RELEASE",
+            "Data provider" : "NCBI",
+            "Data source" : "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/015/586/225/GCF_015586225.1_ASM1558622v1/GCF_015586225.1_ASM1558622v1_genomic.gff.gz",
+            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "container-16px",
+            "description" : "product, note, description",
+            "subfeatureClasses" : {
+               "CDS" : "gnomon_CDS",
+               "UTR" : "gnomon_UTR",
+               "exon" : "container-100pct",
+               "wholeCDS" : null
+            }
+         },
+         "trackType" : "HTMLFeatures",
+         "type" : "HTMLFeatures",
+         "urlTemplate" : "tracks/NCBI_Annotation_Release_100_Pseudogene/{refseq}/trackData.json"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "0.5",
+         "category" : "Reference Assembly",
+         "key" : "GC Content",
+         "label" : "GC Content",
+         "metadata" : {
+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+            "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+         },
+         "scoreType" : "avgScore",
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "neg_color" : "rgba(255,255,0,50)",
+            "pos_color" : "rgba(0,0,255,50)"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/Density",
+         "urlTemplate" : "bigwig/GCF_015586225.1_ASM1558622v1_genomic.fna.gc.bigwig"
+      },
+      {
+         "category" : "RNA-Seq/Mapped Reads",
+         "key" : "Lucser_ASM1558622v1_RNA-Seq-alignments_2021-08-11",
+         "label" : "Lucser_ASM1558622v1_RNA-Seq-alignments_2021-08-11",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR14883001'>SRR14883001</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11814677'>SRR11814677</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR14883004'>SRR14883004</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11814669'>SRR11814669</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR14882999'>SRR14882999</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR350015'>SRR350015</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR14882997'>SRR14882997</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=ERR658157'>ERR658157</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11814676'>SRR11814676</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR14882996'>SRR14882996</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Dark red alignments: Mapped portion of read aligned to forward strand<br>Light red alignments: Spliced portion of read aligned to forward strand<br>Dark blue alignments: Mapped portion of read aligned to reverse strand<br>Light blue alignments: Spliced portion of read aligned to reverse strand<br>Red marking - deletion in the read relative to the reference<br>Green marking - insertion in the read relative to the reference<br>Yellow marking  - mismatch (hover over the mismatch to see what the snp is)"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "analyses/Lucilia-sericata-RNA-Seq_2021-08-11_v1.0/Lucser_ASM1558622v1_RNA-Seq-alignments_2021-08-11.bam"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "RNA-Seq/Coverage Plots",
+         "key" : "Lucser_ASM1558622v1_RNA-Seq-alignments_2021-08-11_coverage",
+         "label" : "Lucser_ASM1558622v1_RNA-Seq-alignments_2021-08-11_coverage",
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "analyses/Lucilia-sericata-RNA-Seq_2021-08-11_v1.0/Lucser_ASM1558622v1_RNA-Seq-alignments_2021-08-11.bigwig"
+      },
+      {
+         "category" : "RNA-Seq/Splice junctions",
+         "compress" : 0,
+         "key" : "Lucser_ASM1558622v1_RNA-Seq-alignments_2021-08-11_junctions",
+         "label" : "Lucser_ASM1558622v1_RNA-Seq-alignments_2021-08-11_junctions",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR14883001'>SRR14883001</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11814677'>SRR11814677</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR14883004'>SRR14883004</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11814669'>SRR11814669</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR14882999'>SRR14882999</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR350015'>SRR350015</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR14882997'>SRR14882997</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=ERR658157'>ERR658157</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11814676'>SRR11814676</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR14882996'>SRR14882996</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Junction reads generated by Hisat2 aligner and regtools. The number of alignments supporting the junction read is listed in blue."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "className" : "feature",
+	    "description" : "score"
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/Lucser_ASM1558622v1_RNA-Seq-alignments_2021-08-11_junctions/{refseq}/trackData.json"
+      }
+   ]
+}
diff --git a/organisms/stage/stage-v2/Mamestra_configurata/trackList.json b/organisms/stage/stage-v2/Mamestra_configurata/trackList.json
new file mode 100644
index 0000000..2420965
--- /dev/null
+++ b/organisms/stage/stage-v2/Mamestra_configurata/trackList.json
@@ -0,0 +1,163 @@
+{
+  "formatVersion": 1,
+  "names": {
+    "type": "Hash",
+    "url": "names/"
+  },
+  "tracks": [
+    {
+      "category": "Reference sequence",
+      "faiUrlTemplate": "seq/GCA_002192655.1_ASM219265v1_genomic.fna.fai",
+      "key": "Reference sequence",
+      "label": "DNA",
+      "seqType": "dna",
+      "storeClass": "JBrowse/Store/Sequence/IndexedFasta",
+      "type": "SequenceTrack",
+      "urlTemplate": "seq/GCA_002192655.1_ASM219265v1_genomic.fna",
+      "useAsRefSeqStore": 1
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Reference Assembly",
+      "key": "Gaps in assembly",
+      "label": "Gaps in assembly",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "white",
+        "pos_color": "black"
+      },
+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "bigwig/GCA_002192655.1_ASM219265v1_genomic.fna.gaps.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "0.5",
+      "category": "Reference Assembly",
+      "key": "GC Content",
+      "label": "GC Content",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+      },
+      "scoreType": "avgScore",
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "rgba(255,255,0,50)",
+        "pos_color": "rgba(0,0,255,50)"
+      },
+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "bigwig/GCA_002192655.1_ASM219265v1_genomic.fna.gc.bigwig"
+    },
+    {
+      "category": "5. Transcriptome/Mapped Reads",
+      "histograms": {
+        "color": "#00BFFF",
+        "height": 75,
+        "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+        "urlTemplate": "bigwig/BAW_454_and_Sanger.bw"
+      },
+      "key": "long_read_RNA_mapped_to_genome",
+      "label": "long_read_RNA_mapped_to_genome",
+      "metadata": {
+        "Alignment method": "CLC genomics workbench",
+        "Data Provider": "Cathy Coutu",
+        "Geographic location (latitude and longitude)": "52.133560, -106.635252",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Read cleaning method": "None",
+        "Sequencing method": "illumina",
+        "Tissues/Life stage included": "larval midgut and adult head",
+        "Track legend": "Blue glyphs represent reads mapped to the forward strand, and red glyphs represent reads mapped to the reverse strand. If a read is discontinuously mapped (e.g. representing a splice junction), mapped segments are connected with a thinner black line. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "bam/BAW_454_and_Sanger.bam"
+    },
+    {
+      "category": "5. Transcriptome/Mapped Reads",
+      "featureScale": 0.005,
+      "histograms": {
+        "color": "#00BFFF",
+        "height": 75,
+        "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+        "urlTemplate": "bigwig/merged.reduced-coverage-RGmod.bw"
+      },
+      "key": "Short_read_RNA_mapped_to_genome",
+      "label": "Short_read_RNA_mapped_to_genome",
+      "maxFeatureScreenDensity": 0.08,
+      "metadata": {
+        "Alignment method": "CLC genomics workbench Version 10",
+        "Data provider": "Cathy Coutu",
+        "Geographic location (latitude and longitude)": "52.133560, -106.635252",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Sequencing method": "illumina",
+        "Tissues/Life stage included": "larval midgut and adult head",
+        "Track legend": "Blue glyphs represent reads mapped to the forward strand, and red glyphs represent reads mapped to the reverse strand. If a read is discontinuously mapped (e.g. representing a splice junction), mapped segments are connected with a thinner black line. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "bam/merged.reduced-coverage-RGmod.bam"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "5. Transcriptome/Coverage Plots (BigWig)",
+      "key": "long_read_RNA_mapped_to_genome_coverage",
+      "label": "long_read_RNA_mapped_to_genome_coverage",
+      "metadata": {
+        "Alignment method": "CLC genomics workbench",
+        "Data Provider": "Cathy Coutu",
+        "Geographic location (latitude and longitude)": "52.133560, -106.635252",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Read cleaning method": "None",
+        "Sequencing method": "illumina",
+        "Tissues/Life stage included": "larval midgut and adult head",
+        "Track legend": "This track represents an X-Y plot of RNA-Seq coverage."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "clip_marker_color": "red",
+        "height": 50,
+        "neg_color": "#005EFF",
+        "origin_color": "#888",
+        "pos_color": "#FFA600",
+        "variance_band_color": "rgba(0,0,0,0.3)"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "bigwig/BAW_454_and_Sanger.bw"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "5. Transcriptome/Coverage Plots (BigWig)",
+      "key": "Short_read_RNA_mapped_to_genome_coverage",
+      "label": "Short_read_RNA_mapped_to_genome_coverage",
+      "metadata": {
+        "Alignment method": "CLC genomics workbench Version 10",
+        "Data provider": "Cathy Coutu",
+        "Geographic location (latitude and longitude)": "52.133560, -106.635252",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Sequencing method": "illumina",
+        "Tissues/Life stage included": "larval midgut and adult head",
+        "Track legend": "This track represents an X-Y plot of RNA-Seq coverage."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "clip_marker_color": "red",
+        "height": 50,
+        "neg_color": "#005EFF",
+        "origin_color": "#888",
+        "pos_color": "#FFA600",
+        "variance_band_color": "rgba(0,0,0,0.3)"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "bigwig/merged.reduced-coverage-RGmod.bw"
+    }
+  ]
+}
diff --git a/organisms/stage/stage-v2/Manduca_sexta/trackList.json b/organisms/stage/stage-v2/Manduca_sexta/trackList.json
new file mode 100644
index 0000000..291adbc
--- /dev/null
+++ b/organisms/stage/stage-v2/Manduca_sexta/trackList.json
@@ -0,0 +1,207 @@
+{
+  "formatVersion": 1,
+  "names": {
+    "type": "Hash",
+    "url": "names/"
+  },
+  "tracks": [
+    {
+      "category": "Reference sequence",
+      "chunkSize": 20000,
+      "key": "Reference sequence",
+      "label": "DNA",
+      "seqType": "dna",
+      "storeClass": "JBrowse/Store/Sequence/StaticChunked",
+      "type": "SequenceTrack",
+      "urlTemplate": "seq/{refseq_dirpath}/{refseq}-"
+    },
+    {
+      "category": "NCBI Annotation Release 102",
+      "compress": 0,
+      "key": "NCBI_Annotation_Release_102_Pseudogene",
+      "label": "NCBI_Annotation_Release_102_Pseudogene",
+      "metadata": {
+        "Data description": "ftp://ftp.ncbi.nlm.nih.gov/genomes/Manduca_sexta/README_CURRENT_RELEASE",
+        "Data provider": "NCBI",
+        "Data source": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/014/839/805/GCF_014839805.1_JHU_Msex_v1.0/GCF_014839805.1_JHU_Msex_v1.0_genomic.gff.gz",
+        "Method": "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "description": "product, note, description",
+        "subfeatureClasses": {
+          "CDS": "gnomon_CDS",
+          "UTR": "gnomon_UTR",
+          "exon": "container-100pct",
+          "wholeCDS": null
+        }
+      },
+      "trackType": "HTMLFeatures",
+      "type": "HTMLFeatures",
+      "urlTemplate": "tracks/NCBI_Annotation_Release_102_Pseudogene/{refseq}/trackData.json"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Reference Assembly",
+      "key": "Gaps in assembly",
+      "label": "Gaps in assembly",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "white",
+        "pos_color": "black"
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+      "urlTemplate": "bigwig/GCF_014839805.1_JHU_Msex_v1.0_genomic.fna.gaps.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "0.5",
+      "category": "Reference Assembly",
+      "key": "GC Content",
+      "label": "GC Content",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+      },
+      "scoreType": "avgScore",
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "rgba(255,255,0,50)",
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+      "urlTemplate": "bigwig/GCF_014839805.1_JHU_Msex_v1.0_genomic.fna.gc.bigwig"
+    },
+    {
+      "category": "Official Gene Set",
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+      "label": "OGSv2.2_Gene",
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+        "Publication status": "Published, please cite https://doi.org/10.1016/j.ibmb.2016.07.005",
+        "Track legend": "Consensus gene models from the PASA2 program, lifted over to assembly JHU_Msex_v1.0."
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+          "exon": "container-100pct",
+          "wholeCDS": null
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+      "trackType": "HTMLFeatures",
+      "type": "HTMLFeatures",
+      "urlTemplate": "tracks/OGSv2.2_Gene/{refseq}/trackData.json"
+    },
+    {
+      "category": "RNA-Seq/Mapped Reads",
+      "key": "Mansex_JHU_Msex_v1.0_RNA-Seq-alignments_2021-05-13",
+      "label": "Mansex_JHU_Msex_v1.0_RNA-Seq-alignments_2021-05-13",
+      "metadata": {
+        "Analysis method": "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+        "Analysis provider": "i5k Workspace@NAL",
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+        "Publication status": "Analysis: NA; Source data: see individual SRA accessions",
+        "Track legend": "Dark red alignments: Mapped portion of read aligned to forward strand<br>Light red alignments: Spliced portion of read aligned to forward strand<br>Dark blue alignments: Mapped portion of read aligned to reverse strand<br>Light blue alignments: Spliced portion of read aligned to reverse strand<br>Red marking - deletion in the read relative to the reference<br>Green marking - insertion in the read relative to the reference<br>Yellow marking  - mismatch (hover over the mismatch to see what the snp is)"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "analyses/Manduca-sexta-RNA-Seq_2021-05-13_v1.0/Mansex_JHU_Msex_v1.0_RNA-Seq-alignments_2021-05-13.bam"
+    },
+    {
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+      "bicolor_pivot": "zero",
+      "category": "RNA-Seq/Coverage Plots",
+      "key": "Mansex_JHU_Msex_v1.0_RNA-Seq-alignments_2021-05-13_coverage",
+      "label": "Mansex_JHU_Msex_v1.0_RNA-Seq-alignments_2021-05-13_coverage",
+      "metadata": {
+        "Analysis method": "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+        "Analysis provider": "i5k Workspace@NAL",
+        "Data source": "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11085711'>SRR11085711</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR10963231'>SRR10963231</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR2660035'>SRR2660035</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11085686'>SRR11085686</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR3467224'>SRR3467224</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11085604'>SRR11085604</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11085618'>SRR11085618</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR1577021'>SRR1577021</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR10963211'>SRR10963211</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR2659997'>SRR2659997</a>",
+        "Publication status": "Analysis: NA; Source data: see individual SRA accessions",
+        "Track legend": "This track represents an X-Y plot of RNA-Seq coverage."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "pos_color": "#00BFFF"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "analyses/Manduca-sexta-RNA-Seq_2021-05-13_v1.0/Mansex_JHU_Msex_v1.0_RNA-Seq-alignments_2021-05-13.bigwig"
+    },
+    {
+      "category": "RNA-Seq/Splice junctions",
+      "compress": 0,
+      "key": "Mansex_JHU_Msex_v1.0_RNA-Seq-alignments_2021-05-13_junctions",
+      "label": "Mansex_JHU_Msex_v1.0_RNA-Seq-alignments_2021-05-13_junctions",
+      "metadata": {
+        "Analysis method": "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+        "Analysis provider": "i5k Workspace@NAL",
+        "Data source": "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11085711'>SRR11085711</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR10963231'>SRR10963231</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR2660035'>SRR2660035</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11085686'>SRR11085686</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR3467224'>SRR3467224</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11085604'>SRR11085604</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR11085618'>SRR11085618</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR1577021'>SRR1577021</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR10963211'>SRR10963211</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR2659997'>SRR2659997</a>",
+        "Publication status": "Analysis: NA; Source data: see individual SRA accessions",
+        "Track legend": "Junction reads generated by Hisat2 aligner and regtools"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "className": "feature",
+        "description": "score"
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/Mansex_JHU_Msex_v1.0_RNA-Seq-alignments_2021-05-13_junctions/{refseq}/trackData.json"
+    },
+    {
+      "category": "NCBI Annotation Release 102",
+      "compress": 0,
+      "key": "NCBI_Annotation_Release_102_Gene",
+      "label": "mansex_current_models",
+      "menuTemplate": [
+        {
+          "label": "View details"
+        },
+        {
+          "action": "newWindow",
+          "iconClass": "dijitIconDatabase",
+          "label": "function(track,feature){ return 'Find gene page for '+feature.get('id')}",
+          "title": "function(track,feature){ return 'Find gene page for '+feature.get('id')}",
+          "url": "function(track,feature){ return 'https://i5k.nal.usda.gov/'+feature.get('id')}"
+        }
+      ],
+      "metadata": {
+        "Data description": "ftp://ftp.ncbi.nlm.nih.gov/genomes/Manduca_sexta/README_CURRENT_RELEASE",
+        "Data provider": "NCBI",
+        "Data source": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/014/839/805/GCF_014839805.1_JHU_Msex_v1.0/GCF_014839805.1_JHU_Msex_v1.0_genomic.gff.gz",
+        "Method": "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "description": "product, note, description",
+        "subfeatureClasses": {
+          "CDS": "gnomon_CDS",
+          "UTR": "gnomon_UTR",
+          "exon": "container-100pct",
+          "wholeCDS": null
+        }
+      },
+      "trackType": "HTMLFeatures",
+      "type": "HTMLFeatures",
+      "urlTemplate": "tracks/mansex_current_models/{refseq}/trackData.json"
+    }
+  ]
+}
diff --git a/organisms/stage/stage-v2/Mayetiola_destructor/trackList.json b/organisms/stage/stage-v2/Mayetiola_destructor/trackList.json
new file mode 100644
index 0000000..78e6f97
--- /dev/null
+++ b/organisms/stage/stage-v2/Mayetiola_destructor/trackList.json
@@ -0,0 +1,361 @@
+{
+  "alwaysOnTracks": "DNA,Annotations",
+  "favicon": "./plugins/WebApollo/img/webapollo_favicon.ico",
+  "formatVersion": 1,
+  "names": {
+    "type": "Hash",
+    "url": "names/"
+  },
+  "share_link": 0,
+  "tracks": [
+    {
+      "category": "Reference sequence",
+      "chunkSize": 20000,
+      "key": "Reference sequence",
+      "label": "DNA",
+      "storeClass": "JBrowse/Store/Sequence/StaticChunked",
+      "type": "SequenceTrack",
+      "urlTemplate": "seq/{refseq_dirpath}/{refseq}-"
+    },
+    {
+      "autocomplete": "none",
+      "compress": 0,
+      "key": "User-created Annotations",
+      "label": "Annotations",
+      "phase": 0,
+      "storeClass": "WebApollo/Store/SeqFeature/ScratchPad",
+      "style": {
+        "alternateClasses": {
+          "miRNA": {
+            "className": "brightgreen-80pct",
+            "renderClassName": "gray-center-30pct"
+          },
+          "ncRNA": {
+            "className": "brightgreen-80pct",
+            "renderClassName": "gray-center-30pct"
+          },
+          "pseudogene": {
+            "className": "light-purple-80pct",
+            "renderClassName": "gray-center-30pct"
+          },
+          "rRNA": {
+            "className": "brightgreen-80pct",
+            "renderClassName": "gray-center-30pct"
+          },
+          "repeat_region": {
+            "className": "magenta-80pct"
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+          "snRNA": {
+            "className": "brightgreen-80pct",
+            "renderClassName": "gray-center-30pct"
+          },
+          "snoRNA": {
+            "className": "brightgreen-80pct",
+            "renderClassName": "gray-center-30pct"
+          },
+          "tRNA": {
+            "className": "brightgreen-80pct",
+            "renderClassName": "gray-center-30pct"
+          },
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+            "className": "blue-ibeam",
+            "renderClassName": "blue-ibeam-render"
+          }
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+        "arrowheadClass": "annot-arrowhead",
+        "centerSubFeature": {
+          "non_canonical_five_prime_splice_site": false,
+          "non_canonical_three_prime_splice_site": false
+        },
+        "className": "annot",
+        "renderClassName": "annot-render",
+        "subfeatureClasses": {
+          "CDS": "annot-CDS",
+          "UTR": "annot-UTR",
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+      "label": "augustus_masked",
+      "metadata": {
+        "Analysis contact": "Jeff Stuart, Department of Entomology, Purdue University, West Lafayette, IN",
+        "Analysis description": "Augustus results as part of the MAKER 2.22 pipeline",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Augustus gene models from the MAKER 2.22 pipeline"
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+      "urlTemplate": "tracks/augustus_masked/{refseq}/trackData.json"
+    },
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+      "key": "blastn",
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+        "Analysis contact": "Jeff Stuart, Department of Entomology, Purdue University, West Lafayette, IN",
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+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Blastn results from the MAKER 2.22 pipeline"
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/blastn/{refseq}/trackData.json"
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+    {
+      "category": "OGS1.0/3. Mapped Proteins/Supplementary: BlastX",
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+      "key": "blastx",
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+        "Analysis contact": "Jeff Stuart, Department of Entomology, Purdue University, West Lafayette, IN",
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+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Blastx results from the MAKER 2.22 pipeline"
+      },
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+      "style": {
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/blastx/{refseq}/trackData.json"
+    },
+    {
+      "category": "OGS1.0/3. Mapped DNA/est2genome",
+      "compress": 0,
+      "key": "est2genome",
+      "label": "est2genome",
+      "metadata": {
+        "Analysis contact": "Jeff Stuart, Department of Entomology, Purdue University, West Lafayette, IN",
+        "Analysis description": "est2genome results as part of the MAKER 2.22 pipeline",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "est2genome results from the MAKER 2.22 pipeline"
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+        "className": "{type}",
+        "subfeatureClasses": {
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/est2genome/{refseq}/trackData.json"
+    },
+    {
+      "category": "OGS1.0/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome",
+      "label": "protein2genome",
+      "metadata": {
+        "Analysis contact": "Jeff Stuart, Department of Entomology, Purdue University, West Lafayette, IN",
+        "Analysis description": "protein2genome results as part of the MAKER 2.22 pipeline",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "protein2genome results from the MAKER 2.22 pipeline"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome/{refseq}/trackData.json"
+    },
+    {
+      "category": "OGS1.0/2. Evidence/Repeats",
+      "compress": 0,
+      "key": "repeatmasker",
+      "label": "repeatmasker",
+      "metadata": {
+        "Analysis contact": "Jeff Stuart, Department of Entomology, Purdue University, West Lafayette, IN",
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diff --git a/organisms/stage/stage-v2/Medauroidea_extradentata/trackList.json b/organisms/stage/stage-v2/Medauroidea_extradentata/trackList.json
new file mode 100644
index 0000000..48036f5
--- /dev/null
+++ b/organisms/stage/stage-v2/Medauroidea_extradentata/trackList.json
@@ -0,0 +1,85 @@
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diff --git a/organisms/stage/stage-v2/Megachile_rotundata/trackList.json b/organisms/stage/stage-v2/Megachile_rotundata/trackList.json
new file mode 100644
index 0000000..cfd706d
--- /dev/null
+++ b/organisms/stage/stage-v2/Megachile_rotundata/trackList.json
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+}
diff --git a/organisms/stage/stage-v2/Melipona_quadrifasciata/trackList.json b/organisms/stage/stage-v2/Melipona_quadrifasciata/trackList.json
new file mode 100644
index 0000000..32a0ac2
--- /dev/null
+++ b/organisms/stage/stage-v2/Melipona_quadrifasciata/trackList.json
@@ -0,0 +1,151 @@
+{
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diff --git a/organisms/stage/stage-v2/Microplitis_demolitor/trackList.json b/organisms/stage/stage-v2/Microplitis_demolitor/trackList.json
new file mode 100644
index 0000000..57a0b5d
--- /dev/null
+++ b/organisms/stage/stage-v2/Microplitis_demolitor/trackList.json
@@ -0,0 +1,593 @@
+{
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+        "Data provider": "Gaelen Burke and Mike Strand, University of Georgia",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Source data": "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByStudy/sra/SRP/SRP028/SRP028964/SRR955076/SRR955076.sra",
+        "Track legend": "Mapped reads are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)",
+        "alignment summary": "http://de.iplantcollaborative.org/dl/d/0AD340BA-F2AC-4E60-BCD3-7082201ED087/align_summary.txt"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "user_contributed_data/Microplitis_demolitor/Microplitis_demolitor_teratocytes_accepted_hits_refSeq_IDs.bam"
+    },
+    {
+      "category": "RNA-Seq/Mapped Reads",
+      "key": "Microplitis demolitor venom_gland",
+      "label": "Microplitis demolitor venom_gland",
+      "metadata": {
+        "Analysis method": "Tophat v2.0.9",
+        "Analysis parameters": "--align_reads 'together' --mate-inner-dist '50' --file_query 'SRR955397_1.fastq' --file_query2 'SRR955397_2.fastq' --library-type 'fr-unstranded' --min-anchor-length '8' --splice-mismatches '0' --min-intron-length '70' --max-intron-length '50000' --min-isoform-fraction '0.15' --max-multihits '20' --min-segment-intron '50' --max-segment-intron '500000' --segment-mismatches '2' --segment-length '20' --num-threads '6' --user_database '69319_ref_Mdem2_chrUn.fa' --b2-sensitive  --tophat_version '2.0.9' --bowtie_version '2.1.0'",
+        "Data provider": "Gaelen Burke and Mike Strand, University of Georgia",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Source data": "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByStudy/sra/SRP/SRP028/SRP028964/SRR955397/SRR955397.sra",
+        "Track legend": "Mapped reads are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)",
+        "alignment summary": "http://de.iplantcollaborative.org/dl/d/7A0402D9-53BA-4ACF-8D71-F74BAAF3DF2B/align_summary.txt"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "user_contributed_data/Microplitis_demolitor/Microplitis_demolitor_venom_gland_accepted_hits_refSeq_IDs.bam"
+    },
+    {
+      "category": "RNA-Seq/Mapped Reads",
+      "key": "Microplitis demolitor ovary",
+      "label": "Microplitis demolitor ovary",
+      "metadata": {
+        "Analysis method": "Tophat v2.0.9",
+        "Analysis parameters": "--align_reads 'together' --mate-inner-dist '50' --file_query 'SRR955015.sra_1.fastq' --file_query2 'SRR955015.sra_2.fastq' --library-type 'fr-unstranded' --min-anchor-length '8' --splice-mismatches '0' --min-intron-length '70' --max-intron-length '50000' --min-isoform-fraction '0.15' --max-multihits '20' --min-segment-intron '50' --max-segment-intron '500000' --segment-mismatches '2' --segment-length '20' --num-threads '6' --user_database '69319_ref_Mdem2_chrUn.fa' --b2-sensitive  --tophat_version '2.0.9' --bowtie_version '2.1.0'",
+        "Data provider": "Gaelen Burke and Mike Strand, University of Georgia",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Source data": "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByStudy/sra/SRP/SRP028/SRP028964/SRR955015/SRR955015.sra",
+        "Track legend": "Mapped reads are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)",
+        "alignment summary": "http://de.iplantcollaborative.org/dl/d/73DDC58C-C75F-4C1E-B1F7-7CF83E0A89BA/align_summary.txt"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "user_contributed_data/Microplitis_demolitor/Microplitis_demolitor_ovary_accepted_hits_refSeq_IDs.bam"
+    },
+    {
+      "category": "RNA-Seq/Mapped Reads",
+      "key": "Microplitis demolitor larvae",
+      "label": "Microplitis demolitor larvae",
+      "metadata": {
+        "Analysis method": "Tophat v2.0.9",
+        "Analysis parameters": "--align_reads 'together' --mate-inner-dist '50' --file_query 'SRR955374_1.fastq' --file_query2 'SRR955374_2.fastq' --library-type 'fr-unstranded' --min-anchor-length '8' --splice-mismatches '0' --min-intron-length '70' --max-intron-length '50000' --min-isoform-fraction '0.15' --max-multihits '20' --min-segment-intron '50' --max-segment-intron '500000' --segment-mismatches '2' --segment-length '20' --num-threads '6' --user_database '69319_ref_Mdem2_chrUn.fa' --b2-sensitive  --tophat_version '2.0.9' --bowtie_version '2.1.0'",
+        "Data provider": "Gaelen Burke and Mike Strand, University of Georgia",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Source data": "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByStudy/sra/SRP/SRP028/SRP028964/SRR955374/SRR955374.sra",
+        "Track legend": "Mapped reads are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)",
+        "alignment summary": "http://de.iplantcollaborative.org/dl/d/25F3B191-FD45-481F-B236-022EC0B20089/align_summary.txt"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "user_contributed_data/Microplitis_demolitor/Microplitis_demolitor_larvae_accepted_hits_refSeq_IDs.bam"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "RNA-Seq/Coverage Plots (BigWig)",
+      "key": "Microplitis demolitor ovary (Coverage Plot)",
+      "label": "Microplitis demolitor ovary (Coverage Plot)",
+      "metadata": {
+        "Analysis method": "Tophat v2.0.9",
+        "Analysis parameters": "--align_reads 'together' --mate-inner-dist '50' --file_query 'SRR955015.sra_1.fastq' --file_query2 'SRR955015.sra_2.fastq' --library-type 'fr-unstranded' --min-anchor-length '8' --splice-mismatches '0' --min-intron-length '70' --max-intron-length '50000' --min-isoform-fraction '0.15' --max-multihits '20' --min-segment-intron '50' --max-segment-intron '500000' --segment-mismatches '2' --segment-length '20' --num-threads '6' --user_database '69319_ref_Mdem2_chrUn.fa' --b2-sensitive  --tophat_version '2.0.9' --bowtie_version '2.1.0'",
+        "Data provider": "Gaelen Burke and Mike Strand, University of Georgia",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Source data": "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByStudy/sra/SRP/SRP028/SRP028964/SRR955015/SRR955015.sra",
+        "Track legend": "This track represents an X-Y plot of RNA-Seq coverage.",
+        "alignment summary": "http://de.iplantcollaborative.org/dl/d/73DDC58C-C75F-4C1E-B1F7-7CF83E0A89BA/align_summary.txt"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "pos_color": "#00BFFF"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "user_contributed_data/Microplitis_demolitor/Microplitis_demolitor_ovary_accepted_hits_refSeq_IDs.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "RNA-Seq/Coverage Plots (BigWig)",
+      "key": "Microplitis demolitor larvae (Coverage Plot)",
+      "label": "Microplitis demolitor larvae (Coverage Plot)",
+      "metadata": {
+        "Analysis method": "Tophat v2.0.9",
+        "Analysis parameters": "--align_reads 'together' --mate-inner-dist '50' --file_query 'SRR955374_1.fastq' --file_query2 'SRR955374_2.fastq' --library-type 'fr-unstranded' --min-anchor-length '8' --splice-mismatches '0' --min-intron-length '70' --max-intron-length '50000' --min-isoform-fraction '0.15' --max-multihits '20' --min-segment-intron '50' --max-segment-intron '500000' --segment-mismatches '2' --segment-length '20' --num-threads '6' --user_database '69319_ref_Mdem2_chrUn.fa' --b2-sensitive  --tophat_version '2.0.9' --bowtie_version '2.1.0'",
+        "Data provider": "Gaelen Burke and Mike Strand, University of Georgia",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Source data": "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByStudy/sra/SRP/SRP028/SRP028964/SRR955374/SRR955374.sra",
+        "Track legend": "This track represents an X-Y plot of RNA-Seq coverage.",
+        "alignment summary": "http://de.iplantcollaborative.org/dl/d/25F3B191-FD45-481F-B236-022EC0B20089/align_summary.txt"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "pos_color": "#00BFFF"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "user_contributed_data/Microplitis_demolitor/Microplitis_demolitor_larvae_accepted_hits_refSeq_IDs.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "RNA-Seq/Coverage Plots (BigWig)",
+      "key": "Microplitis demolitor venom_gland (Coverage Plot)",
+      "label": "Microplitis demolitor venom_gland (Coverage Plot)",
+      "metadata": {
+        "Analysis method": "Tophat v2.0.9",
+        "Analysis parameters": "--align_reads 'together' --mate-inner-dist '50' --file_query 'SRR955397_1.fastq' --file_query2 'SRR955397_2.fastq' --library-type 'fr-unstranded' --min-anchor-length '8' --splice-mismatches '0' --min-intron-length '70' --max-intron-length '50000' --min-isoform-fraction '0.15' --max-multihits '20' --min-segment-intron '50' --max-segment-intron '500000' --segment-mismatches '2' --segment-length '20' --num-threads '6' --user_database '69319_ref_Mdem2_chrUn.fa' --b2-sensitive  --tophat_version '2.0.9' --bowtie_version '2.1.0'",
+        "Data provider": "Gaelen Burke and Mike Strand, University of Georgia",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Source data": "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByStudy/sra/SRP/SRP028/SRP028964/SRR955397/SRR955397.sra",
+        "Track legend": "This track represents an X-Y plot of RNA-Seq coverage.",
+        "alignment summary": "http://de.iplantcollaborative.org/dl/d/7A0402D9-53BA-4ACF-8D71-F74BAAF3DF2B/align_summary.txt"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "pos_color": "#00BFFF"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "user_contributed_data/Microplitis_demolitor/Microplitis_demolitor_venom_gland_accepted_hits_refSeq_IDs.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "RNA-Seq/Coverage Plots (BigWig)",
+      "key": "Microplitis demolitor teratocytes (Coverage Plot)",
+      "label": "Microplitis demolitor teratocytes (Coverage Plot)",
+      "metadata": {
+        "Analysis method": "Tophat v2.0.9",
+        "Analysis parameters": "--align_reads 'together' --mate-inner-dist '50' --file_query 'SRR955076.sra_1.fastq' --file_query2 'SRR955076.sra_2.fastq' --library-type 'fr-unstranded' --min-anchor-length '8' --splice-mismatches '0' --min-intron-length '70' --max-intron-length '50000' --min-isoform-fraction '0.15' --max-multihits '20' --min-segment-intron '50' --max-segment-intron '500000' --segment-mismatches '2' --segment-length '20' --num-threads '6' --user_database '69319_ref_Mdem2_chrUn.fa' --b2-sensitive  --tophat_version '2.0.9' --bowtie_version '2.1.0'",
+        "Data provider": "Gaelen Burke and Mike Strand, University of Georgia",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Source data": "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByStudy/sra/SRP/SRP028/SRP028964/SRR955076/SRR955076.sra",
+        "Track legend": "This track represents an X-Y plot of RNA-Seq coverage.",
+        "alignment summary": "http://de.iplantcollaborative.org/dl/d/0AD340BA-F2AC-4E60-BCD3-7082201ED087/align_summary.txt"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "pos_color": "#00BFFF"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "user_contributed_data/Microplitis_demolitor/Microplitis_demolitor_teratocytes_accepted_hits_refSeq_IDs.bigwig"
+    },
+    {
+      "category": "Mapped DNA/Microplitis demolitor ovary DNA",
+      "key": "Microplitis demolitor ovary DNA, mapped reads",
+      "label": "Microplitis demolitor ovary DNA, mapped reads",
+      "metadata": {
+        "Data description": "https://i5k.nal.usda.gov/node/739298/",
+        "Data provider": "Gaelen Burke, University of Georgia",
+        "Data source": "https://www.ncbi.nlm.nih.gov/sra/SRR3420507",
+        "Method": "bwa 0.7.15",
+        "Publication status": "Published - please cite 10.1128/JVI.01388-15",
+        "Track legend": "Mapped reads are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "user_contributed_data/UGA_March_2018/3t4wo_sort.bam"
+    },
+    {
+      "category": "Mapped DNA/Microplitis demolitor bracovirus DNA",
+      "key": "Microplitis demolitor bracovirus DNA, mapped reads",
+      "label": "Microplitis demolitor bracovirus DNA, mapped reads",
+      "metadata": {
+        "Data description": "https://i5k.nal.usda.gov/node/739297/",
+        "Data provider": "Gaelen Burke, University of Georgia",
+        "Data source": "https://www.ncbi.nlm.nih.gov/sra/SRR3420508",
+        "Method": "bwa 0.7.15",
+        "Publication status": "Published - please cite 10.1371/journal.pgen.1004660",
+        "Track legend": "Mapped reads are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "user_contributed_data/UGA_March_2018/mdbv_all_sort.bam"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Mapped DNA/Microplitis demolitor ovary DNA",
+      "key": "Microplitis demolitor ovary DNA (Coverage Plot)",
+      "label": "Microplitis demolitor ovary DNA (Coverage Plot)",
+      "metadata": {
+        "Data description": "https://i5k.nal.usda.gov/node/739298/",
+        "Data provider": "Gaelen Burke, University of Georgia",
+        "Data source": "https://www.ncbi.nlm.nih.gov/sra/SRR3420507",
+        "Method": "bwa 0.7.15",
+        "Publication status": "Published - please cite 10.1128/JVI.01388-15",
+        "Track legend": "This track represents an X-Y plot of RNA-Seq coverage."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "pos_color": "#00BFFF"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "user_contributed_data/UGA_March_2018/3t4wo_sort.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Mapped DNA/Microplitis demolitor bracovirus DNA",
+      "key": "Microplitis demolitor bracovirus DNA (Coverage Plot)",
+      "label": "Microplitis demolitor bracovirus DNA (Coverage Plot)",
+      "metadata": {
+        "Data description": "https://i5k.nal.usda.gov/node/739297/",
+        "Data provider": "Gaelen Burke, University of Georgia",
+        "Data source": "https://www.ncbi.nlm.nih.gov/sra/SRR3420508",
+        "Method": "bwa 0.7.15",
+        "Publication status": "Published - please cite 10.1371/journal.pgen.1004660",
+        "Track legend": "This track represents an X-Y plot of RNA-Seq coverage."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "pos_color": "#00BFFF"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "user_contributed_data/UGA_March_2018/mdbv_all_sort.bigwig"
+    },
+    {
+      "category": "Mapped DNA/Mapped Reads",
+      "key": "Infected Chrysodeixis includens hemocytes",
+      "label": "Infected Chrysodeixis includens hemocytes",
+      "metadata": {
+        "Data description": "https://i5k.nal.usda.gov/node/739316/",
+        "Data provider": "Gaelen Burke, University of Georgia",
+        "Data source": "https://www.ncbi.nlm.nih.gov/sra/SRX1047183/",
+        "Method": "hisat2 v2.1.0",
+        "Publication status": "Published - please cite 10.1371/journal.pgen.1004660",
+        "Track legend": "Mapped reads are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "user_contributed_data/UGA_March_2018/p_hemo_sort_mdbv.bam"
+    },
+    {
+      "category": "Mapped DNA/Mapped Reads",
+      "key": "Infected Chrysodeixis includens",
+      "label": "Infected Chrysodeixis includens",
+      "metadata": {
+        "Data description": "https://i5k.nal.usda.gov/node/739318",
+        "Data provider": "Gaelen Burke, University of Georgia",
+        "Data source": "SRX3766325,SRX3766326,SRX3766328,SRX3766330,SRX3766333,SRX3766334",
+        "Method": "hisat2 v2.1.0",
+        "Publication status": "Published - please cite 10.1016/j.virol.2016.02.023",
+        "Track legend": "Mapped reads are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "user_contributed_data/UGA_March_2018/p_sort_mdbv.bam"
+    },
+    {
+      "category": "Mapped DNA/Mapped Reads",
+      "key": "Infected Trichoplusia ni",
+      "label": "Infected Trichoplusia ni",
+      "metadata": {
+        "Data description": "https://i5k.nal.usda.gov/node/739317/",
+        "Data provider": "Gaelen Burke, University of Georgia",
+        "Data source": "SRX3766323,SRX3766324,SRX3766327,SRX3766329,SRX3766331,SRX3766332",
+        "Method": "hisat2 v2.1.0",
+        "Publication status": "Published - please cite 10.1016/j.virol.2016.02.023",
+        "Track legend": "Mapped reads are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "user_contributed_data/UGA_March_2018/t_sort_mdbv.bam"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Mapped DNA/Coverage Plots (BigWig)",
+      "key": "Infected Chrysodeixis includens hemocytes (Coverage Plot)",
+      "label": "Infected Chrysodeixis includens hemocytes (Coverage Plot)",
+      "metadata": {
+        "Data description": "https://i5k.nal.usda.gov/node/739316/",
+        "Data provider": "Gaelen Burke, University of Georgia",
+        "Data source": "https://www.ncbi.nlm.nih.gov/sra/SRX1047183/",
+        "Method": "hisat2 v2.1.0",
+        "Publication status": "Published - please cite 10.1371/journal.pgen.1004660",
+        "Track legend": "This track represents an X-Y plot of RNA-Seq coverage."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "pos_color": "#00BFFF"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "user_contributed_data/UGA_March_2018/p_hemo_sort_mdbv.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Mapped DNA/Coverage Plots (BigWig)",
+      "key": "Infected Chrysodeixis includens (Coverage Plot)",
+      "label": "Infected Chrysodeixis includens (Coverage Plot)",
+      "metadata": {
+        "Data description": "https://i5k.nal.usda.gov/node/739318",
+        "Data provider": "Gaelen Burke, University of Georgia",
+        "Data source": "SRX3766325,SRX3766326,SRX3766328,SRX3766330,SRX3766333,SRX3766334",
+        "Method": "hisat2 v2.1.0",
+        "Publication status": "Published - please cite 10.1016/j.virol.2016.02.023",
+        "Track legend": "This track represents an X-Y plot of RNA-Seq coverage."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "pos_color": "#00BFFF"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "user_contributed_data/UGA_March_2018/p_sort_mdbv.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Mapped DNA/Coverage Plots (BigWig)",
+      "key": "Infected Trichoplusia ni (Coverage Plot)",
+      "label": "Infected Trichoplusia ni (Coverage Plot)",
+      "metadata": {
+        "Data description": "https://i5k.nal.usda.gov/node/739317",
+        "Data provider": "Gaelen Burke, University of Georgia",
+        "Data source": "SRX3766323,SRX3766324,SRX3766327,SRX3766329,SRX3766331,SRX3766332",
+        "Method": "hisat2 v2.1.0",
+        "Publication status": "Published - please cite 10.1016/j.virol.2016.02.023",
+        "Track legend": "This track represents an X-Y plot of RNA-Seq coverage."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "pos_color": "#00BFFF"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "user_contributed_data/UGA_March_2018/t_sort_mdbv.bigwig"
+    },
+    {
+      "category": "Mapped DNA/Microplitis demolitor ovary DNA",
+      "key": "Microplitis demolitor ovary DNA, mapped reads (1% coverage)",
+      "label": "Microplitis demolitor ovary DNA, mapped reads (1% coverage)",
+      "metadata": {
+        "Data description": "https://i5k.nal.usda.gov/node/739298/",
+        "Data provider": "Gaelen Burke, University of Georgia",
+        "Data source": "https://www.ncbi.nlm.nih.gov/sra/SRR3420507",
+        "Method": "bwa 0.7.15; Coverage reduced to 1% with GATK",
+        "Publication status": "Published - please cite 10.1128/JVI.01388-15",
+        "Track legend": "Mapped reads are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "user_contributed_data/UGA_March_2018/3t4wo_sort.RG.Reordered.RCfrac.bam"
+    },
+    {
+      "category": "Mapped DNA/Microplitis demolitor bracovirus DNA",
+      "key": "Microplitis demolitor bracovirus DNA, mapped reads (0.1% coverage)",
+      "label": "Microplitis demolitor bracovirus DNA, mapped reads (0.1% coverage)",
+      "metadata": {
+        "Data description": "https://i5k.nal.usda.gov/node/739297/",
+        "Data provider": "Gaelen Burke, University of Georgia",
+        "Data source": "https://www.ncbi.nlm.nih.gov/sra/SRR3420508",
+        "Method": "bwa 0.7.15; Coverage reduced to 0.1% with GATK",
+        "Publication status": "Published - please cite 10.1371/journal.pgen.1004660",
+        "Track legend": "Mapped reads are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "user_contributed_data/UGA_March_2018/mdbv_all_sort.RG.Reordered.RCfrac.bam"
+    },
+    {
+      "category": "Mapped DNA/Microplitis demolitor bracovirus DNA",
+      "compress": 0,
+      "key": "Proviral segments",
+      "label": "proviral_segment",
+      "metadata": {
+        "Data description": "https://i5k.nal.usda.gov/node/739297/",
+        "Data provider": "Gaelen Burke, University of Georgia",
+        "Data source": "https://www.ncbi.nlm.nih.gov/sra/SRR3420508",
+        "Method": "bwa 0.7.15",
+        "Publication status": "Published - please cite 10.1371/journal.pgen.1004660"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "renderClassName": "genemark"
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/proviral_segment/{refseq}/trackData.json"
+    },
+    {
+      "category": "Mapped DNA/Microplitis demolitor ovary DNA",
+      "compress": 0,
+      "key": "Replication units",
+      "label": "replication_unit",
+      "metadata": {
+        "Data description": "https://i5k.nal.usda.gov/node/739298/",
+        "Data provider": "Gaelen Burke, University of Georgia",
+        "Data source": "https://www.ncbi.nlm.nih.gov/sra/SRR3420507",
+        "Method": "bwa 0.7.15",
+        "Publication status": "Published - please cite 10.1128/JVI.01388-15"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "renderClassName": "genemark"
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/replication_unit/{refseq}/trackData.json"
+    },
+    {
+      "category": "Official Gene Set v1.0",
+      "compress": 0,
+      "key": "OGSv1.0 Gene",
+      "label": "micdem_current_models",
+      "menuTemplate": [
+        {
+          "label": "View details"
+        },
+        {
+          "action": "newWindow",
+          "iconClass": "dijitIconDatabase",
+          "label": "function(track,feature){ return 'Find gene page for '+feature.get('id')}",
+          "title": "function(track,feature){ return 'Find gene page for '+feature.get('id')}",
+          "url": "function(track,feature){ return 'https://i5k.nal.usda.gov/'+feature.get('id')}"
+        }
+      ],
+      "metadata": {
+        "Data description": "Microplitis demolitor OGSv1.0 is an integration of automatic gene predictions from *Microplitis demolitor* genome annotations NCBI-RefSeq's gene set NCBI Microplitis demolitor Annotation Release 101 (https://www.ncbi.nlm.nih.gov/genome/annotation_euk/Microplitis_demolitor/101/), with manual annotations by the research community, performed via the Apollo manual curation software (https://zenodo.org/record/1295754#.YDgLyJNKivg), and QC'd via the GFF3toolkit (https://github.com/NAL-i5K/gff3toolkit) and NCBI's table2asn_GFF software (https://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/table2asn_GFF/), and merged via the GFF3toolkit (https://github.com/NAL-i5K/gff3toolkit).",
+        "Data source": "https://data.nal.usda.gov/dataset/microplitis-demolitor-official-gene-set-micdemogsv10",
+        "Publication status": "Published dataset, please cite (dataset) Tims, Kelly; Poelchau, Monica; Burke, Gaelen. (unpublished). Microplitis demolitor Official Gene Set micdem_OGSv1.0. Ag Data Commons. https://data.nal.usda.gov/dataset/microplitis-demolitor-official-gene-set-micdemogsv10."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "description": "product, note, description",
+        "subfeatureClasses": {
+          "CDS": "gnomon_CDS",
+          "UTR": "gnomon_UTR",
+          "exon": "container-100pct",
+          "wholeCDS": null
+        }
+      },
+      "trackType": "HTMLFeatures",
+      "type": "HTMLFeatures",
+      "urlTemplate": "tracks/micdem_current_models/{refseq}/trackData.json"
+    },
+    {
+      "category": "Official Gene Set v1.0",
+      "compress": 0,
+      "key": "OGSv1.0 Pseudogene",
+      "label": "OGSv1.0_Pseudogene",
+      "metadata": {
+        "Data description": "Microplitis demolitor OGSv1.0 is an integration of automatic gene predictions from *Microplitis demolitor* genome annotations NCBI-RefSeq's gene set NCBI Microplitis demolitor Annotation Release 101 (https://www.ncbi.nlm.nih.gov/genome/annotation_euk/Microplitis_demolitor/101/), with manual annotations by the research community, performed via the Apollo manual curation software (https://zenodo.org/record/1295754#.YDgLyJNKivg), and QC'd via the GFF3toolkit (https://github.com/NAL-i5K/gff3toolkit) and NCBI's table2asn_GFF software (https://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/table2asn_GFF/), and merged via the GFF3toolkit (https://github.com/NAL-i5K/gff3toolkit).",
+        "Data source": "https://data.nal.usda.gov/dataset/microplitis-demolitor-official-gene-set-micdemogsv10",
+        "Publication status": "Published dataset, please cite (dataset) Tims, Kelly; Poelchau, Monica; Burke, Gaelen. (unpublished). Microplitis demolitor Official Gene Set micdem_OGSv1.0. Ag Data Commons. https://data.nal.usda.gov/dataset/microplitis-demolitor-official-gene-set-micdemogsv10."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "description": "product, note, description",
+        "subfeatureClasses": {
+          "CDS": "gnomon_CDS",
+          "UTR": "gnomon_UTR",
+          "exon": "container-100pct",
+          "wholeCDS": null
+        }
+      },
+      "trackType": "HTMLFeatures",
+      "type": "HTMLFeatures",
+      "urlTemplate": "tracks/OGSv1.0_Pseudogene/{refseq}/trackData.json"
+    }
+  ]
+}
diff --git a/organisms/stage/stage-v2/Neodiprion_lecontei/trackList.json b/organisms/stage/stage-v2/Neodiprion_lecontei/trackList.json
new file mode 100644
index 0000000..48b0ddd
--- /dev/null
+++ b/organisms/stage/stage-v2/Neodiprion_lecontei/trackList.json
@@ -0,0 +1,441 @@
+{
+  "formatVersion": 1,
+  "names": {
+    "type": "Hash",
+    "url": "names/"
+  },
+  "tracks": [
+    {
+      "category": "Reference sequence",
+      "faiUrlTemplate": "seq/GCA_001263575.2_Nlec1.1_genomic.fna.fai",
+      "key": "Reference sequence",
+      "label": "DNA",
+      "seqType": "dna",
+      "storeClass": "JBrowse/Store/Sequence/IndexedFasta",
+      "type": "SequenceTrack",
+      "urlTemplate": "seq/GCA_001263575.2_Nlec1.1_genomic.fna",
+      "useAsRefSeqStore": 1
+    },
+    {
+      "category": "Official Gene Set",
+      "compress": 0,
+      "key": "neolec_OGSv1.1",
+      "label": "neolec_current_models",
+      "metadata": {
+        "Data URL": "",
+        "Data provider": "Scott Geib, USDA-ARS Pacific Basin Agricultural Research Center",
+        "Method": "Maker v2.31.8, followed by CrossMap re-mapping of coordinates to new genome assembly version",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "CDS": "primary_gene_set-cds",
+          "UTR": "primary_gene_set-utr",
+          "exon": "container-100pct",
+          "wholeCDS": null
+        }
+      },
+      "trackType": "HTMLFeatures",
+      "type": "HTMLFeatures",
+      "urlTemplate": "tracks/neolec_current_models/{refseq}/trackData.json"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Reference Assembly",
+      "key": "Gaps in assembly",
+      "label": "Gaps in assembly",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "white",
+        "pos_color": "black"
+      },
+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "bigwig/GCA_001263575.2_Nlec1.1_genomic.fna.gaps.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "0.5",
+      "category": "Reference Assembly",
+      "key": "GC Content",
+      "label": "GC Content",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+      },
+      "scoreType": "avgScore",
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "rgba(255,255,0,50)",
+        "pos_color": "rgba(0,0,255,50)"
+      },
+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "bigwig/GCA_001263575.2_Nlec1.1_genomic.fna.gc.bigwig"
+    },
+    {
+      "category": "NCBI Annotation Release 100",
+      "compress": 0,
+      "key": "NCBI Annotation Release 100 Gene",
+      "label": "NCBI_Annotation_Release_100_Gene",
+      "metadata": {
+        "Data description": "ftp://ftp.ncbi.nlm.nih.gov/genomes/Neodiprion_lecontei/README_CURRENT_RELEASE",
+        "Data provider": "NCBI",
+        "Data source": "ftp://ftp.ncbi.nih.gov/genomes/Neodiprion_lecontei/GFF/ref_Nlec1.0_top_level.gff3.gz",
+        "Method": "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "description": "product, note, description",
+        "subfeatureClasses": {
+          "CDS": "gnomon_CDS",
+          "UTR": "gnomon_UTR",
+          "exon": "container-100pct",
+          "wholeCDS": null
+        }
+      },
+      "trackType": "HTMLFeatures",
+      "type": "HTMLFeatures",
+      "urlTemplate": "tracks/NCBI_Annotation_Release_100_Gene/{refseq}/trackData.json"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Transcriptome/Coverage Plots (BigWig)",
+      "key": "Adult female body RNA-seq (Coverage Plot)",
+      "label": "Adult_female_body_RNA-seq_Coverage_Plot",
+      "metadata": {
+        "Analysis method": "STAR v2.4.0j",
+        "File provider": "Kim Vertacnik, University of Kentucky",
+        "Geographical location of specimen collection": "USA, Lexington KY, 37.983767, -84.510784",
+        "NCBI SRA accession #": "SRR2970129",
+        "Other methods": "Trimmomatic v0.32 used for adaptor trimming and quality filtering",
+        "Other notes": "pooled adult female body tissue from eight wild-caught insects",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Sequencing platform and version": "Illumina HiSeq 2000",
+        "Sex": "female",
+        "Strain": "RB017",
+        "Tissues included": "pooled adult female body"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "pos_color": "#00BFFF"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "analyses/Nlec_AFB_v1.1/Nlec_AFB_v1.1.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Transcriptome/Coverage Plots (BigWig)",
+      "key": "Adult female head RNA-seq (Coverage Plot)",
+      "label": "Adult_female_head_RNA-seq_Coverage_Plot",
+      "metadata": {
+        "Analysis method": "STAR v2.4.0j",
+        "File provider": "Kim Vertacnik, University of Kentucky",
+        "Geographical location of specimen collection": "USA, Lexington KY, 37.983767, -84.510784",
+        "NCBI SRA accession #": "SRR2970128",
+        "Other methods": "Trimmomatic v0.32 used for adaptor trimming and quality filtering",
+        "Other notes": "pooled adult female head tissue from eight wild-caught insects",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Sequencing platform and version": "Illumina HiSeq 2000",
+        "Sex": "female",
+        "Strain": "RB017",
+        "Tissues included": "pooled adult female head"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "pos_color": "#00BFFF"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "analyses/Nlec_AFH_v1.1/Nlec_AFH_v1.1.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Transcriptome/Coverage Plots (BigWig)",
+      "key": "Adult male body RNA-seq (Coverage Plot)",
+      "label": "Adult_male_body_RNA-seq_Coverage_Plot",
+      "metadata": {
+        "Analysis method": "STAR v2.4.0j",
+        "File provider": "Kim Vertacnik, University of Kentucky",
+        "Geographical location of specimen collection": "USA, Lexington KY, 37.983767, -84.510784",
+        "NCBI SRA accession #": "SRR2970131",
+        "Other methods": "Trimmomatic v0.32 used for adaptor trimming and quality filtering",
+        "Other notes": "pooled adult male body tissue from eight wild-caught insects",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Sequencing platform and version": "Illumina HiSeq 2000",
+        "Sex": "female",
+        "Strain": "RB017",
+        "Tissues included": "pooled adult male body"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "pos_color": "#00BFFF"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "analyses/Nlec_AMB_v1.1/Nlec_AMB_v1.1.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Transcriptome/Coverage Plots (BigWig)",
+      "key": "Adult male head RNA-seq (Coverage Plot)",
+      "label": "Adult_male_head_RNA-seq_Coverage_Plot",
+      "metadata": {
+        "Analysis method": "STAR v2.4.0j",
+        "File provider": "Kim Vertacnik, University of Kentucky",
+        "Geographical location of specimen collection": "USA, Lexington KY, 37.983767, -84.510784",
+        "NCBI SRA accession #": "SRR2970130",
+        "Other methods": "Trimmomatic v0.32 used for adaptor trimming and quality filtering",
+        "Other notes": "pooled adult male head tissue from eight wild-caught insects",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Sequencing platform and version": "Illumina HiSeq 2000",
+        "Sex": "female",
+        "Strain": "RB017",
+        "Tissues included": "pooled adult male head"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "pos_color": "#00BFFF"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "analyses/Nlec_AMH_v1.1/Nlec_AMH_v1.1.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Transcriptome/Coverage Plots (BigWig)",
+      "key": "Eonymph body RNA-seq (Coverage Plot)",
+      "label": "Eonymph_body_RNA-seq_Coverage_Plot",
+      "metadata": {
+        "Analysis method": "STAR v2.4.0j",
+        "File provider": "Kim Vertacnik, University of Kentucky",
+        "Geographical location of specimen collection": "USA, Lexington KY, 37.983767, -84.510784",
+        "NCBI SRA accession #": "SRR2970134",
+        "Other methods": "Trimmomatic v0.32 used for adaptor trimming and quality filtering",
+        "Other notes": "pooled eonymph body tissue from eight insects reared for one generation in the lab",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Sequencing platform and version": "Illumina HiSeq 2000",
+        "Sex": "pooled",
+        "Strain": "RB017",
+        "Tissues included": "pooled eonymph body"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "pos_color": "#00BFFF"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "analyses/Nlec_EB_v1.1/Nlec_EB_v1.1.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Transcriptome/Coverage Plots (BigWig)",
+      "key": "Larval body RNA-seq (Coverage Plot)",
+      "label": "Larval_body_RNA-seq_Coverage_Plot",
+      "metadata": {
+        "Analysis method": "STAR v2.4.0j",
+        "File provider": "Kim Vertacnik, University of Kentucky",
+        "Geographical location of specimen collection": "USA, Lexington KY, 37.983767, -84.510784",
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+        "Other methods": "Trimmomatic v0.32 used for adaptor trimming and quality filtering",
+        "Other notes": "pooled larval body tissue from eight insects reared for one generation in the lab",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Sequencing platform and version": "Illumina HiSeq 2000",
+        "Sex": "pooled",
+        "Strain": "RB017",
+        "Tissues included": "pooled feeding larva body"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "pos_color": "#00BFFF"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "analyses/Nlec_FLB_v1.1/Nlec_FLB_v1.1.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
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diff --git a/organisms/stage/stage-v2/Neodiprion_lecontei_training/trackList.json b/organisms/stage/stage-v2/Neodiprion_lecontei_training/trackList.json
new file mode 100644
index 0000000..2131ccf
--- /dev/null
+++ b/organisms/stage/stage-v2/Neodiprion_lecontei_training/trackList.json
@@ -0,0 +1,682 @@
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diff --git a/organisms/stage/stage-v2/Nicrophorus_vespilloides/trackList.json b/organisms/stage/stage-v2/Nicrophorus_vespilloides/trackList.json
new file mode 100644
index 0000000..b89b3eb
--- /dev/null
+++ b/organisms/stage/stage-v2/Nicrophorus_vespilloides/trackList.json
@@ -0,0 +1,337 @@
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+      "type": "WebApollo/View/Track/AnnotTrack"
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+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "white",
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+    },
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+      "key": "GC Content",
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+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+      },
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+      "urlTemplate": "bigwig/GCF_001412225.1_Nicves_v1.0_genomic_RefSeqIDs.fna.gc.bigwig"
+    },
+    {
+      "category": "Official Gene Set 1.0/1. Gene Sets/Protein Coding",
+      "compress": 0,
+      "key": "Official Gene Set 1.0, protein-coding genes",
+      "label": "official-gene-set-1-0_protein",
+      "metadata": {
+        "Data description": "Gene set accompanying GBE publication with RefSeq Accession numbers.",
+        "Data provider": "Chris Cunningham, Swansea University",
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+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/official-gene-set-1-0_protein/{refseq}/trackData.json"
+    },
+    {
+      "category": "Official Gene Set 1.0/1. Gene Sets/Noncoding",
+      "compress": 0,
+      "key": "Official Gene Set 1.0, non-coding RNA",
+      "label": "official-gene-set-1-0_RNA-motif",
+      "metadata": {
+        "Data description": "Gene set accompanying GBE publication with RefSeq Accession numbers.",
+        "Data provider": "Chris Cunningham, Swansea University",
+        "Method": "MAKER 2.0",
+        "Publication status": "Cunningham et al. 2015. Genome Biology and Evolution 7: 3383-3396."
+      },
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+      },
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/official-gene-set-1-0_RNA-motif/{refseq}/trackData.json"
+    },
+    {
+      "category": "Official Gene Set 1.0/2. Evidence",
+      "compress": 0,
+      "key": "Official Gene Set 1.0, repeatmasker evidence",
+      "label": "official-gene-set-1-0_repeatmasker",
+      "metadata": {
+        "Data description": "Gene set accompanying GBE publication with RefSeq Accession numbers.",
+        "Data provider": "Chris Cunningham, Swansea University",
+        "Method": "MAKER 2.0",
+        "Publication status": "Cunningham et al. 2015. Genome Biology and Evolution 7: 3383-3396."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
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+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/official-gene-set-1-0_repeatmasker/{refseq}/trackData.json"
+    }
+  ]
+}
diff --git a/organisms/stage/stage-v2/Nylanderia_fulva/trackList.json b/organisms/stage/stage-v2/Nylanderia_fulva/trackList.json
new file mode 100644
index 0000000..4518ba6
--- /dev/null
+++ b/organisms/stage/stage-v2/Nylanderia_fulva/trackList.json
@@ -0,0 +1,124 @@
+{
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+  "names": {
+    "type": "Hash",
+    "url": "names/"
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+  "tracks": [
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+      "chunkSize": 20000,
+      "key": "Reference sequence",
+      "label": "DNA",
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+      "type": "SequenceTrack",
+      "urlTemplate": "seq/{refseq_dirpath}/{refseq}-"
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+    {
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+      "bicolor_pivot": "zero",
+      "category": "Reference Assembly",
+      "key": "Gaps in assembly",
+      "label": "Gaps in assembly",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "white",
+        "pos_color": "black"
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+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "bigwig/GCF_005281655.1_TAMU_Nfulva_1.0_genomic.fna.gaps.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "0.5",
+      "category": "Reference Assembly",
+      "key": "GC Content",
+      "label": "GC Content",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+      },
+      "scoreType": "avgScore",
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "rgba(255,255,0,50)",
+        "pos_color": "rgba(0,0,255,50)"
+      },
+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "bigwig/GCF_005281655.1_TAMU_Nfulva_1.0_genomic.fna.gc.bigwig"
+    },
+    {
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+      "key": "OGSv1.0 Gene",
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+        {
+          "action": "newWindow",
+          "iconClass": "dijitIconDatabase",
+          "label": "function(track,feature){ return 'Find gene page for '+feature.get('id')}",
+          "title": "function(track,feature){ return 'Find gene page for '+feature.get('id')}",
+          "url": "function(track,feature){ return 'https://i5k.nal.usda.gov/'+feature.get('id')}"
+        }
+      ],
+      "metadata": {
+        "Data provider": "Kranti Konganti, Texas A&M University; Ed Vargo, Texas A&M University; Aaron Tarone, Texas A&M University; Lukas Schrader, University of Muenster",
+        "Data source": "https://data.nal.usda.gov/dataset/nylanderia-fulva-annotations-ogsv10",
+        "Materials and Methods": "The Nylanderia fulva OGSv1.0 is the Official Gene Set of genome assembly TAMU_Nfulva_1.0 (https://www.ncbi.nlm.nih.gov/assembly/GCF_005281655.1/). It is a merge of NCBI Nylanderia fulva Annotation Release 100 (https://www.ncbi.nlm.nih.gov/genome/annotation_euk/Nylanderia_fulva/100/) and semi-automated predictions of odorant receptors.",
+        "Publication status": "Unpublished, please refer to Fort Lauderdale/Toronto conditions of data re-use"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
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+          "exon": "container-100pct",
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+      },
+      "trackType": "HTMLFeatures",
+      "type": "HTMLFeatures",
+      "urlTemplate": "tracks/nylful_current_models/{refseq}/trackData.json"
+    },
+    {
+      "category": "Official Gene Set",
+      "compress": 0,
+      "key": "OGSv1.0 Pseudogene",
+      "label": "OGSv1.0_Pseudogene",
+      "metadata": {
+        "Data provider": "Kranti Konganti, Texas A&M University; Ed Vargo, Texas A&M University; Aaron Tarone, Texas A&M University; Lukas Schrader, University of Muenster",
+        "Data source": "https://data.nal.usda.gov/dataset/nylanderia-fulva-annotations-ogsv10",
+        "Materials and Methods": "The Nylanderia fulva OGSv1.0 is the Official Gene Set of genome assembly TAMU_Nfulva_1.0 (https://www.ncbi.nlm.nih.gov/assembly/GCF_005281655.1/). It is a merge of NCBI Nylanderia fulva Annotation Release 100 (https://www.ncbi.nlm.nih.gov/genome/annotation_euk/Nylanderia_fulva/100/) and semi-automated predictions of odorant receptors.",
+        "Publication status": "Unpublished, please refer to Fort Lauderdale/Toronto conditions of data re-use"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
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+      "trackType": "HTMLFeatures",
+      "type": "HTMLFeatures",
+      "urlTemplate": "tracks/OGSv1.0_Pseudogene/{refseq}/trackData.json"
+    }
+  ]
+}
diff --git a/organisms/stage/stage-v2/Odontomachus_brunneus/trackList.json b/organisms/stage/stage-v2/Odontomachus_brunneus/trackList.json
new file mode 100644
index 0000000..d6e3990
--- /dev/null
+++ b/organisms/stage/stage-v2/Odontomachus_brunneus/trackList.json
@@ -0,0 +1,718 @@
+{
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+  "names": {
+    "type": "Hash",
+    "url": "names/"
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+      "key": "Reference sequence",
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+      "type": "SequenceTrack",
+      "urlTemplate": "seq/{refseq_dirpath}/{refseq}-"
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+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Reference Assembly",
+      "key": "Gaps in assembly",
+      "label": "Gaps in assembly",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "white",
+        "pos_color": "black"
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+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "bigwig/GCF_010583005.1_Obru_v1_genomic.fna.gaps.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "0.5",
+      "category": "Reference Assembly",
+      "key": "GC Content",
+      "label": "GC Content",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+      },
+      "scoreType": "avgScore",
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "rgba(255,255,0,50)",
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+      "urlTemplate": "bigwig/GCF_010583005.1_Obru_v1_genomic.fna.gc.bigwig"
+    },
+    {
+      "category": "NCBI Annotation Release 100",
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+      "key": "NCBI_Annotation_Release_100_Pseudogene",
+      "label": "NCBI_Annotation_Release_100_Pseudogene",
+      "metadata": {
+        "Data description": "ftp://ftp.ncbi.nlm.nih.gov/genomes/Odontomachus_brunneus/README_CURRENT_RELEASE",
+        "Data provider": "NCBI",
+        "Data source": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/010/583/005/GCF_010583005.1_Obru_v1/GCF_010583005.1_Obru_v1_genomic.gff.gz",
+        "Method": "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
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+      "style": {
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+      "type": "HTMLFeatures",
+      "urlTemplate": "tracks/NCBI_Annotation_Release_100_Pseudogene/{refseq}/trackData.json"
+    },
+    {
+      "category": "RNA-Seq/Mapped Reads",
+      "key": "Odobru_Obru_v1_RNA-Seq-alignments_2020-06-02",
+      "label": "Odobru_Obru_v1_RNA-Seq-alignments_2020-06-02",
+      "metadata": {
+        "Analysis method": "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+        "Analysis provider": "i5k Workspace@NAL",
+        "Data source": "SRR6984027,SRR6984020,SRR6984034,SRR6984030,SRR6984019,SRR6984018,SRR6984056,SRR6984023,SRR6984021,SRR6984036",
+        "Publication status": "Analysis: NA; Source data: see individual SRA accessions",
+        "Track legend": "Dark red alignments: Mapped portion of read aligned to forward strand<br>Light red alignments: Spliced portion of read aligned to forward strand<br>Dark blue alignments: Mapped portion of read aligned to reverse strand<br>Light blue alignments: Spliced portion of read aligned to reverse strand<br>Red marking - deletion in the read relative to the reference<br>Green marking - insertion in the read relative to the reference<br>Yellow marking  - mismatch (hover over the mismatch to see what the snp is)"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "analyses/Odontomachus-brunneus-RNA-Seq_2020-06-02_v1.0/Odobru_Obru_v1_RNA-Seq-alignments_2020-06-02.bam"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "RNA-Seq/Coverage Plots",
+      "key": "Odobru_Obru_v1_RNA-Seq-alignments_2020-06-02_coverage",
+      "label": "Odobru_Obru_v1_RNA-Seq-alignments_2020-06-02_coverage",
+      "metadata": {
+        "Analysis method": "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+        "Analysis provider": "i5k Workspace@NAL",
+        "Data source": "SRR6984027,SRR6984020,SRR6984034,SRR6984030,SRR6984019,SRR6984018,SRR6984056,SRR6984023,SRR6984021,SRR6984036",
+        "Publication status": "Analysis: NA; Source data: see individual SRA accessions",
+        "Track legend": "This track represents an X-Y plot of RNA-Seq coverage."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "pos_color": "#00BFFF"
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+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "analyses/Odontomachus-brunneus-RNA-Seq_2020-06-02_v1.0/Odobru_Obru_v1_RNA-Seq-alignments_2020-06-02.bigwig"
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+      "label": "Odobru_Obru_v1_RNA-Seq-alignments_2020-06-02_junctions",
+      "metadata": {
+        "Analysis method": "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+        "Analysis provider": "i5k Workspace@NAL",
+        "Data source": "SRR6984027,SRR6984020,SRR6984034,SRR6984030,SRR6984019,SRR6984018,SRR6984056,SRR6984023,SRR6984021,SRR6984036",
+        "Publication status": "Analysis: NA; Source data: see individual SRA accessions",
+        "Track legend": "Junction reads generated by Hisat2 aligner and regtools"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "className": "feature",
+        "description": "score"
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/Odobru_Obru_v1_RNA-Seq-alignments_2020-06-02_junctions/{refseq}/trackData.json"
+    },
+    {
+      "category": "RNA-Seq/Mapped Reads",
+      "key": "Male",
+      "label": "Male",
+      "metadata": {
+        "Analysis method": "Reads were trimmed with Trimmomatic (0.32) and aligned to the genome assembly by caste/life-stage using STAR (2.7.3a) in paired-end mode with the available NCBI genome gtf file. The reads were aligned to the genome in a second pass using all the available splice junction information from the first pass alignments. Bam files were indexed with SAMtools (1.10).The second pass splice junction output files were converted to bed files using the custom script available at: https://gist.github.com/fabiolib/ffb21853e3eb3780150074aeffc54901",
+        "Analysis provider": "Kim Walden, University of Illinois at Urbana-Champaign",
+        "Data source": "SRR6984018, SRR6984012, SRR6984056",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale re-use guidelines",
+        "Track legend": "Dark red alignments: Mapped portion of read aligned to forward strand<br>Light red alignments: Spliced portion of read aligned to forward strand<br>Dark blue alignments: Mapped portion of read aligned to reverse strand<br>Light blue alignments: Spliced portion of read aligned to reverse strand<br>Red marking - deletion in the read relative to the reference<br>Green marking - insertion in the read relative to the reference<br>Yellow marking  - mismatch (hover over the mismatch to see what the snp is)",
+        "development stage": "Adult male"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "analyses/Odontomachus-brunneus-RNA-Seq_2020-06-09_v1.0/Odontomachus_male_2nd_passAligned.sortedByCoord.out.bam"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "RNA-Seq/Coverage Plots",
+      "key": "Male, coverage",
+      "label": "Male, coverage",
+      "metadata": {
+        "Analysis method": "Reads were trimmed with Trimmomatic (0.32) and aligned to the genome assembly by caste/life-stage using STAR (2.7.3a) in paired-end mode with the available NCBI genome gtf file. The reads were aligned to the genome in a second pass using all the available splice junction information from the first pass alignments. Bam files were indexed with SAMtools (1.10). The second pass splice junction output files were converted to bed files using the custom script available at: https://gist.github.com/fabiolib/ffb21853e3eb3780150074aeffc54901",
+        "Analysis provider": "Kim Walden, University of Illinois at Urbana-Champaign",
+        "Data source": "SRR6984018, SRR6984012, SRR6984056",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale re-use guidelines",
+        "Track legend": "This track represents an X-Y plot of RNA-Seq coverage.",
+        "development stage": "Adult Male"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "pos_color": "#00BFFF"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "analyses/Odontomachus-brunneus-RNA-Seq_2020-06-09_v1.0/Odontomachus_male_2nd_passAligned.sortedByCoord.out.bigwig"
+    },
+    {
+      "category": "RNA-Seq/Mapped Reads",
+      "key": "Larva",
+      "label": "Larva",
+      "metadata": {
+        "Analysis method": "Reads were trimmed with Trimmomatic (0.32) and aligned to the genome assembly by caste/life-stage using STAR (2.7.3a) in paired-end mode with the available NCBI genome gtf file. The reads were aligned to the genome in a second pass using all the available splice junction information from the first pass alignments. Bam files were indexed with SAMtools (1.10).The second pass splice junction output files were converted to bed files using the custom script available at: https://gist.github.com/fabiolib/ffb21853e3eb3780150074aeffc54901",
+        "Analysis provider": "Kim Walden, University of Illinois at Urbana-Champaign",
+        "Data source": "SRR6984019, SRR6984036, SRR6984027",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale re-use guidelines",
+        "Track legend": "Dark red alignments: Mapped portion of read aligned to forward strand<br>Light red alignments: Spliced portion of read aligned to forward strand<br>Dark blue alignments: Mapped portion of read aligned to reverse strand<br>Light blue alignments: Spliced portion of read aligned to reverse strand<br>Red marking - deletion in the read relative to the reference<br>Green marking - insertion in the read relative to the reference<br>Yellow marking  - mismatch (hover over the mismatch to see what the snp is)",
+        "development stage": "Larva"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "analyses/Odontomachus-brunneus-RNA-Seq_2020-06-09_v1.0/Odontomachus_larva_2nd_passAligned.sortedByCoord.out.bam"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "RNA-Seq/Coverage Plots",
+      "key": "Larva, coverage",
+      "label": "Larva, coverage",
+      "metadata": {
+        "Analysis method": "Reads were trimmed with Trimmomatic (0.32) and aligned to the genome assembly by caste/life-stage using STAR (2.7.3a) in paired-end mode with the available NCBI genome gtf file. The reads were aligned to the genome in a second pass using all the available splice junction information from the first pass alignments. Bam files were indexed with SAMtools (1.10). The second pass splice junction output files were converted to bed files using the custom script available at: https://gist.github.com/fabiolib/ffb21853e3eb3780150074aeffc54901",
+        "Analysis provider": "Kim Walden, University of Illinois at Urbana-Champaign",
+        "Data source": "SRR6984019, SRR6984036, SRR6984027",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale re-use guidelines",
+        "Track legend": "This track represents an X-Y plot of RNA-Seq coverage.",
+        "development stage": "Larva"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "pos_color": "#00BFFF"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "analyses/Odontomachus-brunneus-RNA-Seq_2020-06-09_v1.0/Odontomachus_larva_2nd_passAligned.sortedByCoord.out.bigwig"
+    },
+    {
+      "category": "RNA-Seq/Mapped Reads",
+      "key": "Egg",
+      "label": "Egg",
+      "metadata": {
+        "Analysis method": "Reads were trimmed with Trimmomatic (0.32) and aligned to the genome assembly by caste/life-stage using STAR (2.7.3a) in paired-end mode with the available NCBI genome gtf file. The reads were aligned to the genome in a second pass using all the available splice junction information from the first pass alignments. Bam files were indexed with SAMtools (1.10).The second pass splice junction output files were converted to bed files using the custom script available at: https://gist.github.com/fabiolib/ffb21853e3eb3780150074aeffc54901",
+        "Analysis provider": "Kim Walden, University of Illinois at Urbana-Champaign",
+        "Data source": "SRR6984010, SRR6984024, SRR6984030",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale re-use guidelines",
+        "Track legend": "Dark red alignments: Mapped portion of read aligned to forward strand<br>Light red alignments: Spliced portion of read aligned to forward strand<br>Dark blue alignments: Mapped portion of read aligned to reverse strand<br>Light blue alignments: Spliced portion of read aligned to reverse strand<br>Red marking - deletion in the read relative to the reference<br>Green marking - insertion in the read relative to the reference<br>Yellow marking  - mismatch (hover over the mismatch to see what the snp is)",
+        "development stage": "Egg"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "analyses/Odontomachus-brunneus-RNA-Seq_2020-06-09_v1.0/Odontomachus_egg_2nd_passAligned.sortedByCoord.out.bam"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "RNA-Seq/Coverage Plots",
+      "key": "Egg, coverage",
+      "label": "Egg, coverage",
+      "metadata": {
+        "Analysis method": "Reads were trimmed with Trimmomatic (0.32) and aligned to the genome assembly by caste/life-stage using STAR (2.7.3a) in paired-end mode with the available NCBI genome gtf file. The reads were aligned to the genome in a second pass using all the available splice junction information from the first pass alignments. Bam files were indexed with SAMtools (1.10). The second pass splice junction output files were converted to bed files using the custom script available at: https://gist.github.com/fabiolib/ffb21853e3eb3780150074aeffc54901",
+        "Analysis provider": "Kim Walden, University of Illinois at Urbana-Champaign",
+        "Data source": "SRR6984010, SRR6984024, SRR6984030",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale re-use guidelines",
+        "Track legend": "This track represents an X-Y plot of RNA-Seq coverage.",
+        "development stage": "Egg"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "pos_color": "#00BFFF"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "analyses/Odontomachus-brunneus-RNA-Seq_2020-06-09_v1.0/Odontomachus_egg_2nd_passAligned.sortedByCoord.out.bigwig"
+    },
+    {
+      "category": "RNA-Seq/Mapped Reads",
+      "key": "Reproductive Adult Worker",
+      "label": "Reproductive Adult Worker",
+      "metadata": {
+        "Analysis method": "Reads were trimmed with Trimmomatic (0.32) and aligned to the genome assembly by caste/life-stage using STAR (2.7.3a) in paired-end mode with the available NCBI genome gtf file. The reads were aligned to the genome in a second pass using all the available splice junction information from the first pass alignments. Bam files were indexed with SAMtools (1.10).The second pass splice junction output files were converted to bed files using the custom script available at: https://gist.github.com/fabiolib/ffb21853e3eb3780150074aeffc54901",
+        "Analysis provider": "Kim Walden, University of Illinois at Urbana-Champaign",
+        "Data source": "SRR6984022, SRR6984034, SRR6984031",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale re-use guidelines",
+        "Track legend": "Dark red alignments: Mapped portion of read aligned to forward strand<br>Light red alignments: Spliced portion of read aligned to forward strand<br>Dark blue alignments: Mapped portion of read aligned to reverse strand<br>Light blue alignments: Spliced portion of read aligned to reverse strand<br>Red marking - deletion in the read relative to the reference<br>Green marking - insertion in the read relative to the reference<br>Yellow marking  - mismatch (hover over the mismatch to see what the snp is)",
+        "development stage": "Reproductive Adult Worker"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "analyses/Odontomachus-brunneus-RNA-Seq_2020-06-09_v1.0/Odontomachus_RAW_2nd_passAligned.sortedByCoord.out.bam"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "RNA-Seq/Coverage Plots",
+      "key": "Reproductive Adult Worker, coverage",
+      "label": "Reproductive Adult Worker, coverage",
+      "metadata": {
+        "Analysis method": "Reads were trimmed with Trimmomatic (0.32) and aligned to the genome assembly by caste/life-stage using STAR (2.7.3a) in paired-end mode with the available NCBI genome gtf file. The reads were aligned to the genome in a second pass using all the available splice junction information from the first pass alignments. Bam files were indexed with SAMtools (1.10). The second pass splice junction output files were converted to bed files using the custom script available at: https://gist.github.com/fabiolib/ffb21853e3eb3780150074aeffc54901",
+        "Analysis provider": "Kim Walden, University of Illinois at Urbana-Champaign",
+        "Data source": "SRR6984022, SRR6984034, SRR6984031",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale re-use guidelines",
+        "Track legend": "This track represents an X-Y plot of RNA-Seq coverage.",
+        "development stage": "Reproductive Adult Worker"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "pos_color": "#00BFFF"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "analyses/Odontomachus-brunneus-RNA-Seq_2020-06-09_v1.0/Odontomachus_RAW_2nd_passAligned.sortedByCoord.out.bigwig"
+    },
+    {
+      "category": "RNA-Seq/Mapped Reads",
+      "key": "Non-reproductive Adult Worker",
+      "label": "Non-reproductive Adult Worker",
+      "metadata": {
+        "Analysis method": "Reads were trimmed with Trimmomatic (0.32) and aligned to the genome assembly by caste/life-stage using STAR (2.7.3a) in paired-end mode with the available NCBI genome gtf file. The reads were aligned to the genome in a second pass using all the available splice junction information from the first pass alignments. Bam files were indexed with SAMtools (1.10).The second pass splice junction output files were converted to bed files using the custom script available at: https://gist.github.com/fabiolib/ffb21853e3eb3780150074aeffc54901",
+        "Analysis provider": "Kim Walden, University of Illinois at Urbana-Champaign",
+        "Data source": "SRR6984021, SRR6984013, SRR6984057",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale re-use guidelines",
+        "Track legend": "Dark red alignments: Mapped portion of read aligned to forward strand<br>Light red alignments: Spliced portion of read aligned to forward strand<br>Dark blue alignments: Mapped portion of read aligned to reverse strand<br>Light blue alignments: Spliced portion of read aligned to reverse strand<br>Red marking - deletion in the read relative to the reference<br>Green marking - insertion in the read relative to the reference<br>Yellow marking  - mismatch (hover over the mismatch to see what the snp is)",
+        "development stage": "Non-reproductive Adult Worker"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "analyses/Odontomachus-brunneus-RNA-Seq_2020-06-09_v1.0/Odontomachus_NRW_2nd_passAligned.sortedByCoord.out.bam"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "RNA-Seq/Coverage Plots",
+      "key": "Non-reproductive Adult Worker, coverage",
+      "label": "Non-reproductive Adult Worker, coverage",
+      "metadata": {
+        "Analysis method": "Reads were trimmed with Trimmomatic (0.32) and aligned to the genome assembly by caste/life-stage using STAR (2.7.3a) in paired-end mode with the available NCBI genome gtf file. The reads were aligned to the genome in a second pass using all the available splice junction information from the first pass alignments. Bam files were indexed with SAMtools (1.10). The second pass splice junction output files were converted to bed files using the custom script available at: https://gist.github.com/fabiolib/ffb21853e3eb3780150074aeffc54901",
+        "Analysis provider": "Kim Walden, University of Illinois at Urbana-Champaign",
+        "Data source": "SRR6984021, SRR6984013, SRR6984057",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale re-use guidelines",
+        "Track legend": "This track represents an X-Y plot of RNA-Seq coverage.",
+        "development stage": "Non-reproductive Adult Worker"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "pos_color": "#00BFFF"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "analyses/Odontomachus-brunneus-RNA-Seq_2020-06-09_v1.0/Odontomachus_NRW_2nd_passAligned.sortedByCoord.out.bigwig"
+    },
+    {
+      "category": "RNA-Seq/Mapped Reads",
+      "key": "Queen",
+      "label": "Queen",
+      "metadata": {
+        "Analysis method": "Reads were trimmed with Trimmomatic (0.32) and aligned to the genome assembly by caste/life-stage using STAR (2.7.3a) in paired-end mode with the available NCBI genome gtf file. The reads were aligned to the genome in a second pass using all the available splice junction information from the first pass alignments. Bam files were indexed with SAMtools (1.10).The second pass splice junction output files were converted to bed files using the custom script available at: https://gist.github.com/fabiolib/ffb21853e3eb3780150074aeffc54901",
+        "Analysis provider": "Kim Walden, University of Illinois at Urbana-Champaign",
+        "Data source": "SRR6984023, SRR6984033, SRR6984032",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale re-use guidelines",
+        "Track legend": "Dark red alignments: Mapped portion of read aligned to forward strand<br>Light red alignments: Spliced portion of read aligned to forward strand<br>Dark blue alignments: Mapped portion of read aligned to reverse strand<br>Light blue alignments: Spliced portion of read aligned to reverse strand<br>Red marking - deletion in the read relative to the reference<br>Green marking - insertion in the read relative to the reference<br>Yellow marking  - mismatch (hover over the mismatch to see what the snp is)",
+        "development stage": "Queen"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "analyses/Odontomachus-brunneus-RNA-Seq_2020-06-09_v1.0/Odontomachus_queen_2nd_passAligned.sortedByCoord.out.bam"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "RNA-Seq/Coverage Plots",
+      "key": "Queen, coverage",
+      "label": "Queen, coverage",
+      "metadata": {
+        "Analysis method": "Reads were trimmed with Trimmomatic (0.32) and aligned to the genome assembly by caste/life-stage using STAR (2.7.3a) in paired-end mode with the available NCBI genome gtf file. The reads were aligned to the genome in a second pass using all the available splice junction information from the first pass alignments. Bam files were indexed with SAMtools (1.10). The second pass splice junction output files were converted to bed files using the custom script available at: https://gist.github.com/fabiolib/ffb21853e3eb3780150074aeffc54901",
+        "Analysis provider": "Kim Walden, University of Illinois at Urbana-Champaign",
+        "Data source": "SRR6984023, SRR6984033, SRR6984032",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale re-use guidelines",
+        "Track legend": "This track represents an X-Y plot of RNA-Seq coverage.",
+        "development stage": "Queen"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "pos_color": "#00BFFF"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "analyses/Odontomachus-brunneus-RNA-Seq_2020-06-09_v1.0/Odontomachus_queen_2nd_passAligned.sortedByCoord.out.bigwig"
+    },
+    {
+      "category": "RNA-Seq/Mapped Reads",
+      "key": "Pupa",
+      "label": "Pupa",
+      "metadata": {
+        "Analysis method": "Reads were trimmed with Trimmomatic (0.32) and aligned to the genome assembly by caste/life-stage using STAR (2.7.3a) in paired-end mode with the available NCBI genome gtf file. The reads were aligned to the genome in a second pass using all the available splice junction information from the first pass alignments. Bam files were indexed with SAMtools (1.10).The second pass splice junction output files were converted to bed files using the custom script available at: https://gist.github.com/fabiolib/ffb21853e3eb3780150074aeffc54901",
+        "Analysis provider": "Kim Walden, University of Illinois at Urbana-Champaign",
+        "Data source": "SRR6984020",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale re-use guidelines",
+        "Track legend": "Dark red alignments: Mapped portion of read aligned to forward strand<br>Light red alignments: Spliced portion of read aligned to forward strand<br>Dark blue alignments: Mapped portion of read aligned to reverse strand<br>Light blue alignments: Spliced portion of read aligned to reverse strand<br>Red marking - deletion in the read relative to the reference<br>Green marking - insertion in the read relative to the reference<br>Yellow marking  - mismatch (hover over the mismatch to see what the snp is)",
+        "development stage": "Pupa"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "analyses/Odontomachus-brunneus-RNA-Seq_2020-06-09_v1.0/Odontomachus_pupa_2nd_passAligned.sortedByCoord.out.bam"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "RNA-Seq/Coverage Plots",
+      "key": "Pupa, coverage",
+      "label": "Pupa, coverage",
+      "metadata": {
+        "Analysis method": "Reads were trimmed with Trimmomatic (0.32) and aligned to the genome assembly by caste/life-stage using STAR (2.7.3a) in paired-end mode with the available NCBI genome gtf file. The reads were aligned to the genome in a second pass using all the available splice junction information from the first pass alignments. Bam files were indexed with SAMtools (1.10). The second pass splice junction output files were converted to bed files using the custom script available at: https://gist.github.com/fabiolib/ffb21853e3eb3780150074aeffc54901",
+        "Analysis provider": "Kim Walden, University of Illinois at Urbana-Champaign",
+        "Data source": "SRR6984020",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale re-use guidelines",
+        "Track legend": "This track represents an X-Y plot of RNA-Seq coverage.",
+        "development stage": "Pupa"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "pos_color": "#00BFFF"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "analyses/Odontomachus-brunneus-RNA-Seq_2020-06-09_v1.0/Odontomachus_pupa_2nd_passAligned.sortedByCoord.out.bigwig"
+    },
+    {
+      "category": "RNA-Seq/Splice junctions",
+      "compress": 0,
+      "key": "Larva, junction reads",
+      "label": "Larva, junction reads",
+      "metadata": {
+        "Analysis method": "Reads were trimmed with Trimmomatic (0.32) and aligned to the genome assembly by caste/life-stage using STAR (2.7.3a) in paired-end mode with the available NCBI genome gtf file. The reads were aligned to the genome in a second pass using all the available splice junction information from the first pass alignments. Bam files were indexed with SAMtools (1.10). The second pass splice junction output files were converted to bed files using the custom script available at: https://gist.github.com/fabiolib/ffb21853e3eb3780150074aeffc54901",
+        "Analysis provider": "Kim Walden, University of Illinois at Urbana-Champaign",
+        "Data source": "SRR6984019, SRR6984036, SRR6984027",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale re-use guidelines",
+        "Track legend": "Junction reads",
+        "development stage": "Larva"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "CDS": "junction-cds",
+          "UTR": "webapollo-UTR",
+          "exon": "container-100pct",
+          "intron": null,
+          "match_part": "darkblue-80pct",
+          "start_codon": null,
+          "stop_codon": null,
+          "wholeCDS": null
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/Larva, junction reads/{refseq}/trackData.json"
+    },
+    {
+      "category": "RNA-Seq/Splice junctions",
+      "compress": 0,
+      "key": "Non-reproductive Adult Worker, junction reads",
+      "label": "Non-reproductive Adult Worker, junction reads",
+      "metadata": {
+        "Analysis method": "Reads were trimmed with Trimmomatic (0.32) and aligned to the genome assembly by caste/life-stage using STAR (2.7.3a) in paired-end mode with the available NCBI genome gtf file. The reads were aligned to the genome in a second pass using all the available splice junction information from the first pass alignments. Bam files were indexed with SAMtools (1.10). The second pass splice junction output files were converted to bed files using the custom script available at: https://gist.github.com/fabiolib/ffb21853e3eb3780150074aeffc54901",
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+}
diff --git a/organisms/stage/stage-v2/Oncopeltus_fasciatus/trackList.json b/organisms/stage/stage-v2/Oncopeltus_fasciatus/trackList.json
new file mode 100644
index 0000000..216ab15
--- /dev/null
+++ b/organisms/stage/stage-v2/Oncopeltus_fasciatus/trackList.json
@@ -0,0 +1,2144 @@
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+    },
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+      "compress": 0,
+      "key": "protein2genome_Cephalochordata",
+      "label": "protein2genome_Cephalochordata",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Cephalochordata proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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+          "match_part": "protein2genome"
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+      "urlTemplate": "tracks/protein2genome_Cephalochordata/{refseq}/trackData.json"
+    },
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+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Chelicerata",
+      "label": "protein2genome_Chelicerata",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Chelicerata proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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+          "match_part": "protein2genome"
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+    },
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+      "compress": 0,
+      "key": "protein2genome_Cnidaria",
+      "label": "protein2genome_Cnidaria",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Cnidaria proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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+          "match_part": "protein2genome"
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Cnidaria/{refseq}/trackData.json"
+    },
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+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Craniata",
+      "label": "protein2genome_Craniata",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Craniata proteins as part of the MAKER automated annotation pipeline."
+      },
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+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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+          "match_part": "protein2genome"
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+    },
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+      "compress": 0,
+      "key": "protein2genome_Crustacea",
+      "label": "protein2genome_Crustacea",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Crustacea proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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+          "match_part": "protein2genome"
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+      "type": "FeatureTrack",
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+    },
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+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Echinodermata",
+      "label": "protein2genome_Echinodermata",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Echinodermata proteins as part of the MAKER automated annotation pipeline."
+      },
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+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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+          "match_part": "protein2genome"
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Echinodermata/{refseq}/trackData.json"
+    },
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+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Mollusca",
+      "label": "protein2genome_Mollusca",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Mollusca proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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+          "match_part": "protein2genome"
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Mollusca/{refseq}/trackData.json"
+    },
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+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Nemata",
+      "label": "protein2genome_Nemata",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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+          "match_part": "protein2genome"
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+      "urlTemplate": "tracks/protein2genome_Nemata/{refseq}/trackData.json"
+    },
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+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Nematomorpha",
+      "label": "protein2genome_Nematomorpha",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Nematomorpha proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Nematomorpha/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Onychophora",
+      "label": "protein2genome_Onychophora",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Onychophora proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
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+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Onychophora/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Parazoa",
+      "label": "protein2genome_Parazoa",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Parazoa/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Placozoa",
+      "label": "protein2genome_Placozoa",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Placozoa/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Platyhelminthes",
+      "label": "protein2genome_Platyhelminthes",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Platyhelminthes/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Priapulida",
+      "label": "protein2genome_Priapulida",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Priapulida/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Tardigrada",
+      "label": "protein2genome_Tardigrada",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Tardigrada/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Tunicata",
+      "label": "protein2genome_Tunicata",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Tunicata/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_UNCATEGORISED",
+      "label": "protein2genome_UNCATEGORISED",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_UNCATEGORISED/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/2. Evidence/Repeats",
+      "compress": 0,
+      "key": "repeatmasker",
+      "label": "repeatmasker",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from RepeatMasker as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "repeat"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/repeatmasker/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/2. Evidence/Repeats",
+      "compress": 0,
+      "key": "repeatrunner",
+      "label": "repeatrunner",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Repeatrunner as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "repeat"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/repeatrunner/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/1. Gene Sets/Supplementary Gene Predictions",
+      "compress": 0,
+      "key": "snap_masked",
+      "label": "snap_masked",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "snap"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/snap_masked/{refseq}/trackData.json"
+    },
+    {
+      "category": "RNA-Seq/Mapped Reads",
+      "key": "pooled RNA-seq - cleaned reads",
+      "label": "pooled_RNA-seq_cleaned_reads",
+      "metadata": {
+        "Alignment method": "TopHat 2.0.9, option --b2-very-sensitive",
+        "Alignment summary": "http://de.iplantcollaborative.org/dl/d/C1F07955-A133-4B73-85B5-4D5E57AC764C/align_summary.txt",
+        "Data Provider": "Baylor College of Medicine",
+        "Data Source 1": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-adult-female-1-1_1pA_C1M7KACXX-7-ID03_1_sequence.txt.bz2",
+        "Data Source 2": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-adult-female-1-1_1pA_C1M7KACXX-7-ID03_2_sequence.txt.bz2",
+        "Data Source 3": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-adult-male-1-1_1pA_C22AGACXX-4-ID02_1_sequence.txt.bz2",
+        "Data Source 4": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-adult-male-1-1_1pA_C22AGACXX-4-ID02_2_sequence.txt.bz2",
+        "Data Source 5": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-juveniles-1-1_1pA_C22AGACXX-4-ID01_1_sequence.txt.bz2",
+        "Data Source 6": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-juveniles-1-1_1pA_C22AGACXX-4-ID01_2_sequence.txt.bz2",
+        "Read cleaning method": "Quality and adapter trimming with Trimmomatic3.0 (parameters ILLUMINACLIP:Trimmomatic-0.30/adapters/TruSeq3-PE.fa:2:30:10:8:true LEADING:3  TRAILING:3  SLIDINGWINDOW:4:15  MINLEN:36)",
+        "Track legend": "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)"
+      },
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+      },
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+    },
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+        "Track legend": "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)"
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+      "category": "RNA-Seq/Mapped Reads",
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+        "Read cleaning method": "None",
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+      },
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+        "Data Source": "http://genomics-pubs.princeton.edu/insect_genomics/data/Oncopeltus_fasciatus.tar",
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+      "urlTemplate": "bam/ivargas/andolfatto_raw_reads/accepted_hits.bigwig",
+      "variance_band": false
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+      "key": "Maternal and early embryonic 454 transcriptome",
+      "label": "mat_embr_454_transcriptome",
+      "metadata": {
+        "Alignment contact": "Iris Vargas-Jentzsch, University of Cologne",
+        "Alignment program and Parameters": "GMAP version 2014-05-15 called with args: Ofas_454.transcriptome_complete_short.fasta -d Ofas.scaffolds -f 2",
+        "BioProject": "PRJNA79671; Accession #s SRX022011, SRX022012, SRX022013, SRX022014",
+        "Data Source": "http://www.extavourlab.com/resources/Oncopeltus_454transcriptome_BLASTnames_01_2011.fasta<br> Here we used the complete transcriptome dataset, including singletons, obtained directly from Ben Ewen-Campen (bewencampen at oeb dot harvard dot edu).",
+        "PMCID": "PMC3040728",
+        "PMID": "21266083",
+        "Reference": "Ewen-Campen B., Shaner N., Panfilio K. A., Suzuki Y., Roth S., and Extavour C. G. (2011). The maternal and early embryonic transcriptome of the milkweed bug Oncopeltus fasciatus. BMC Genomics 12: 61."
+      },
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+        "Data Source": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/",
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+      },
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+      "metadata": {
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+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+      },
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+        "neg_color": "white",
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+      "urlTemplate": "bigwig/Ofas.scaffolds-GAPS.bigwig"
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+      "bicolor_pivot": "0.5",
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+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+      },
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+      "style": {
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+      "urlTemplate": "bigwig/Ofas.scaffolds_GC.bigwig"
+    },
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+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Official Gene Set OGS_v1.1. Note that stop codon read-through features are visualized as red bars above and below the CDS."
+      },
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+    },
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+      "label": "OGS_v1.1_rRNA",
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+        "Analysis description": "The Official Gene Set OGSv1.1 has been superseded by OGSv1.2. OGSv1.1 was generated from the computationally predicted gene set OFAS_v0.5.3 and manually curated models.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
+      },
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+      "urlTemplate": "tracks/OGS_v1.1_rRNA/{refseq}/trackData.json"
+    },
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+      "category": "Official Gene Set v1.1/2. Noncoding Genes",
+      "compress": 0,
+      "key": "OGS_v1.1_pseudogene",
+      "label": "OGS_v1.1_pseudogene",
+      "metadata": {
+        "Analysis description": "The Official Gene Set OGSv1.1 has been superseded by OGSv1.2. OGSv1.1 was generated from the computationally predicted gene set OFAS_v0.5.3 and manually curated models.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
+      },
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/OGS_v1.1_pseudogene/{refseq}/trackData.json"
+    },
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+      "compress": 0,
+      "fmtDetailValue_Id": "function(id, feature) { var name2 = id.replace(/-R./, ''); if(feature.get('type')=='mRNA') { return '<a href=\"https://i5k.nal.usda.gov/'+name2+'\" target=\"_blank\"><b>'+id+'</a> (Click for Gene page)</b>';} else {return id}}",
+      "key": "OGSv1.2 protein-coding genes",
+      "label": "oncfas_current_models",
+      "menuTemplate": [
+        {
+          "label": "View details"
+        },
+        {
+          "action": "newWindow",
+          "iconClass": "dijitIconDatabase",
+          "label": "function(track,feature){ return 'Open gene page for '+feature.get('id').replace(/-R./, '')}",
+          "title": "function(track,feature){ return 'Open gene page for '+feature.get('id').replace(/-R./, '')}",
+          "url": "function(track,feature){ return 'https://i5k.nal.usda.gov/'+feature.get('id').replace(/-R./, '')}"
+        }
+      ],
+      "metadata": {
+        "Analysis description": "The Official Gene Set OGSv1.2 is an update of OGSv1.1.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Official Gene Set OGS_v1.2. Note that stop codon read-through features are visualized as red bars above and below the CDS."
+      },
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+      "style": {
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+      "urlTemplate": "tracks/oncfas_current_models/{refseq}/trackData.json"
+    },
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+      "key": "OGSv1.2 pseudogenes",
+      "label": "OGS_v1.2_pseudogenes",
+      "metadata": {
+        "Analysis description": "The Official Gene Set OGSv1.2 is an update of OGSv1.1.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
+      },
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+      "urlTemplate": "tracks/OGS_v1.2_pseudogenes/{refseq}/trackData.json"
+    },
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+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
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+        "Analysis description": "The Official Gene Set OGSv1.2 is an update of OGSv1.1.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use."
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/OGS_v1.2_sequence_modifications/{refseq}/trackData.json"
+    },
+    {
+      "category": "RNA-Seq/Mapped Reads",
+      "key": "posterior embryo, 19 hours after egg laying",
+      "label": "posterior embryo, 19 hours after egg laying",
+      "metadata": {
+        "Analysis provider": "Ariel Chipman, The Hebrew University of Jerusalem; Agustin Baricalla, Universidad Nacional del Noroeste de Buenos Aires",
+        "Data description": "https://i5k.nal.usda.gov/node/933164",
+        "Data source": "https://doi.org/10.1002/dvg.23027",
+        "Materials and Methods": "https://doi.org/10.1002/dvg.23027",
+        "Program": "FastQC, trimomatic, MultiQC, STARaligner",
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+        "Track legend": "Dark red alignments: Mapped portion of read aligned to forward strand<br>Light red alignments: Spliced portion of read aligned to forward strand<br>Dark blue alignments: Mapped portion of read aligned to reverse strand<br>Light blue alignments: Spliced portion of read aligned to reverse strand<br>Red marking - deletion in the read relative to the reference<br>Green marking - insertion in the read relative to the reference<br>Yellow marking  - mismatch (hover over the mismatch to see what the snp is)",
+        "age": "19 hours after egg laying",
+        "development stage": "embryo",
+        "host tissue sampled": "posterior"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "analyses/Oncopeltus-fasciatus-RNA-Seq_04-24-2020_v1.0/19P.sorted.bam"
+    },
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+      "bicolor_pivot": "zero",
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diff --git a/organisms/stage/stage-v2/Oncopeltus_fasciatus_training/trackList.json b/organisms/stage/stage-v2/Oncopeltus_fasciatus_training/trackList.json
new file mode 100644
index 0000000..216ab15
--- /dev/null
+++ b/organisms/stage/stage-v2/Oncopeltus_fasciatus_training/trackList.json
@@ -0,0 +1,2144 @@
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+        "Track legend": "Results from Protein2genome alignments of a set of Mollusca proteins as part of the MAKER automated annotation pipeline."
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+        "arrowheadClass": "webapollo-arrowhead",
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+    },
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+      "label": "protein2genome_Nemata",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline."
+      },
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+        "arrowheadClass": "webapollo-arrowhead",
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+    },
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+      "key": "protein2genome_Nematomorpha",
+      "label": "protein2genome_Nematomorpha",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Nematomorpha proteins as part of the MAKER automated annotation pipeline."
+      },
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+          "match_part": "protein2genome"
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+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+      "key": "protein2genome_Onychophora",
+      "label": "protein2genome_Onychophora",
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+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Onychophora proteins as part of the MAKER automated annotation pipeline."
+      },
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+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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+          "match_part": "protein2genome"
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+      "type": "FeatureTrack",
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+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
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+      "label": "protein2genome_Parazoa",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline."
+      },
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+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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+      "urlTemplate": "tracks/protein2genome_Parazoa/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Placozoa",
+      "label": "protein2genome_Placozoa",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline."
+      },
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+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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+          "match_part": "protein2genome"
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+      "urlTemplate": "tracks/protein2genome_Placozoa/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Platyhelminthes",
+      "label": "protein2genome_Platyhelminthes",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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+          "match_part": "protein2genome"
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Platyhelminthes/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Priapulida",
+      "label": "protein2genome_Priapulida",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
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+          "match_part": "protein2genome"
+        }
+      },
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Priapulida/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Tardigrada",
+      "label": "protein2genome_Tardigrada",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Tardigrada/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Tunicata",
+      "label": "protein2genome_Tunicata",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Tunicata/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_UNCATEGORISED",
+      "label": "protein2genome_UNCATEGORISED",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_UNCATEGORISED/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/2. Evidence/Repeats",
+      "compress": 0,
+      "key": "repeatmasker",
+      "label": "repeatmasker",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from RepeatMasker as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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+        "subfeatureClasses": {
+          "match_part": "repeat"
+        }
+      },
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+      "urlTemplate": "tracks/repeatmasker/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/2. Evidence/Repeats",
+      "compress": 0,
+      "key": "repeatrunner",
+      "label": "repeatrunner",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Repeatrunner as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
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+        }
+      },
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/repeatrunner/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/1. Gene Sets/Supplementary Gene Predictions",
+      "compress": 0,
+      "key": "snap_masked",
+      "label": "snap_masked",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/snap_masked/{refseq}/trackData.json"
+    },
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+      "key": "pooled RNA-seq - cleaned reads",
+      "label": "pooled_RNA-seq_cleaned_reads",
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+        "Data Provider": "Baylor College of Medicine",
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+        "Data Source 3": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-adult-male-1-1_1pA_C22AGACXX-4-ID02_1_sequence.txt.bz2",
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+        "Data Source 5": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-juveniles-1-1_1pA_C22AGACXX-4-ID01_1_sequence.txt.bz2",
+        "Data Source 6": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-juveniles-1-1_1pA_C22AGACXX-4-ID01_2_sequence.txt.bz2",
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+        "Track legend": "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)"
+      },
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+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "bam/ivargas/cleaned_reads/accepted_hits.bam"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "RNA-Seq/Coverage Plots",
+      "key": "pooled RNA-seq - cleaned reads, XY-plot",
+      "label": "pooled RNA-seq - cleaned reads, XY-plot",
+      "metadata": {
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+        "Alignment summary": "http://de.iplantcollaborative.org/dl/d/C1F07955-A133-4B73-85B5-4D5E57AC764C/align_summary.txt",
+        "Data Provider": "Baylor College of Medicine",
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+        "Data Source 2": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-adult-female-1-1_1pA_C1M7KACXX-7-ID03_2_sequence.txt.bz2",
+        "Data Source 3": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-adult-male-1-1_1pA_C22AGACXX-4-ID02_1_sequence.txt.bz2",
+        "Data Source 4": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-adult-male-1-1_1pA_C22AGACXX-4-ID02_2_sequence.txt.bz2",
+        "Data Source 5": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-juveniles-1-1_1pA_C22AGACXX-4-ID01_1_sequence.txt.bz2",
+        "Data Source 6": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-juveniles-1-1_1pA_C22AGACXX-4-ID01_2_sequence.txt.bz2",
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+        "Track legend": "This track represents an X-Y plot of RNA-Seq coverage. The y-axis represents the number of mapped reads. The scale of the y-axis changes with the maximum number of reads aligned in the browser region. The y-axis has a minimum value of abs(2000); areas with higher coverage are indicated by a red clip."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "clip_marker_color": "red",
+        "height": 50,
+        "neg_color": "#005EFF",
+        "pos_color": "#FFA600"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "bam/ivargas/cleaned_reads/accepted_hits.bigwig"
+    },
+    {
+      "category": "RNA-Seq/Mapped Reads",
+      "key": "pooled RNA-seq - raw reads",
+      "label": "pooled_RNA-seq_raw_reads",
+      "metadata": {
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+        "Read cleaning method": "None",
+        "Track legend": "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "bam/ivargas/raw_reads/accepted_hits.bam"
+    },
+    {
+      "category": "RNA-Seq/Mapped Reads",
+      "key": "RNA-seq raw PE reads Andolfatto et al.",
+      "label": "RNA-seq_Andolfatto_raw_PE_reads",
+      "metadata": {
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+        "PMCID": "PMC3040728",
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+        "Reference": "Ewen-Campen B., Shaner N., Panfilio K. A., Suzuki Y., Roth S., and Extavour C. G. (2011). The maternal and early embryonic transcriptome of the milkweed bug Oncopeltus fasciatus. BMC Genomics 12: 61."
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diff --git a/organisms/stage/stage-v2/Onthophagus_taurus/trackList.json b/organisms/stage/stage-v2/Onthophagus_taurus/trackList.json
new file mode 100644
index 0000000..fbd2ce9
--- /dev/null
+++ b/organisms/stage/stage-v2/Onthophagus_taurus/trackList.json
@@ -0,0 +1,1595 @@
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+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Platyhelminthes/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Priapulida",
+      "label": "protein2genome_Priapulida",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Priapulida/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Tardigrada",
+      "label": "protein2genome_Tardigrada",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
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+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Tardigrada/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Tunicata",
+      "label": "protein2genome_Tunicata",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Tunicata/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_UNCATEGORISED",
+      "label": "protein2genome_UNCATEGORISED",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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+        "subfeatureClasses": {
+          "match_part": "protein2genome"
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+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_UNCATEGORISED/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/2. Evidence/Repeats",
+      "compress": 0,
+      "key": "repeatmasker",
+      "label": "repeatmasker",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from RepeatMasker as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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+        "subfeatureClasses": {
+          "match_part": "repeat"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/repeatmasker/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/2. Evidence/Repeats",
+      "compress": 0,
+      "key": "repeatrunner",
+      "label": "repeatrunner",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Repeatrunner as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "repeat"
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+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/repeatrunner/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/1. Gene Sets/Supplementary Gene Predictions",
+      "compress": 0,
+      "key": "snap_masked",
+      "label": "snap_masked",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "snap"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/snap_masked/{refseq}/trackData.json"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Reference Assembly",
+      "key": "Gaps in assembly",
+      "label": "Gaps in assembly",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "white",
+        "pos_color": "black"
+      },
+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "bigwig/Otaur.scaffolds.fa.gaps.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "0.5",
+      "category": "Reference Assembly",
+      "key": "GC Content",
+      "label": "GC Content",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+      },
+      "scoreType": "avgScore",
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "rgba(255,255,0,50)",
+        "pos_color": "rgba(0,0,255,50)"
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+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "bigwig/Otaur.scaffolds.fa.gc.bigwig"
+    },
+    {
+      "category": "Transcriptome/Mapped Reads",
+      "key": "Onthophagus taurus early male pupa brain transcripts",
+      "label": "Onthophagus taurus early male pupa brain transcripts",
+      "metadata": {
+        "Analysis method": "tophat2 v2.1.0",
+        "Date completed": "Nov-15",
+        "File provider": "Eduardo E Zattara, Indiana University Bloomington",
+        "Geographical location of specimen collection": "United States, Mapple View Farm, NC",
+        "NCBI TaxID": "166361",
+        "Other methods": "Trimmomatic 0.32",
+        "Other notes on methods": "Part of a larger project still unpublished",
+        "Other organism notes": "Large male",
+        "Publication Status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+        "Sequencing platform and version": "Illumina NextSeq 500, High Output 75 cycles ",
+        "Sex": "Male",
+        "Strain": "NC",
+        "Tissues included": "Brain"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlM-BRN_S22.sorted.bam"
+    },
+    {
+      "category": "Transcriptome/Mapped Reads",
+      "key": "Onthophagus taurus early female pupa brain transcripts",
+      "label": "Onthophagus taurus early female pupa brain transcripts",
+      "metadata": {
+        "Analysis method": "tophat2 v2.1.0",
+        "Date completed": "Nov-15",
+        "File provider": "Eduardo E Zattara, Indiana University Bloomington",
+        "Geographical location of specimen collection": "United States, Mapple View Farm, NC",
+        "NCBI TaxID": "166361",
+        "Other methods": "Trimmomatic 0.32",
+        "Other notes on methods": "Part of a larger project still unpublished",
+        "Other organism notes": "Large female",
+        "Publication Status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+        "Sequencing platform and version": "Illumina NextSeq 500, High Output 75 cycles ",
+        "Sex": "Female",
+        "Strain": "NC",
+        "Tissues included": "Brain"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlF-BRN_S18.sorted.bam"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Transcriptome/Coverage Plots (BigWig)",
+      "key": "Onthophagus taurus early male pupa brain transcripts (Coverage Plot)",
+      "label": "Onthophagus taurus early male pupa brain transcripts (Coverage Plot)",
+      "metadata": {
+        "Analysis method": "tophat2 v2.1.0",
+        "Date completed": "Nov-15",
+        "File provider": "Eduardo E Zattara, Indiana University Bloomington",
+        "Geographical location of specimen collection": "United States, Mapple View Farm, NC",
+        "NCBI TaxID": "166361",
+        "Other methods": "Trimmomatic 0.32",
+        "Other notes on methods": "Part of a larger project still unpublished",
+        "Other organism notes": "Large male",
+        "Publication Status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+        "Sequencing platform and version": "Illumina NextSeq 500, High Output 75 cycles ",
+        "Sex": "Male",
+        "Strain": "NC",
+        "Tissues included": "Brain"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "pos_color": "#00BFFF"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlM-BRN_S22.sorted.bigwig"
+    },
+    {
+      "autoscale": "local",
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+      "key": "Onthophagus taurus early female pupa brain transcripts (Coverage Plot)",
+      "label": "Onthophagus taurus early female pupa brain transcripts (Coverage Plot)",
+      "metadata": {
+        "Analysis method": "tophat2 v2.1.0",
+        "Date completed": "Nov-15",
+        "File provider": "Eduardo E Zattara, Indiana University Bloomington",
+        "Geographical location of specimen collection": "United States, Mapple View Farm, NC",
+        "NCBI TaxID": "166361",
+        "Other methods": "Trimmomatic 0.32",
+        "Other notes on methods": "Part of a larger project still unpublished",
+        "Other organism notes": "Large female",
+        "Publication Status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+        "Sequencing platform and version": "Illumina NextSeq 500, High Output 75 cycles ",
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+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "user_contributed_data/ezattara/pupal_brain_transcripts_feb2016/ctrlF-BRN_S18.sorted.bigwig"
+    },
+    {
+      "category": "Gene Silhouette Models/1. Gene Sets/Protein Coding",
+      "compress": 0,
+      "key": "Gene Silhouette Models v4",
+      "label": "Gene_Silhouette_Models_v4",
+      "metadata": {
+        "Analysis method": "Gene Silhouette Algorithm, alpha version, unpublished",
+        "Analysis provider": "Douglas B. Rusch, Centre for Genomics and Bioinformatics, Indiana University Bloomington",
+        "Other notes": "Novel algorithm predicts genes based on mapped RNAseq reads; based on data from early pupae, brain, dorsal head and pronotal epidermis, and posterior abdominal epidermis only"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "CDS": "gnomon_CDS",
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+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/Gene_Silhouette_Models_v4/{refseq}/trackData.json"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Transcriptome/Coverage Plots (BigWig)",
+      "key": "O. taurus M PD1 BRN+CHE+THE+GEN transcripts",
+      "label": "O. taurus M PD1 BRN+CHE+THE+GEN transcripts",
+      "metadata": {
+        "Analysis method": "tophat2 v2.1.0",
+        "Date completed": "Nov-15",
+        "File provider": "Eduardo E Zattara, Indiana University Bloomington",
+        "Geographical location of specimen collection": "United States, Mapple View Farm, NC",
+        "Other methods": "Trimmomatic 0.32",
+        "Other notes on methods": "Part of a larger project still unpublished",
+        "Other organism notes": "Large male",
+        "Publication Status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Sequencing platform and version": "Illumina NextSeq 500, High Output 75 cycles ",
+        "Sex": "Male",
+        "Strain": "NC",
+        "Tissues included": "pooled brain, dorsal head epidermis, pronotum epidermis, posterior abdominal epidermis"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
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+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "user_contributed_data/ezattara/mixed_transcripts_march_2016/ctrlM-ALL.merged.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Transcriptome/Coverage Plots (BigWig)",
+      "key": "O. taurus F PD1 BRN+CHE+THE+GEN transcripts",
+      "label": "O. taurus F PD1 BRN+CHE+THE+GEN transcripts",
+      "metadata": {
+        "Analysis method": "tophat2 v2.1.0",
+        "Date completed": "Nov-15",
+        "File provider": "Eduardo E Zattara, Indiana University Bloomington",
+        "Geographical location of specimen collection": "United States, Mapple View Farm, NC",
+        "Other methods": "Trimmomatic 0.32",
+        "Other notes on methods": "Part of a larger project still unpublished",
+        "Other organism notes": "Large female",
+        "Publication Status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Sequencing platform and version": "Illumina NextSeq 500, High Output 75 cycles ",
+        "Sex": "Female",
+        "Strain": "NC",
+        "Tissues included": "pooled brain, dorsal head epidermis, pronotum epidermis, posterior abdominal epidermis"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
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+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "user_contributed_data/ezattara/mixed_transcripts_march_2016/ctrlF-ALL.merged.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Transcriptome/Coverage Plots (BigWig)",
+      "key": "O. taurus M NC L3L+PP1+PD1+AD4",
+      "label": "O. taurus M NC L3L+PP1+PD1+AD4",
+      "metadata": {
+        "Analysis method": "tophat2 v2.0.14",
+        "File provider": "Eduardo E Zattara, Indiana University Bloomington",
+        "Geographical location of specimen collection": "United States, Mapple View Farm, NC",
+        "Other methods": "Trimmomatic 0.32",
+        "Other notes": "Part of a larger project still unpublished",
+        "Other organism notes": "Large male",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Sequencing platform and version": "Illumina HiSeq 100PE",
+        "Sex": "Male",
+        "Strain": "NC",
+        "Tissues included": "whole body, pooled late 3 larvae, prepupa 1, pupa day 1, adult day 4"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "pos_color": "#00BFFF"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "user_contributed_data/ezattara/NC-L3L_PP1_PD1_AD4/NC_M_merged.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Transcriptome/Coverage Plots (BigWig)",
+      "key": "O. taurus F NC L3L+PP1+PD1+AD4",
+      "label": "O. taurus F NC L3L+PP1+PD1+AD4",
+      "metadata": {
+        "Analysis method": "tophat2 v2.0.14",
+        "File provider": "Eduardo E Zattara, Indiana University Bloomington",
+        "Geographical location of specimen collection": "United States, Mapple View Farm, NC",
+        "Other methods": "Trimmomatic 0.32",
+        "Other notes": "Part of a larger project still unpublished",
+        "Other organism notes": "Large female",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Sequencing platform and version": "Illumina HiSeq 100PE",
+        "Sex": "Female",
+        "Strain": "NC",
+        "Tissues included": "whole body, pooled late 3 larvae, prepupa 1, pupa day 1, adult day 4"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
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+        "pos_color": "#00BFFF"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "user_contributed_data/ezattara/NC-L3L_PP1_PD1_AD4/NC_F_merged.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Transcriptome/Coverage Plots (BigWig)",
+      "key": "O. taurus embryonic reads",
+      "label": "O. taurus embryonic",
+      "metadata": {
+        "Analysis method": "tophat2 v2.0.14",
+        "Date completed": "Nov-15",
+        "File provider": "Eduardo E Zattara, Indiana University Bloomington",
+        "Geographical location of specimen collection": "Western Australia, Busselton",
+        "NCBI TaxID": "166361",
+        "Other methods": "Trimmomatic 0.32",
+        "Other notes on methods": "Part of a larger project still unpublished",
+        "Publication Status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+        "Sequencing platform and version": "Illumina NextSeq500, 75SE",
+        "Sex": "pooled",
+        "Strain": "WA",
+        "Tissues included": "whole embryos, pooled mixed stages"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "pos_color": "#00BFFF"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "user_contributed_data/ezattara/whole_embryos/Otau-embryos.bigwig"
+    },
+    {
+      "category": "Transcriptome/Mapped Reads",
+      "key": "O. taurus embryonic reads",
+      "label": "O. taurus embryonic reads",
+      "metadata": {
+        "Analysis method": "tophat2 v2.0.14",
+        "Date completed": "Nov-15",
+        "File provider": "Eduardo E Zattara, Indiana University Bloomington",
+        "Geographical location of specimen collection": "Western Australia, Busselton",
+        "NCBI TaxID": "166361",
+        "Other methods": "Trimmomatic 0.32",
+        "Other notes on methods": "Part of a larger project still unpublished",
+        "Publication Status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
+        "Sequencing platform and version": "Illumina NextSeq500, 75SE",
+        "Sex": "pooled",
+        "Strain": "WA",
+        "Tissues included": "whole embryos, pooled mixed stages"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "user_contributed_data/ezattara/whole_embryos/Otau-embryos.accepted_hits.sorted.bam"
+    },
+    {
+      "category": "Transcriptome/Splice Junctions",
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+      "label": "O. taurus whole body, mixed stage RNAseq, reduced coverage, females",
+      "metadata": {
+        "Analysis method": "tophat2 v2.1.0",
+        "Date completed": "June-16-2016",
+        "File provider": "Eduardo E Zattara, Indiana University Bloomington",
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+        "NCBI TaxID": "166361",
+        "Other methods": "Trimmomatic 0.32, normalized coverage with samtools, picard and GATK",
+        "Other notes on methods": "Part of a larger project still unpublished",
+        "Other tissue notes": "Mix of late larvae, prepupae, pupae and adult RNA; pool of 12 individuals",
+        "Publication Status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
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+        "File provider": "Eduardo E Zattara, Indiana University Bloomington",
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+        "NCBI TaxID": "166361",
+        "Other methods": "Trimmomatic 0.32, normalized coverage with samtools, picard and GATK",
+        "Other notes on methods": "Part of a larger project still unpublished",
+        "Other tissue notes": "Mix of late larvae, prepupae, pupae and adult RNA; pool of 12 individuals",
+        "Publication Status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. ",
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+      "urlTemplate": "user_contributed_data/ezattara/reduced_coverage_june_2016/NC_M_merged.reduced.bam"
+    }
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+}
diff --git a/organisms/stage/stage-v2/Orussus_abietinus/trackList.json b/organisms/stage/stage-v2/Orussus_abietinus/trackList.json
new file mode 100755
index 0000000..29eae44
--- /dev/null
+++ b/organisms/stage/stage-v2/Orussus_abietinus/trackList.json
@@ -0,0 +1,1532 @@
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+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Parazoa/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Placozoa",
+      "label": "protein2genome_Placozoa",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Placozoa/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Platyhelminthes",
+      "label": "protein2genome_Platyhelminthes",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Platyhelminthes/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Priapulida",
+      "label": "protein2genome_Priapulida",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Priapulida/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Tardigrada",
+      "label": "protein2genome_Tardigrada",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Tardigrada/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Tunicata",
+      "label": "protein2genome_Tunicata",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Tunicata/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_UNCATEGORISED",
+      "label": "protein2genome_UNCATEGORISED",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_UNCATEGORISED/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/2. Evidence/Repeats",
+      "compress": 0,
+      "key": "repeatmasker",
+      "label": "repeatmasker",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from RepeatMasker as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "repeat"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/repeatmasker/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/2. Evidence/Repeats",
+      "compress": 0,
+      "key": "repeatrunner",
+      "label": "repeatrunner",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Repeatrunner as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "repeat"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/repeatrunner/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/1. Gene Sets/Supplementary Gene Predictions",
+      "compress": 0,
+      "key": "snap_masked",
+      "label": "snap_masked",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "snap"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/snap_masked/{refseq}/trackData.json"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Reference Assembly",
+      "key": "Gaps in assembly",
+      "label": "Gaps in assembly",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "white",
+        "pos_color": "black"
+      },
+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "bigwig/Oabi11242013.GAPS.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "0.5",
+      "category": "Reference Assembly",
+      "key": "GC Content",
+      "label": "GC Content",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+      },
+      "scoreType": "avgScore",
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "rgba(255,255,0,50)",
+        "pos_color": "rgba(0,0,255,50)"
+      },
+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "bigwig/Oabi11242013.genome_GC.bigwig"
+    },
+    {
+      "category": "Transcriptome/Assembly",
+      "compress": 0,
+      "key": "O. abietinus female Trinity transcriptome",
+      "label": "Oabi-female_est2genome",
+      "metadata": {
+        "Analysis provider": "JP Oeyen (Univ. Bonn/ZFMK, ZMB), janphilipoyen@gmail.com)",
+        "Data Source 1": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Parasitic_wood_wasp/RNA_sequence/Oabi_ICD_OAi5ON.BN106-1_1pA_D2FUUACXX-1-ID01_1_sequence.txt.bz2; ftp://ftp.hgsc.bcm.edu/I5K-pilot/Parasitic_wood_wasp/RNA_sequence/Oabi_ICD_OAi5ON.BN106-1_1pA_D2FUUACXX-1-ID01_2_sequence.txt.bz2",
+        "Data description": "Raw reads cleaned with Trimmomatic v0.32, using the options ILLUMINACLIP:costumadapterlist.fa:2:30:10, SLIDINGWINDOW:4:33 and MINLEN:45. Cleaned reads were assembled using Trinity version trinityrnaseq_r20140413p1 using default settings. Assembled transcripts were mapped to the genome using Exonerate-gff3 (https://github.com/hotdogee/exonerate-gff3) with the options: --model est2genome --showtargetgff yes --gff3 yes --showalignment no --showvulgar no --geneseed 250 --bestn 2 --percent 50 --minintron 20 --maxintron 10000. Transcripts mapping to two locations were detected and marked with a note using a custom perl script (available from JP Oeyen (Univ. Bonn/ZFMK, ZMB), janphilipoyen@gmail.com)",
+        "Publication status": "unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "est_gff"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/Oabi-female_est2genome/{refseq}/trackData.json"
+    },
+    {
+      "category": "Transcriptome/Assembly",
+      "compress": 0,
+      "key": "O. abietinus male Trinity transcriptome",
+      "label": "Oabi-male_est2genome",
+      "metadata": {
+        "Analysis provider": "JP Oeyen (Univ. Bonn/ZFMK, ZMB), janphilipoyen@gmail.com)",
+        "Data Source": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Parasitic_wood_wasp/RNA_sequence/Oabi_ICD_OAi5ON.BN108-1_1pA_D2FUUACXX-1-ID02_1_sequence.txt.bz2; ftp://ftp.hgsc.bcm.edu/I5K-pilot/Parasitic_wood_wasp/RNA_sequence/Oabi_ICD_OAi5ON.BN108-1_1pA_D2FUUACXX-1-ID02_2_sequence.txt.bz2",
+        "Data description": "Raw reads cleaned with Trimmomatic v0.32, using the options ILLUMINACLIP:costumadapterlist.fa:2:30:10, SLIDINGWINDOW:4:33 and MINLEN:45. Cleaned reads were assembled using Trinity version trinityrnaseq_r20140413p1 using default settings. Assembled transcripts were mapped to the genome using Exonerate-gff3 (https://github.com/hotdogee/exonerate-gff3) with the options: --model est2genome --showtargetgff yes --gff3 yes --showalignment no --showvulgar no --geneseed 250 --bestn 2 --percent 50 --minintron 20 --maxintron 10000. Transcripts mapping to two locations were detected and marked with a note using a custom perl script (available from JP Oeyen (Univ. Bonn/ZFMK, ZMB), janphilipoyen@gmail.com)",
+        "Publication status": "unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "est_gff"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/Oabi-male_est2genome/{refseq}/trackData.json"
+    },
+    {
+      "category": "Univ. Bonn/Supplementary Gene Predictions",
+      "compress": 0,
+      "key": "O. abietinus two-pass maker",
+      "label": "Maker_Oabi11242013_iterative",
+      "metadata": {
+        "Analysis provider": "JP Oeyen (Univ. Bonn/ZFMK, ZMB), janphilipoyen@gmail.com)",
+        "Data Source": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Parasitic_wood_wasp/genome_assemblies/Oabi11242013.genome.fa",
+        "Data description": "Maker annotation with 2 consequtive runs with transcriptome and protein evidence. More details will be filled in soon!",
+        "Publication status": "unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "className": "{type}",
+        "subfeatureClasses": {
+          "CDS": "alt_gene_set-cds",
+          "UTR": "alt_gene_set-utr",
+          "exon": "container-100pct",
+          "wholeCDS": null
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/Maker_Oabi11242013_iterative/{refseq}/trackData.json"
+    },
+    {
+      "category": "Transcriptome/Mapped Reads",
+      "key": "O. abietinus female cleaned reads",
+      "label": "Oabi-female_tophat-accepted_hits",
+      "metadata": {
+        "Analysis provider": "JP Oeyen (Univ. Bonn/ZFMK, ZMB), janphilipoyen@gmail.com)",
+        "Data Source": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Parasitic_wood_wasp/RNA_sequence/Oabi_ICD_OAi5ON.BN106-1_1pA_D2FUUACXX-1-ID01_1_sequence.txt.bz2; ftp://ftp.hgsc.bcm.edu/I5K-pilot/Parasitic_wood_wasp/RNA_sequence/Oabi_ICD_OAi5ON.BN106-1_1pA_D2FUUACXX-1-ID01_2_sequence.txt.bz2",
+        "Data description": "Raw reads cleaned with Trimmomatic v0.32, using the options ILLUMINACLIP:'costumadapterlist.fa':2:30:10, SLIDINGWINDOW:4:33 and MINLEN:45. Cleaned reads mapped with TopHat v2.0.12 using default settings.",
+        "File note": "This track replaces the previous track, 'Orussus abietinus female RNAseq cleaned unassembled reads, alignments'",
+        "Publication status": "unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use",
+        "Track legend": "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "bam/janphilipoeyen/cleaned-reads-tophat/Oabi-female_tophat-accepted_hits.bam"
+    },
+    {
+      "category": "Transcriptome/Mapped Reads",
+      "key": "O. abietinus male cleaned reads",
+      "label": "Oabi-male_tophat-accepted_hits",
+      "metadata": {
+        "Analysis provider": "JP Oeyen (Univ. Bonn/ZFMK, ZMB), janphilipoyen@gmail.com)",
+        "Data Source": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Parasitic_wood_wasp/RNA_sequence/Oabi_ICD_OAi5ON.BN108-1_1pA_D2FUUACXX-1-ID02_1_sequence.txt.bz2, ftp://ftp.hgsc.bcm.edu/I5K-pilot/Parasitic_wood_wasp/RNA_sequence/Oabi_ICD_OAi5ON.BN108-1_1pA_D2FUUACXX-1-ID02_2_sequence.txt.bz2",
+        "Data description": "Raw reads cleaned with Trimmomatic v0.32, using the options ILLUMINACLIP:'costumadapterlist.fa':2:30:10, SLIDINGWINDOW:4:33 and MINLEN:45. Cleaned reads mapped with TopHat v2.0.12 using default settings.",
+        "File note": "This track replaces the previous track, 'Orussus abietinus male RNAseq cleaned unassembled reads, alignments'",
+        "Publication status": "unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use",
+        "Track legend": "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:<br>Red - deletion in the read relative to the reference<br>Green - insertion in the read relative to the reference<br>Yellow - mismatch (hover over the mismatch to see what the snp is)"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "bam/janphilipoeyen/cleaned-reads-tophat/Oabi-male_tophat-accepted_hits.bam"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Transcriptome/Coverage plots (BigWig)",
+      "key": " O. abietinus male cleaned reads, XY-plots",
+      "label": "Oabi-male_tophat-accepted_hits_bigwig",
+      "metadata": {
+        "Analysis provider": "JP Oeyen (Univ. Bonn/ZFMK, ZMB), janphilipoyen@gmail.com)",
+        "Data Source": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Parasitic_wood_wasp/RNA_sequence/Oabi_ICD_OAi5ON.BN108-1_1pA_D2FUUACXX-1-ID02_1_sequence.txt.bz2, ftp://ftp.hgsc.bcm.edu/I5K-pilot/Parasitic_wood_wasp/RNA_sequence/Oabi_ICD_OAi5ON.BN108-1_1pA_D2FUUACXX-1-ID02_2_sequence.txt.bz2",
+        "Data description": "Raw reads cleaned with Trimmomatic v0.32, using the options ILLUMINACLIP:'costumadapterlist.fa':2:30:10, SLIDINGWINDOW:4:33 and MINLEN:45. Cleaned reads mapped with TopHat v2.0.12 using default settings. Alignment files were converted by the NAL to bigwig format; reads that failed QC, secondary and supplementary alignments, and optical or PCR duplicates were ignored.",
+        "File note": "This track replaces the previous track, 'Orussus abietinus male RNAseq cleaned unassembled reads, XY-Plot'",
+        "Publication status": "unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "clip_marker_color": "red",
+        "height": 50,
+        "neg_color": "#005EFF",
+        "pos_color": "#FFA600"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "bigwig/janphilipoeyen/cleaned-reads-tophat/Oabi-male_tophat-accepted_hits.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Transcriptome/Coverage plots (BigWig)",
+      "key": " O. abietinus female cleaned reads, XY-plots",
+      "label": "Oabi-female_tophat-accepted_hits_bigwig",
+      "metadata": {
+        "Analysis provider": "JP Oeyen (Univ. Bonn/ZFMK, ZMB), janphilipoyen@gmail.com)",
+        "Data Source": "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Parasitic_wood_wasp/RNA_sequence/Oabi_ICD_OAi5ON.BN106-1_1pA_D2FUUACXX-1-ID01_1_sequence.txt.bz2; ftp://ftp.hgsc.bcm.edu/I5K-pilot/Parasitic_wood_wasp/RNA_sequence/Oabi_ICD_OAi5ON.BN106-1_1pA_D2FUUACXX-1-ID01_2_sequence.txt.bz2",
+        "Data description": "Raw reads cleaned with Trimmomatic v0.32, using the options ILLUMINACLIP:'costumadapterlist.fa':2:30:10, SLIDINGWINDOW:4:33 and MINLEN:45. Cleaned reads mapped with TopHat v2.0.12 using default settings. Alignment files were converted by the NAL to bigwig format; reads that failed QC, secondary and supplementary alignments, and optical or PCR duplicates were ignored.",
+        "File note": "This track replaces the previous track, 'Orussus abietinus female RNAseq cleaned unassembled reads, XY-Plot'",
+        "Publication status": "unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "clip_marker_color": "red",
+        "height": 50,
+        "neg_color": "#005EFF",
+        "pos_color": "#FFA600"
+      },
+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "bigwig/janphilipoeyen/cleaned-reads-tophat/Oabi-female_tophat-accepted_hits.bigwig"
+    },
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+      "urlTemplate": "tracks/OGSv.1.0-ncRNA/{refseq}/trackData.json"
+    },
+    {
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+      "key": "Official Gene Set v1.0, rRNA",
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+        "Track legend": "Official Gene Set OGS_v1.0."
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+    },
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+    },
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+}
diff --git a/organisms/stage/stage-v2/Osmia_lignaria/trackList.json b/organisms/stage/stage-v2/Osmia_lignaria/trackList.json
new file mode 100644
index 0000000..c96d0b5
--- /dev/null
+++ b/organisms/stage/stage-v2/Osmia_lignaria/trackList.json
@@ -0,0 +1,105 @@
+{
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+        {
+          "label": "View details"
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+        {
+          "action": "newWindow",
+          "iconClass": "dijitIconDatabase",
+          "label": "function(track,feature){ return 'Find gene page for '+feature.get('id')}",
+          "title": "function(track,feature){ return 'Find gene page for '+feature.get('id')}",
+          "url": "function(track,feature){ return 'https://i5k.nal.usda.gov/'+feature.get('id')}"
+        }
+      ],
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+      "trackType": "HTMLFeatures",
+      "type": "HTMLFeatures",
+      "urlTemplate": "tracks/osmlig_current_models/{refseq}/trackData.json"
+    },
+    {
+      "category": "NCBI Annotation Release 100",
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+      "key": "NCBI_Annotation_Release_100_Pseudogene",
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+      "trackType": "HTMLFeatures",
+      "type": "HTMLFeatures",
+      "urlTemplate": "tracks/NCBI_Annotation_Release_100_Pseudogene/{refseq}/trackData.json"
+    }
+  ]
+}
diff --git a/organisms/stage/stage-v2/Pachypsylla_venusta/trackList.json b/organisms/stage/stage-v2/Pachypsylla_venusta/trackList.json
new file mode 100644
index 0000000..f324f3e
--- /dev/null
+++ b/organisms/stage/stage-v2/Pachypsylla_venusta/trackList.json
@@ -0,0 +1,1209 @@
+{
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+  "names": {
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diff --git a/organisms/stage/stage-v2/Parasteatoda_tepidariorum/trackList.json b/organisms/stage/stage-v2/Parasteatoda_tepidariorum/trackList.json
new file mode 100644
index 0000000..968bb69
--- /dev/null
+++ b/organisms/stage/stage-v2/Parasteatoda_tepidariorum/trackList.json
@@ -0,0 +1,1277 @@
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+      "key": "protein2genome_Craniata",
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+      "key": "protein2genome_Crustacea",
+      "label": "protein2genome_Crustacea",
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+      "key": "protein2genome_Echinodermata",
+      "label": "protein2genome_Echinodermata",
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+      "key": "protein2genome_Mollusca",
+      "label": "protein2genome_Mollusca",
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+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
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+      "key": "protein2genome_Nemata",
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+      "key": "protein2genome_Nematomorpha",
+      "label": "protein2genome_Nematomorpha",
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+        "Track legend": "Results from Protein2genome alignments of a set of Nematomorpha proteins as part of the MAKER automated annotation pipeline."
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+      "key": "protein2genome_Onychophora",
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+      "key": "protein2genome_Parazoa",
+      "label": "protein2genome_Parazoa",
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+        "Track legend": "Results from Protein2genome alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline."
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+      "key": "protein2genome_Placozoa",
+      "label": "protein2genome_Placozoa",
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+        "Track legend": "Results from Protein2genome alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline."
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+      "key": "protein2genome_Platyhelminthes",
+      "label": "protein2genome_Platyhelminthes",
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+        "Track legend": "Results from Protein2genome alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline."
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+      "key": "protein2genome_Priapulida",
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+        "Track legend": "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline."
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+      "key": "protein2genome_Tardigrada",
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+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Tardigrada/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Tunicata",
+      "label": "protein2genome_Tunicata",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research",
+        "Track legend": "Results from Protein2genome alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Tunicata/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_UNCATEGORISED",
+      "label": "protein2genome_UNCATEGORISED",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research",
+        "Track legend": "Results from Protein2genome alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline."
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+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_UNCATEGORISED/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/2. Evidence/Repeats",
+      "compress": 0,
+      "key": "repeatmasker",
+      "label": "repeatmasker",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research",
+        "Track legend": "Results from RepeatMasker as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "repeat"
+        }
+      },
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/repeatmasker/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/2. Evidence/Repeats",
+      "compress": 0,
+      "key": "repeatrunner",
+      "label": "repeatrunner",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research",
+        "Track legend": "Results from Repeatrunner as part of the MAKER automated annotation pipeline."
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+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
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+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
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+          "match_part": "repeat"
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+      },
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/repeatrunner/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/1. Gene Sets/Supplementary Gene Predictions",
+      "compress": 0,
+      "key": "snap_masked",
+      "label": "snap_masked",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research",
+        "Track legend": "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline."
+      },
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+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "snap"
+        }
+      },
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/snap_masked/{refseq}/trackData.json"
+    },
+    {
+      "category": "Transcriptome/Assembly",
+      "compress": 0,
+      "key": "Jpn_Pt_gene.model_oda",
+      "label": "Jpn_Pt_gene.model_oda",
+      "metadata": {
+        "Analysis method": "Mapped the RNA-seq reads to Baylor's Pt-genome (Ptep01282013genome) with BLAT, and predicted genes and transcripts with cufflinks and cuffmerge using the RNA-seq mapping data together with EST and cDNA mapping data. We removed multiple-hit (>= 3) reads and one (scaffold with larger number) of two loci of two-hit reads",
+        "Data provider": "Yasuko Akiyama-Oda and Hiroki Oda, JT Biohistory Research Hall",
+        "Source of materials": "RNA-seq of embryonic libraries (stages 3, 5, 7, and 10)",
+        "Track information": "Gene models predicted by Cufflinks/Cuffmerge based on mapping of RNA-seq reads"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "CDS": "transcriptome-cds",
+          "UTR": "transcriptome-utr",
+          "exon": "container-100pct",
+          "wholeCDS": null
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/Jpn_Pt_gene.model_oda/{refseq}/trackData.json"
+    },
+    {
+      "category": "Transcriptome/Mapped ESTs",
+      "key": "EST_oda",
+      "label": "EST_oda",
+      "metadata": {
+        "Accession number": "The EST data are deposited in the DNA Data Bank of Japan under accession numbers FY216297–FY225483 and FY368221–FY381845.",
+        "Data provider": "Yasuko Akiyama-Oda and Hiroki Oda, JT Biohistory Research Hall",
+        "Source of materials": "The EST data are derived from the 5′ end of five  P. tepidariorum embryo cDNA libraries at different stages: At_eW: mixed segmentation stages; eS6: early stage 6; eS7: early stage 7; S7: stage 7.  The cDNA data are mostly from cDNAs cloned and sequenced in our laboratory but include several cDNAs retrieved from NCBI.",
+        "Track information": "cDNA and EST data mapped with BLAT",
+        "Track legend": "This track is displayed so that aligned exons are colored in dark blue while the introns spanning the predicted splicing sites are light blue."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "user_contributed_files/yaoda/EST_cDNA_Oda.bam"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Reference Assembly",
+      "key": "Gaps in assembly",
+      "label": "Gaps in assembly",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "white",
+        "pos_color": "black"
+      },
+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "bigwig/Ptep01282013.GAPS.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "0.5",
+      "category": "Reference Assembly",
+      "key": "GC Content",
+      "label": "GC Content",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+      },
+      "scoreType": "avgScore",
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "rgba(255,255,0,50)",
+        "pos_color": "rgba(0,0,255,50)"
+      },
+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "bigwig/Ptep01282013.genome_GC.bigwig"
+    }
+  ]
+}
diff --git a/organisms/stage/stage-v2/Photinus_pyralis/trackList.json b/organisms/stage/stage-v2/Photinus_pyralis/trackList.json
new file mode 100644
index 0000000..f6b8849
--- /dev/null
+++ b/organisms/stage/stage-v2/Photinus_pyralis/trackList.json
@@ -0,0 +1,337 @@
+{
+  "formatVersion": 1,
+  "names": {
+    "type": "Hash",
+    "url": "names/"
+  },
+  "tracks": [
+    {
+      "category": "Reference sequence",
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+      "key": "Reference sequence",
+      "label": "DNA",
+      "seqType": "dna",
+      "storeClass": "JBrowse/Store/Sequence/StaticChunked",
+      "type": "SequenceTrack",
+      "urlTemplate": "seq/{refseq_dirpath}/{refseq}-"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Reference Assembly",
+      "key": "Gaps in assembly",
+      "label": "Gaps in assembly",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "white",
+        "pos_color": "black"
+      },
+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "bigwig/GCF_008802855.1_Ppyr1.3_genomic.fna.gaps.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "0.5",
+      "category": "Reference Assembly",
+      "key": "GC Content",
+      "label": "GC Content",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+      },
+      "scoreType": "avgScore",
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "rgba(255,255,0,50)",
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+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "bigwig/GCF_008802855.1_Ppyr1.3_genomic.fna.gc.bigwig"
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+    {
+      "category": "RNA-Seq/Mapped Reads",
+      "key": "SRR3883760 Mapped reads",
+      "label": "SRR3883760",
+      "metadata": {
+        "Analysis method": "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+        "Analysis provider": "i5k Workspace@NAL",
+        "Data source": "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR3883760'>SRR3883760</a>",
+        "Publication status": "Analysis: NA; Source data: see individual SRA accessions",
+        "Track legend": "Dark red alignments: Mapped portion of read aligned to forward strand<br>Light red alignments: Spliced portion of read aligned to forward strand<br>Dark blue alignments: Mapped portion of read aligned to reverse strand<br>Light blue alignments: Spliced portion of read aligned to reverse strand<br>Red marking - deletion in the read relative to the reference<br>Green marking - insertion in the read relative to the reference<br>Yellow marking  - mismatch (hover over the mismatch to see what the snp is)"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "analyses/SRR3883760/Phopyr_Ppyr1.3_RNA-Seq-alignments_2021-02-09.bam"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "RNA-Seq/Coverage Plots",
+      "key": "SRR3883760 Coverage",
+      "label": "SRR3883760 Coverage",
+      "metadata": {
+        "Analysis method": "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+        "Analysis provider": "i5k Workspace@NAL",
+        "Data source": "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR3883760'>SRR3883760</a>",
+        "Publication status": "Analysis: NA; Source data: see individual SRA accessions",
+        "Track legend": "This track represents an X-Y plot of RNA-Seq coverage."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "pos_color": "#00BFFF"
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+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "analyses/SRR3883760/Phopyr_Ppyr1.3_RNA-Seq-alignments_2021-02-09.bigwig"
+    },
+    {
+      "category": "RNA-Seq/Splice junctions",
+      "label": "SRR3883760 Splice junctions",
+      "metadata": {
+        "Analysis method": "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+        "Analysis provider": "i5k Workspace@NAL",
+        "Data source": "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR3883760'>SRR3883760</a>",
+        "Publication status": "Analysis: NA; Source data: see individual SRA accessions",
+        "Track legend": "This track represents an X-Y plot of RNA-Seq coverage."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BEDTabix",
+      "style": {
+        "description": "score"
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+      "type": "CanvasFeatures",
+      "urlTemplate": "analyses/SRR3883760/Phopyr_Ppyr1.3_RNA-Seq-alignments_2021-02-09.bed.gz"
+    },
+    {
+      "category": "RNA-Seq/Splice junctions",
+      "label": "SRR3883768 Splice junctions",
+      "metadata": {
+        "Analysis method": "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+        "Analysis provider": "i5k Workspace@NAL",
+        "Data source": "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR3883768'>SRR3883768</a>",
+        "Publication status": "Analysis: NA; Source data: see individual SRA accessions",
+        "Track legend": "Junction reads generated by Hisat2 aligner and regtools"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BEDTabix",
+      "style": {
+        "description": "score"
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+      "type": "CanvasFeatures",
+      "urlTemplate": "analyses/SRR3883768/Phopyr_Ppyr1.3_RNA-Seq-alignments_2021-02-09.bed.gz"
+    },
+    {
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+      "key": "SRR3883768 Mapped reads",
+      "label": "SRR3883768 Mapped reads",
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+        "Publication status": "Analysis: NA; Source data: see individual SRA accessions",
+        "Track legend": "Dark red alignments: Mapped portion of read aligned to forward strand<br>Light red alignments: Spliced portion of read aligned to forward strand<br>Dark blue alignments: Mapped portion of read aligned to reverse strand<br>Light blue alignments: Spliced portion of read aligned to reverse strand<br>Red marking - deletion in the read relative to the reference<br>Green marking - insertion in the read relative to the reference<br>Yellow marking  - mismatch (hover over the mismatch to see what the snp is)"
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+      "urlTemplate": "analyses/SRR3883768/Phopyr_Ppyr1.3_RNA-Seq-alignments_2021-02-09.bam"
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+    {
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+      "bicolor_pivot": "zero",
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+      "label": "SRR3883768 Coverage",
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+        "Analysis provider": "i5k Workspace@NAL",
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+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
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+        "Publication status": "Analysis: NA; Source data: see individual SRA accessions",
+        "Track legend": "Dark red alignments: Mapped portion of read aligned to forward strand<br>Light red alignments: Spliced portion of read aligned to forward strand<br>Dark blue alignments: Mapped portion of read aligned to reverse strand<br>Light blue alignments: Spliced portion of read aligned to reverse strand<br>Red marking - deletion in the read relative to the reference<br>Green marking - insertion in the read relative to the reference<br>Yellow marking  - mismatch (hover over the mismatch to see what the snp is)"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
+      "type": "WebApollo/View/Track/DraggableAlignments",
+      "urlTemplate": "analyses/SRR6345445/Phopyr_Ppyr1.3_RNA-Seq-alignments_2021-02-09.bam"
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+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "RNA-Seq/Coverage Plots",
+      "key": "SRR6345445 Coverage",
+      "label": "SRR6345445 Coverage",
+      "metadata": {
+        "Analysis method": "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+        "Analysis provider": "i5k Workspace@NAL",
+        "Data source": "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR6345445'>SRR6345445</a>",
+        "Publication status": "Analysis: NA; Source data: see individual SRA accessions",
+        "Track legend": "This track represents an X-Y plot of RNA-Seq coverage."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
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+      "type": "JBrowse/View/Track/Wiggle/XYPlot",
+      "urlTemplate": "analyses/SRR6345445/Phopyr_Ppyr1.3_RNA-Seq-alignments_2021-02-09.bigwig"
+    },
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+      "category": "RNA-Seq/Mapped Reads",
+      "key": "SRR3883762 Mapped reads",
+      "label": "SRR3883762 Mapped reads",
+      "metadata": {
+        "Analysis method": "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+        "Analysis provider": "i5k Workspace@NAL",
+        "Data source": "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR3883762'>SRR3883762</a>",
+        "Publication status": "Analysis: NA; Source data: see individual SRA accessions",
+        "Track legend": "Dark red alignments: Mapped portion of read aligned to forward strand<br>Light red alignments: Spliced portion of read aligned to forward strand<br>Dark blue alignments: Mapped portion of read aligned to reverse strand<br>Light blue alignments: Spliced portion of read aligned to reverse strand<br>Red marking - deletion in the read relative to the reference<br>Green marking - insertion in the read relative to the reference<br>Yellow marking  - mismatch (hover over the mismatch to see what the snp is)"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BAM",
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+      "urlTemplate": "analyses/SRR3883762/Phopyr_Ppyr1.3_RNA-Seq-alignments_2021-02-09.bam"
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+      "key": "SRR3883762 Coverage",
+      "label": "SRR3883762 Coverage",
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+        "Analysis method": "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+        "Analysis provider": "i5k Workspace@NAL",
+        "Data source": "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR3883762'>SRR3883762</a>",
+        "Publication status": "Analysis: NA; Source data: see individual SRA accessions",
+        "Track legend": "This track represents an X-Y plot of RNA-Seq coverage."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
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+      "urlTemplate": "analyses/SRR3883762/Phopyr_Ppyr1.3_RNA-Seq-alignments_2021-02-09.bigwig"
+    },
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+      "key": "NCBI_Annotation_Release_100_Gene",
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+        },
+        {
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+          "url": "function(track,feature){ return 'https://i5k.nal.usda.gov/'+feature.get('name')}"
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diff --git a/organisms/stage/stage-v2/Rhagoletis_zephyria/trackList.json b/organisms/stage/stage-v2/Rhagoletis_zephyria/trackList.json
new file mode 100644
index 0000000..f5232d7
--- /dev/null
+++ b/organisms/stage/stage-v2/Rhagoletis_zephyria/trackList.json
@@ -0,0 +1,255 @@
+{
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+}
diff --git a/organisms/stage/stage-v2/Rhipicephalus_microplus/trackList.json b/organisms/stage/stage-v2/Rhipicephalus_microplus/trackList.json
new file mode 100644
index 0000000..82e0220
--- /dev/null
+++ b/organisms/stage/stage-v2/Rhipicephalus_microplus/trackList.json
@@ -0,0 +1,179 @@
+{
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+      "url" : "names/"
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+               "title" : "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
+               "url" : "function(track,feature){ return 'https://i5k.nal.usda.gov/tripal_elasticsearch/search_website/?search_box='+feature.get('name')}"
+            }
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+         "type" : "HTMLFeatures",
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+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
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diff --git a/organisms/stage/stage-v2/Rhyzopertha_dominica/trackList.json b/organisms/stage/stage-v2/Rhyzopertha_dominica/trackList.json
new file mode 100644
index 0000000..39aa9b5
--- /dev/null
+++ b/organisms/stage/stage-v2/Rhyzopertha_dominica/trackList.json
@@ -0,0 +1,426 @@
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diff --git a/organisms/stage/stage-v2/Tigriopus_californicus/trackList.json b/organisms/stage/stage-v2/Tigriopus_californicus/trackList.json
new file mode 100644
index 0000000..85693dd
--- /dev/null
+++ b/organisms/stage/stage-v2/Tigriopus_californicus/trackList.json
@@ -0,0 +1,1044 @@
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+        "File provider": "Thiago Lima, Scripps Institution of Oceanography",
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+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
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+      },
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+      "urlTemplate": "user_contributed_data/Tigriopus_californicus_i5k/CAT_to_SD_genome4_opt_15_merged_sort.bam"
+    },
+    {
+      "category": "DNASeq/Mapped Reads",
+      "key": "Bodega Bay population (mapped reads)",
+      "label": "Bodega Bay population (mapped reads)",
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+        "Date completed": "4/25/14",
+        "File provider": "Thiago Lima, Scripps Institution of Oceanography",
+        "Geographical location of specimen collection": "USA, Bodega Bay, 38°19'4”N, 123°4'23”W",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
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+      },
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+        "File provider": "Thiago Lima, Scripps Institution of Oceanography",
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+      "urlTemplate": "user_contributed_data/Tigriopus_californicus_i5k/BR_to_SD_genome4_opt_15_merged_sort.bam"
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+      "key": "Friday Harbor population (mapped reads)",
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+        "File provider": "Thiago Lima, Scripps Institution of Oceanography",
+        "Geographical location of specimen collection": "USA, Friday Harbor, 48°32'47”N, 123°0'35”W",
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diff --git a/organisms/stage/stage-v2/Tribolium_castaneum/trackList.json b/organisms/stage/stage-v2/Tribolium_castaneum/trackList.json
new file mode 100644
index 0000000..f130530
--- /dev/null
+++ b/organisms/stage/stage-v2/Tribolium_castaneum/trackList.json
@@ -0,0 +1,433 @@
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+      },
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/NCBI_Annotation_Release_103_miRNA/{refseq}/trackData.json"
+    },
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+        "Method": "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
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+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/NCBI_Annotation_Release_103_tRNA/{refseq}/trackData.json"
+    },
+    {
+      "category": "NCBI Annotation Release 103/2. Evidence",
+      "compress": 0,
+      "key": "cDNA match evidence from NCBI Annotation Release 103",
+      "label": "NCBI_Annotation_Release_103_cDNA_match",
+      "metadata": {
+        "Data description": "ftp://ftp.ncbi.nih.gov/genomes/all/GCF_000002335.3_Tcas5.2/README.txt",
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+        "Data source": "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF_000002335.3_Tcas5.2/GCF_000002335.3_Tcas5.2_genomic.gff.gz",
+        "Method": "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/NCBI_Annotation_Release_103_cDNA_match/{refseq}/trackData.json"
+    },
+    {
+      "category": "NCBI Annotation Release 103/1. Gene Sets/Noncoding",
+      "compress": 0,
+      "key": "NCBI Predicted miRNA, primary transcripts, Annotation Release 103",
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+      "metadata": {
+        "Data description": "ftp://ftp.ncbi.nih.gov/genomes/all/GCF_000002335.3_Tcas5.2/README.txt",
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+        "Data source": "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF_000002335.3_Tcas5.2/GCF_000002335.3_Tcas5.2_genomic.gff.gz",
+        "Method": "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
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+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/NCBI_Annotation_Release_103_miRNA_primary_transcript/{refseq}/trackData.json"
+    }
+  ]
+}
diff --git a/organisms/stage/stage-v2/Tribolium_madens/trackList.json b/organisms/stage/stage-v2/Tribolium_madens/trackList.json
new file mode 100644
index 0000000..690a7ca
--- /dev/null
+++ b/organisms/stage/stage-v2/Tribolium_madens/trackList.json
@@ -0,0 +1,180 @@
+{
+   "formatVersion" : 1,
+   "names" : {
+      "type" : "Hash",
+      "url" : "names/"
+   },
+   "tracks" : [
+      {
+         "category" : "Reference sequence",
+         "chunkSize" : 20000,
+         "key" : "Reference sequence",
+         "label" : "DNA",
+         "seqType" : "dna",
+         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
+         "type" : "SequenceTrack",
+         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-"
+      },
+      {
+         "category" : "NCBI Annotation Release 100",
+         "compress" : 0,
+         "key" : "NCBI_Annotation_Release_100_Gene",
+         "label" : "trimad_current_models",
+         "menuTemplate" : [
+            {
+               "label" : "View details"
+            },
+            {
+               "action" : "newWindow",
+               "iconClass" : "dijitIconDatabase",
+               "label" : "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
+               "title" : "function(track,feature){ return 'Find gene page for '+feature.get('name')}",
+               "url" : "function(track,feature){ return 'https://i5k.nal.usda.gov/'+feature.get('name')}"
+            }
+         ],
+         "metadata" : {
+            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Tribolium_madens/README_CURRENT_RELEASE",
+            "Data provider" : "NCBI",
+            "Data source" : "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/015/345/945/GCF_015345945.1_Tmad_KSU_1.1/GCF_015345945.1_Tmad_KSU_1.1_genomic.gff.gz",
+            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "arrowheadClass" : "trellis-arrowhead",
+            "className" : "container-16px",
+            "description" : "product, note, description",
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+               "CDS" : "gnomon_CDS",
+               "UTR" : "gnomon_UTR",
+               "exon" : "container-100pct",
+               "wholeCDS" : null
+            }
+         },
+         "trackType" : "HTMLFeatures",
+         "type" : "HTMLFeatures",
+         "urlTemplate" : "tracks/trimad_current_models/{refseq}/trackData.json"
+      },
+      {
+         "category" : "NCBI Annotation Release 100",
+         "compress" : 0,
+         "key" : "NCBI_Annotation_Release_100_Pseudogene",
+         "label" : "NCBI_Annotation_Release_100_Pseudogene",
+         "metadata" : {
+            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Tribolium_madens/README_CURRENT_RELEASE",
+            "Data provider" : "NCBI",
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+            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
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+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
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+            "className" : "container-16px",
+            "description" : "product, note, description",
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+               "exon" : "container-100pct",
+               "wholeCDS" : null
+            }
+         },
+         "trackType" : "HTMLFeatures",
+         "type" : "HTMLFeatures",
+         "urlTemplate" : "tracks/NCBI_Annotation_Release_100_Pseudogene/{refseq}/trackData.json"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "Reference Assembly",
+         "key" : "Gaps in assembly",
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+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
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+         "style" : {
+            "neg_color" : "white",
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+         "urlTemplate" : "bigwig/GCF_015345945.1_Tmad_KSU_1.1_genomic.fna.gaps.bigwig"
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+            "Track contact" : "The i5k workspace@NAL",
+            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
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+         },
+         "scoreType" : "avgScore",
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+            "neg_color" : "rgba(255,255,0,50)",
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+         "urlTemplate" : "bigwig/GCF_015345945.1_Tmad_KSU_1.1_genomic.fna.gc.bigwig"
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+      {
+         "category" : "RNA-Seq/Mapped Reads",
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+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+         "type" : "WebApollo/View/Track/DraggableAlignments",
+         "urlTemplate" : "analyses/Tribolium-madens-RNA-Seq_2021-10-25_v1.0/Trimad_Tmad_KSU_1.1_RNA-Seq-alignments_2021-10-25.bam"
+      },
+      {
+         "autoscale" : "local",
+         "bicolor_pivot" : "zero",
+         "category" : "RNA-Seq/Coverage Plots",
+         "key" : "Trimad_Tmad_KSU_1.1_RNA-Seq-alignments_2021-10-25_coverage",
+         "label" : "Trimad_Tmad_KSU_1.1_RNA-Seq-alignments_2021-10-25_coverage",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR15809238'>SRR15809238</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR15809237'>SRR15809237</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR15809236'>SRR15809236</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR15809235'>SRR15809235</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR15809234'>SRR15809234</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR15809233'>SRR15809233</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
+         "style" : {
+            "pos_color" : "#00BFFF"
+         },
+         "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+         "urlTemplate" : "analyses/Tribolium-madens-RNA-Seq_2021-10-25_v1.0/Trimad_Tmad_KSU_1.1_RNA-Seq-alignments_2021-10-25.bigwig"
+      },
+      {
+         "category" : "RNA-Seq/Splice junctions",
+         "compress" : 0,
+         "key" : "Trimad_Tmad_KSU_1.1_RNA-Seq-alignments_2021-10-25_junctions",
+         "label" : "Trimad_Tmad_KSU_1.1_RNA-Seq-alignments_2021-10-25_junctions",
+         "metadata" : {
+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR15809238'>SRR15809238</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR15809237'>SRR15809237</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR15809236'>SRR15809236</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR15809235'>SRR15809235</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR15809234'>SRR15809234</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR15809233'>SRR15809233</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Junction reads generated by Hisat2 aligner and regtools. The number of alignments supporting the junction read is listed in blue."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+	    "description":"score",
+            "className" : "feature"
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/Trimad_Tmad_KSU_1.1_RNA-Seq-alignments_2021-10-25_junctions/{refseq}/trackData.json"
+      }
+   ]
+}
diff --git a/organisms/stage/stage-v2/Trichogramma_pretiosum/trackList.json b/organisms/stage/stage-v2/Trichogramma_pretiosum/trackList.json
new file mode 100644
index 0000000..40a6cc8
--- /dev/null
+++ b/organisms/stage/stage-v2/Trichogramma_pretiosum/trackList.json
@@ -0,0 +1,1209 @@
+{
+  "alwaysOnTracks": "DNA,Annotations",
+  "css": "./plugins/NAL_CSS/css/main.css",
+  "favicon": "./plugins/WebApollo/img/webapollo_favicon.ico",
+  "formatVersion": 1,
+  "names": {
+    "type": "Hash",
+    "url": "names/"
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+  "share_link": 0,
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+      "storeClass": "JBrowse/Store/Sequence/StaticChunked",
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+      "urlTemplate": "seq/{refseq_dirpath}/{refseq}-"
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+      "autocomplete": "none",
+      "compress": 0,
+      "key": "User-created Annotations",
+      "label": "Annotations",
+      "phase": 0,
+      "storeClass": "WebApollo/Store/SeqFeature/ScratchPad",
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+            "renderClassName": "gray-center-30pct"
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+            "renderClassName": "gray-center-30pct"
+          },
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+            "className": "light-purple-80pct",
+            "renderClassName": "gray-center-30pct"
+          },
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+            "className": "brightgreen-80pct",
+            "renderClassName": "gray-center-30pct"
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+            "renderClassName": "gray-center-30pct"
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+            "renderClassName": "gray-center-30pct"
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+            "className": "brightgreen-80pct",
+            "renderClassName": "gray-center-30pct"
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+            "renderClassName": "blue-ibeam-render"
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+          "non_canonical_three_prime_splice_site": false
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+      "type": "WebApollo/View/Track/AnnotTrack"
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+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
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+      "urlTemplate": "tracks/tripre_current_models/{refseq}/trackData.json"
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+      "key": "augustus_masked",
+      "label": "augustus_masked",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from the Augustus gene prediction software as part of the MAKER automated annotation pipeline."
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+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/augustus_masked/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX",
+      "compress": 0,
+      "key": "blastx_Annelida",
+      "label": "blastx_Annelida",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Blastx alignments of a set of Annelida proteins as part of the MAKER automated annotation pipeline."
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+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
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+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/blastx_Annelida/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX",
+      "compress": 0,
+      "key": "blastx_Arthropoda",
+      "label": "blastx_Arthropoda",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Blastx alignments of a set of Arthropoda proteins as part of the MAKER automated annotation pipeline."
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+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/blastx_Arthropoda/{refseq}/trackData.json"
+    },
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+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Atelocerata proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
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+        "arrowheadClass": "webapollo-arrowhead",
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+          "match_part": "protein2genome"
+        }
+      },
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Atelocerata/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
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+      "key": "protein2genome_Cephalochordata",
+      "label": "protein2genome_Cephalochordata",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Cephalochordata proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
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+          "match_part": "protein2genome"
+        }
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+      "urlTemplate": "tracks/protein2genome_Cephalochordata/{refseq}/trackData.json"
+    },
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+      "key": "protein2genome_Chelicerata",
+      "label": "protein2genome_Chelicerata",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Chelicerata proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
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+          "match_part": "protein2genome"
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+      "type": "FeatureTrack",
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+    },
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+      "compress": 0,
+      "key": "protein2genome_Cnidaria",
+      "label": "protein2genome_Cnidaria",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Cnidaria proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
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+          "match_part": "protein2genome"
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+      },
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Cnidaria/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Craniata",
+      "label": "protein2genome_Craniata",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Craniata proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Craniata/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Crustacea",
+      "label": "protein2genome_Crustacea",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Crustacea proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Crustacea/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Echinodermata",
+      "label": "protein2genome_Echinodermata",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Echinodermata proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
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+          "match_part": "protein2genome"
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+      },
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Echinodermata/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Mollusca",
+      "label": "protein2genome_Mollusca",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Mollusca proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
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+          "match_part": "protein2genome"
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Mollusca/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Nemata",
+      "label": "protein2genome_Nemata",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Nemata/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Nematomorpha",
+      "label": "protein2genome_Nematomorpha",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Nematomorpha proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
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+      },
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+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Nematomorpha/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Onychophora",
+      "label": "protein2genome_Onychophora",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Onychophora proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
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+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Onychophora/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Parazoa",
+      "label": "protein2genome_Parazoa",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
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+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Parazoa/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Placozoa",
+      "label": "protein2genome_Placozoa",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
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+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Placozoa/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Platyhelminthes",
+      "label": "protein2genome_Platyhelminthes",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Platyhelminthes/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Priapulida",
+      "label": "protein2genome_Priapulida",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Priapulida/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Tardigrada",
+      "label": "protein2genome_Tardigrada",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Tardigrada/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_Tunicata",
+      "label": "protein2genome_Tunicata",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_Tunicata/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/3. Mapped Proteins/Protein2genome",
+      "compress": 0,
+      "key": "protein2genome_UNCATEGORISED",
+      "label": "protein2genome_UNCATEGORISED",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Protein2genome alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "protein2genome"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/protein2genome_UNCATEGORISED/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/2. Evidence/Repeats",
+      "compress": 0,
+      "key": "repeatmasker",
+      "label": "repeatmasker",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from RepeatMasker as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "repeat"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/repeatmasker/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/2. Evidence/Repeats",
+      "compress": 0,
+      "key": "repeatrunner",
+      "label": "repeatrunner",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from Repeatrunner as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "repeat"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/repeatrunner/{refseq}/trackData.json"
+    },
+    {
+      "category": "BCM_v0.5.3/1. Gene Sets/Supplementary Gene Predictions",
+      "compress": 0,
+      "key": "snap_masked",
+      "label": "snap_masked",
+      "metadata": {
+        "Analysis contact": "Daniel Hughes, Baylor College of Medicine",
+        "Analysis description": "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.",
+        "Publication status": "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.",
+        "Track legend": "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline."
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "webapollo-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "match_part": "snap"
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "urlTemplate": "tracks/snap_masked/{refseq}/trackData.json"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Reference Assembly",
+      "key": "Gaps in assembly",
+      "label": "Gaps in assembly",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "white",
+        "pos_color": "black"
+      },
+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "urlTemplate": "bigwig/Tpre_FINAL.GAPS.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "0.5",
+      "category": "Reference Assembly",
+      "key": "GC Content",
+      "label": "GC Content",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
+      },
+      "scoreType": "avgScore",
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "rgba(255,255,0,50)",
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diff --git a/organisms/stage/stage-v2/Varroa_destructor/trackList.json b/organisms/stage/stage-v2/Varroa_destructor/trackList.json
new file mode 100644
index 0000000..f184656
--- /dev/null
+++ b/organisms/stage/stage-v2/Varroa_destructor/trackList.json
@@ -0,0 +1,113 @@
+{
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diff --git a/organisms/stage/stage-v2/Varroa_jacobsoni/trackList.json b/organisms/stage/stage-v2/Varroa_jacobsoni/trackList.json
new file mode 100644
index 0000000..5279c97
--- /dev/null
+++ b/organisms/stage/stage-v2/Varroa_jacobsoni/trackList.json
@@ -0,0 +1,126 @@
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diff --git a/organisms/stage/stage-v2/Venturia_canescens/trackList.json b/organisms/stage/stage-v2/Venturia_canescens/trackList.json
new file mode 100644
index 0000000..9f65716
--- /dev/null
+++ b/organisms/stage/stage-v2/Venturia_canescens/trackList.json
@@ -0,0 +1,190 @@
+{
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+               "url" : "function(track,feature){ return 'https://i5k.nal.usda.gov/'+feature.get('name')}"
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+            "Analysis method" : "https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/",
+            "Analysis provider" : "i5k Workspace@NAL",
+            "Data source" : "<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR8354707'>SRR8354707</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR8354715'>SRR8354715</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR8354705'>SRR8354705</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR14772628'>SRR14772628</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR8354708'>SRR8354708</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR8354711'>SRR8354711</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR14772631'>SRR14772631</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=ERR791800'>ERR791800</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR8354702'>SRR8354702</a>,<a href='https://www.ncbi.nlm.nih.gov/sra/?term=SRR8354698'>SRR8354698</a>",
+            "Publication status" : "Analysis: NA; Source data: see individual SRA accessions",
+            "Track legend" : "Junction reads generated by Hisat2 aligner and regtools. The number of alignments supporting the junction read is listed in blue."
+         },
+         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
+         "style" : {
+            "className" : "feature",
+	     "description" : "score",
+    "subfeatureClasses": {
+      "UTR": "webapollo-UTR",
+      "CDS": "junction-cds",
+      "exon": "container-100pct",
+      "intron": null,
+      "wholeCDS": null,
+      "start_codon": null,
+      "stop_codon": null,
+      "match_part": "darkblue-80pct"
+    }
+         },
+         "trackType" : null,
+         "type" : "FeatureTrack",
+         "urlTemplate" : "tracks/Vencan_ASM1945775v1_RNA-Seq-alignments_2021-09-27_junctions/{refseq}/trackData.json"
+      }
+   ]
+}
diff --git a/organisms/stage/stage-v2/make_dir_script.pl b/organisms/stage/stage-v2/make_dir_script.pl
new file mode 100644
index 0000000..5b2aa5f
--- /dev/null
+++ b/organisms/stage/stage-v2/make_dir_script.pl
@@ -0,0 +1,9 @@
+#!/usr/bin/perl -w
+
+use strict;
+
+while (<>){
+	$_ =~ m/(\S*)\|(\S*)/;
+	print "mkdir $1; cd $1; cp $2/trackList.json .; cd .. \n";
+}
+
diff --git a/organisms/stage/stage-v2/make_dirs_and_cp.sh b/organisms/stage/stage-v2/make_dirs_and_cp.sh
new file mode 100644
index 0000000..0f35577
--- /dev/null
+++ b/organisms/stage/stage-v2/make_dirs_and_cp.sh
@@ -0,0 +1,139 @@
+mkdir Aethina_tumida; cd Aethina_tumida; cp /app/data/other_species/aettum/jbrowse/data/trackList.json .; cd .. 
+mkdir Agrilus_planipennis; cd Agrilus_planipennis; cp /app/data/BCM_i5k_pilot/agrpla/jbrowse/data/trackList.json .; cd .. 
+mkdir Amyelois_transitella; cd Amyelois_transitella; cp /app/data/other_species/amytra/jbrowse/data/trackList.json .; cd .. 
+mkdir Anoplophora_glabripennis; cd Anoplophora_glabripennis; cp /app/data/BCM_i5k_pilot/anogla/BCM/jbrowse/data/trackList.json .; cd .. 
+mkdir Apis_mellifera; cd Apis_mellifera; cp /app/data/other_species/apimel/Amel_4.5/jbrowse/data//trackList.json .; cd .. 
+mkdir Athalia_rosae; cd Athalia_rosae; cp /app/data/BCM_i5k_pilot/athros/BCM/jbrowse/data/trackList.json .; cd .. 
+mkdir Bactrocera_oleae; cd Bactrocera_oleae; cp /app/data/other_species/bacole/jbrowse/data/trackList.json .; cd .. 
+mkdir Bactrocera_dorsalis; cd Bactrocera_dorsalis; cp /app/data/other_species/bacdor/jbrowse/data/trackList.json .; cd .. 
+mkdir Bactrocera_cucurbitae; cd Bactrocera_cucurbitae; cp /app/data/other_species/baccuc/jbrowse/data/trackList.json .; cd .. 
+mkdir Bemisia_tabaci; cd Bemisia_tabaci; cp /app/data/other_species/bemtab/jbrowse/data/trackList.json .; cd .. 
+mkdir Blattella_germanica; cd Blattella_germanica; cp /app/data/BCM_i5k_pilot/blager/BCM/jbrowse/data/trackList.json .; cd .. 
+mkdir Bombus_terrestris; cd Bombus_terrestris; cp /app/data/other_species/bomter/Bter_1.0/jbrowse/data/trackList.json .; cd .. 
+mkdir Bombus_impatiens; cd Bombus_impatiens; cp /app/data/other_species/bomimp/BIMP_2.1/jbrowse/data/trackList.json .; cd .. 
+mkdir Bradysia_coprophila; cd Bradysia_coprophila; cp /app/data/other_species/bracop/BU_Bcop_v1/jbrowse/data/trackList.json .; cd .. 
+mkdir Catajapyx_aquilonaris; cd Catajapyx_aquilonaris; cp /app/data/BCM_i5k_pilot/cataqu/jbrowse/data/trackList.json .; cd .. 
+mkdir Centruroides_sculpturatus; cd Centruroides_sculpturatus; cp /app/data/BCM_i5k_pilot/censcu/jbrowse/data/trackList.json .; cd .. 
+mkdir Cephus_cinctus; cd Cephus_cinctus; cp /app/data/other_species/cepcin/Ccin1/jbrowse/data//trackList.json .; cd .. 
+mkdir Ceratitis_capitata; cd Ceratitis_capitata; cp /app/data/BCM_i5k_pilot/cercap/jbrowse/data/trackList.json .; cd .. 
+mkdir Chelonus_insularis; cd Chelonus_insularis; cp /app/data/other_species/cheins/ASM1335770v1/jbrowse/data/trackList.json .; cd .. 
+mkdir Cimex_lectularius; cd Cimex_lectularius; cp /app/data/BCM_i5k_pilot/cimlec/BCM/jbrowse/data/trackList.json .; cd .. 
+mkdir Clitarchus_hookeri; cd Clitarchus_hookeri; cp /app/data/other_species/clihoo/jbrowse/data/trackList.json .; cd .. 
+mkdir Contarinia_nasturtii; cd Contarinia_nasturtii; cp /app/data/other_species/connas/AAFC_CNas_1.1/jbrowse/data/trackList.json .; cd .. 
+mkdir Copidosoma_floridanum; cd Copidosoma_floridanum; cp /app/data/BCM_i5k_pilot/copflo/jbrowse/data/trackList.json .; cd .. 
+mkdir Culex_quinquefasciatus; cd Culex_quinquefasciatus; cp /app/data/other_species/culqui/VPISU_Cqui_1.0_pri_paternal/jbrowse/data/trackList.json .; cd .. 
+mkdir Diabrotica_virgifera_training; cd Diabrotica_virgifera_training; cp /app/data/other_species/diavir/Dvir_v2.0_RefSeq/jbrowse/data/trackList.json .; cd .. 
+mkdir Diachasma_alloeum; cd Diachasma_alloeum; cp /app/data/other_species/diaall/Dall2.0/jbrowse/data/trackList.json .; cd .. 
+mkdir Diaphorina_citri_legacy; cd Diaphorina_citri_legacy; cp /app/data/other_species/diacit_legacy/jbrowse/data/trackList.json .; cd .. 
+mkdir Diaphorina_citri; cd Diaphorina_citri; cp /app/data/other_species/diacit/jbrowse/data/trackList.json .; cd .. 
+mkdir Drosophila_elegans; cd Drosophila_elegans; cp /app/data/other_species/droele/ASM1815250v1/jbrowse/data/trackList.json .; cd .. 
+mkdir Drosophila_rhopaloa; cd Drosophila_rhopaloa; cp /app/data/modencode/drorho/Drho_2.0/jbrowse/data/trackList.json .; cd .. 
+mkdir Drosophila_ficusphila; cd Drosophila_ficusphila; cp /app/data/other_species/drofic/ASM1815226v1/jbrowse/data/trackList.json .; cd .. 
+mkdir Drosophila_kikkawai; cd Drosophila_kikkawai; cp /app/data/other_species/drokik/ASM1815253v1/jbrowse/data/trackList.json .; cd .. 
+mkdir Drosophila_takahashii; cd Drosophila_takahashii; cp /app/data/modencode/drotak/Dtak_2.0/jbrowse/data/trackList.json .; cd .. 
+mkdir Drosophila_eugracilis; cd Drosophila_eugracilis; cp /app/data/other_species/droeug/ASM1815383v1/jbrowse/data/trackList.json .; cd .. 
+mkdir Drosophila_bipectinata; cd Drosophila_bipectinata; cp /app/data/other_species/drobip/ASM1815384v1/jbrowse/data/trackList.json .; cd .. 
+mkdir Drosophila_biarmipes; cd Drosophila_biarmipes; cp /app/data/modencode/drobia/Dbia_2.0/jbrowse/data/trackList.json .; cd .. 
+mkdir Dufourea_novaeangliae; cd Dufourea_novaeangliae; cp /app/data/other_species/dufnov/jbrowse/data/trackList.json .; cd .. 
+mkdir Ephemera_danica; cd Ephemera_danica; cp /app/data/BCM_i5k_pilot/ephdan/Edan_2.0/jbrowse/data//trackList.json .; cd .. 
+mkdir Eufriesea_mexicana; cd Eufriesea_mexicana; cp /app/data/other_species/eufmex/ASM148370v1/jbrowse/data/trackList.json .; cd .. 
+mkdir Euglossa_dilemma; cd Euglossa_dilemma; cp /app/data/other_species/eugdil/jbrowse/data/trackList.json .; cd .. 
+mkdir Eurytemora_affinis; cd Eurytemora_affinis; cp /app/data/BCM_i5k_pilot/euraff/jbrowse/data/trackList.json .; cd .. 
+mkdir Eurytemora_affinis; cd Eurytemora_affinis; cp /app/data/BCM_i5k_pilot/euraff/jbrowse/data/trackList.json .; cd .. 
+mkdir Eurytemora_affinis_-_training; cd Eurytemora_affinis_-_training; cp /app/data/BCM_i5k_pilot/euraff/jbrowse/data/trackList.json .; cd .. 
+mkdir Fopius_arisanus; cd Fopius_arisanus; cp /app/data/other_species/fopari/jbrowse/data/trackList.json .; cd .. 
+mkdir Frankliniella_occidentalis; cd Frankliniella_occidentalis; cp /app/data/BCM_i5k_pilot/fraocc/Focc_3.0/jbrowse/data/trackList.json .; cd .. 
+mkdir Galleria_mellonella; cd Galleria_mellonella; cp /app/data/other_species/galmel/ASM364042v2/jbrowse/data/trackList.json .; cd .. 
+mkdir Gerris_buenoi; cd Gerris_buenoi; cp /app/data/BCM_i5k_pilot/gerbue/jbrowse/data//trackList.json .; cd .. 
+mkdir Habropoda_laboriosa; cd Habropoda_laboriosa; cp /app/data/other_species/hablab/jbrowse/data/trackList.json .; cd .. 
+mkdir Halyomorpha_halys; cd Halyomorpha_halys; cp /app/data/BCM_i5k_pilot/halhal/Hhal_1.1/jbrowse/data/trackList.json .; cd .. 
+mkdir Heliothis_virescens; cd Heliothis_virescens; cp /app/data/other_species/helvir/jbrowse/data//trackList.json .; cd .. 
+mkdir Holacanthella_duospinosa; cd Holacanthella_duospinosa; cp /app/data/other_species/holduo/ASM273828v1/jbrowse/data/trackList.json .; cd .. 
+mkdir Homalodisca_vitripennis; cd Homalodisca_vitripennis; cp /app/data/BCM_i5k_pilot/homvit/jbrowse/data/trackList.json .; cd .. 
+mkdir Hyalella_azteca; cd Hyalella_azteca; cp /app/data/BCM_i5k_pilot/hyaazt/Hazt_2.0.1/jbrowse/data/trackList.json .; cd .. 
+mkdir Ladona_fulva; cd Ladona_fulva; cp /app/data/other_species/ladful/Lful_2.0/jbrowse/data/trackList.json .; cd .. 
+mkdir Laodelphax_striatellus; cd Laodelphax_striatellus; cp /app/data/other_species/laostr/ASM333518v2/jbrowse/data/trackList.json .; cd .. 
+mkdir Lasioglossum_albipes; cd Lasioglossum_albipes; cp /app/data/other_species/lasalb/jbrowse/data/trackList.json .; cd .. 
+mkdir Latrodectus_hesperus; cd Latrodectus_hesperus; cp /app/data/BCM_i5k_pilot/lathes/GCA_000697925.1/jbrowse/data/trackList.json .; cd .. 
+mkdir Leptinotarsa_decemlineata; cd Leptinotarsa_decemlineata; cp /app/data/BCM_i5k_pilot/lepdec/Ldec_2.0/jbrowse/data/trackList.json .; cd .. 
+mkdir Leptinotarsa_decemlineata_training; cd Leptinotarsa_decemlineata_training; cp /app/data/BCM_i5k_pilot/lepdec/jbrowse/data/trackList.json .; cd .. 
+mkdir Limnephilus_lunatus; cd Limnephilus_lunatus; cp /app/data/BCM_i5k_pilot/limlun/jbrowse/data/trackList.json .; cd .. 
+mkdir Locusta_migratoria; cd Locusta_migratoria; cp /app/data/other_species/locmig/jbrowse/data//trackList.json .; cd .. 
+mkdir Loxosceles_reclusa; cd Loxosceles_reclusa; cp /app/data/BCM_i5k_pilot/loxrec/GCA_001188405.1/jbrowse/data/trackList.json .; cd .. 
+mkdir Lucilia_sericata; cd Lucilia_sericata; cp /app/data/other_species/lucser/ASM1558622v1/jbrowse/data/trackList.json .; cd .. 
+mkdir Manduca_sexta; cd Manduca_sexta; cp /app/data/other_species/mansex/JHU_Msex_v1.0/jbrowse/data/trackList.json .; cd .. 
+mkdir Mayetiola_destructor; cd Mayetiola_destructor; cp /app/data/other_species/maydes/jbrowse/data/trackList.json .; cd .. 
+mkdir Medauroidea_extradentata; cd Medauroidea_extradentata; cp /app/data/other_species/medext/GCA_003012365.1/jbrowse/data/trackList.json .; cd .. 
+mkdir Megachile_rotundata; cd Megachile_rotundata; cp /app/data/other_species/megrot/jbrowse/data/trackList.json .; cd .. 
+mkdir Melipona_quadrifasciata; cd Melipona_quadrifasciata; cp /app/data/other_species/melqua/jbrowse/data/trackList.json .; cd .. 
+mkdir Microplitis_demolitor; cd Microplitis_demolitor; cp /app/data/other_species/micdem/jbrowse/data/trackList.json .; cd .. 
+mkdir Neodiprion_lecontei; cd Neodiprion_lecontei; cp /app/data/other_species/neolec/Nlec1.1/jbrowse/data/trackList.json .; cd .. 
+mkdir Neodiprion_lecontei_training; cd Neodiprion_lecontei_training; cp /app/data/other_species/neolec/jbrowse/data/trackList.json .; cd .. 
+mkdir Nicrophorus_vespilloides; cd Nicrophorus_vespilloides; cp /app/data/other_species/nicves/jbrowse/data/trackList.json .; cd .. 
+mkdir Nylanderia_fulva; cd Nylanderia_fulva; cp /app/data/other_species/nylful/TAMU_Nfulva_1.0/jbrowse/data/trackList.json .; cd .. 
+mkdir Odontomachus_brunneus; cd Odontomachus_brunneus; cp /app/data/other_species/odobru/Obru_v1/jbrowse/data/trackList.json .; cd .. 
+mkdir Oncopeltus_fasciatus_training; cd Oncopeltus_fasciatus_training; cp /app/data/BCM_i5k_pilot/oncfas/jbrowse/data/trackList.json .; cd .. 
+mkdir Oncopeltus_fasciatus; cd Oncopeltus_fasciatus; cp /app/data/BCM_i5k_pilot/oncfas/jbrowse/data/trackList.json .; cd .. 
+mkdir 33_-_Onthophagus_taurus_training; cd 33_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 2_-_Onthophagus_taurus_training; cd 2_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 10_-_Onthophagus_taurus_training; cd 10_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 28_-_Onthophagus_taurus_training; cd 28_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 34_-_Onthophagus_taurus_training; cd 34_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 29_-_Onthophagus_taurus_training; cd 29_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 30_-_Onthophagus_taurus_training; cd 30_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 39_-_Onthophagus_taurus_training; cd 39_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 31_-_Onthophagus_taurus_training; cd 31_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 35_-_Onthophagus_taurus_training; cd 35_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 40_-_Onthophagus_taurus_training; cd 40_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 30_-_Onthophagus_taurus_training; cd 30_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 39_-_Onthophagus_taurus_training; cd 39_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 31_-_Onthophagus_taurus_training; cd 31_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 35_-_Onthophagus_taurus_training; cd 35_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 40_-_Onthophagus_taurus_training; cd 40_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 36_-_Onthophagus_taurus_training; cd 36_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 37_-_Onthophagus_taurus_training; cd 37_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 18_-_Onthophagus_taurus_training; cd 18_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 19_-_Onthophagus_taurus_training; cd 19_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 20_-_Onthophagus_taurus_training; cd 20_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 22_-_Onthophagus_taurus_training; cd 22_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 25_-_Onthophagus_taurus_training; cd 25_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 38_-_Onthophagus_taurus_training; cd 38_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 7_-_Onthophagus_taurus_training; cd 7_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 3_-_Onthophagus_taurus_training; cd 3_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 4_-_Onthophagus_taurus_training; cd 4_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir Onthophagus_taurus; cd Onthophagus_taurus; cp /app/data/BCM_i5k_pilot/onttau/jbrowse/data/trackList.json .; cd .. 
+mkdir 8_-_Onthophagus_taurus_training; cd 8_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 5_-_Onthophagus_taurus_training; cd 5_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 6_-_Onthophagus_taurus_training; cd 6_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 9_-_Onthophagus_taurus_training; cd 9_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 13_-_Onthophagus_taurus_training; cd 13_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 12_-_Onthophagus_taurus_training; cd 12_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 15_-_Onthophagus_taurus_training; cd 15_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 14_-_Onthophagus_taurus_training; cd 14_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 16_-_Onthophagus_taurus_training; cd 16_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 17_-_Onthophagus_taurus_training; cd 17_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 1_-_Onthophagus_taurus_training; cd 1_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 11_-_Onthophagus_taurus_training; cd 11_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 32_-_Onthophagus_taurus_training; cd 32_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 21_-_Onthophagus_taurus_training; cd 21_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 23_-_Onthophagus_taurus_training; cd 23_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 24_-_Onthophagus_taurus_training; cd 24_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 26_-_Onthophagus_taurus_training; cd 26_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir 27_-_Onthophagus_taurus_training; cd 27_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. 
+mkdir Orussus_abietinus; cd Orussus_abietinus; cp /app/data/BCM_i5k_pilot/oruabi/BCM/jbrowse/data/trackList.json .; cd .. 
+mkdir Osmia_lignaria; cd Osmia_lignaria; cp /app/data/other_species/osmlig/USDA_OLig_1.0/jbrowse/data/trackList.json .; cd .. 
+mkdir Pachypsylla_venusta; cd Pachypsylla_venusta; cp /app/data/BCM_i5k_pilot/pacven/jbrowse/data/trackList.json .; cd .. 
+mkdir Parasteatoda_tepidariorum; cd Parasteatoda_tepidariorum; cp /app/data/BCM_i5k_pilot/partep/jbrowse/data/trackList.json .; cd .. 
+mkdir Photinus_pyralis; cd Photinus_pyralis; cp /app/data/other_species/phopyr/Ppyr1.3/jbrowse/data/trackList.json .; cd .. 
+mkdir Rhagoletis_zephyria; cd Rhagoletis_zephyria; cp /app/data/other_species/rhazep/jbrowse/data/trackList.json .; cd .. 
+mkdir Rhipicephalus_microplus; cd Rhipicephalus_microplus; cp /app/data/other_species/rhimic/ASM1333972v1/jbrowse/data/trackList.json .; cd .. 
+mkdir Rhyzopertha_dominica; cd Rhyzopertha_dominica; cp /app/data/other_species/rhydom/RdoDt3_tmp/jbrowse/data/trackList.json .; cd .. 
+mkdir Saccharomyceseubayanus; cd Saccharomyceseubayanus; cp /app/data/other_species/saceub/SEUB3.0/jbrowse/data/trackList.json .; cd .. 
+mkdir Tigriopus_californicus; cd Tigriopus_californicus; cp /app/data/other_species/tigcal/jbrowse/data/trackList.json .; cd .. 
+mkdir Tribolium_castaneum; cd Tribolium_castaneum; cp /app/data/other_species/tricas/jbrowse/data/trackList.json .; cd .. 
+mkdir Tribolium_madens; cd Tribolium_madens; cp /app/data/other_species/trimad/Tmad_KSU_1.1/jbrowse/data/trackList.json .; cd .. 
+mkdir Trichogramma_pretiosum; cd Trichogramma_pretiosum; cp /app/data/BCM_i5k_pilot/tripre/jbrowse/data/trackList.json .; cd .. 
+mkdir Varroa_jacobsoni; cd Varroa_jacobsoni; cp /app/data/other_species/varjac/vjacob_1.0/jbrowse/data/trackList.json .; cd .. 
+mkdir Varroa_destructor; cd Varroa_destructor; cp /app/data/other_species/vardes/Vdes_3.0/jbrowse/data/trackList.json .; cd .. 
+mkdir Venturia_canescens; cd Venturia_canescens; cp /app/data/other_species/vencan/ASM1945775v1/jbrowse/data/trackList.json .; cd .. 
+mkdir Mamestra_configurata; cd Mamestra_configurata; cp /app/data/other_species/mamcon/GCA_002192655.1/jbrowse/data/trackList.json .; cd .. 
diff --git a/organisms/stage/stage-v2/manifest.md5 b/organisms/stage/stage-v2/manifest.md5
new file mode 100644
index 0000000..14d8957
--- /dev/null
+++ b/organisms/stage/stage-v2/manifest.md5
@@ -0,0 +1,132 @@
+9875a5e7cf043a27f48495fab6f8c486  ./10_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./11_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./12_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./13_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./14_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./15_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./16_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./17_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./18_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./19_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./1_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./20_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./21_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./22_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./23_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./24_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./25_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./26_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./27_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./28_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./29_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./2_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./30_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./31_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./32_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./33_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./34_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./35_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./36_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./37_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./38_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./39_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./3_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./40_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./4_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./5_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./6_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./7_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./8_-_Onthophagus_taurus_training/trackList.json
+9875a5e7cf043a27f48495fab6f8c486  ./9_-_Onthophagus_taurus_training/trackList.json
+d8db276ad9aed8370be3e448f1ade2f0  ./Aethina_tumida/trackList.json
+ff685cf03032d84052af658902db8637  ./Agrilus_planipennis/trackList.json
+9851922c6640cb97bff757dbd2159e3e  ./Amyelois_transitella/trackList.json
+7dc065ff1eb1d12373695f31824c181d  ./Anoplophora_glabripennis/trackList.json
+11da269635d0e213cb75b2097f0bf555  ./Apis_mellifera/trackList.json
+6c7259caa7a619ff92b494fb7aa53584  ./Athalia_rosae/trackList.json
+0dd7df524755dc3e8600e8ccf92b9b65  ./Bactrocera_cucurbitae/trackList.json
+1db44adb0f976af41c61572e72b2e650  ./Bactrocera_dorsalis/trackList.json
+75b14700e091c4566207b4050051f234  ./Bactrocera_oleae/trackList.json
+14c7c5d6ca3e75a7da9a94b3752b062c  ./Bemisia_tabaci/trackList.json
+1b098a3fc9af07517ea96312738211b8  ./Blattella_germanica/trackList.json
+c0cd5551c4757f44d968489190f62509  ./Bombus_impatiens/trackList.json
+cabe15288c522c931487b963fe43cd21  ./Bombus_terrestris/trackList.json
+4b1a3309f1989a9eaa745d9fcfc6a3bd  ./Bradysia_coprophila/trackList.json
+6a781e375070334ab8115b59852bdf9d  ./Catajapyx_aquilonaris/trackList.json
+7685a17ef89cdec36c225df2bd1350f5  ./Centruroides_sculpturatus/trackList.json
+9963bbcb94c2c2a3b6b0d8b843e956cd  ./Cephus_cinctus/trackList.json
+ba09e9b4dc8ca1c737eaddbe8cb10077  ./Ceratitis_capitata/trackList.json
+b9f99d10fb298674bca72800203b3d40  ./Chelonus_insularis/trackList.json
+96919b420433e81cc47ef318fc4d884c  ./Cimex_lectularius/trackList.json
+c25c42aec2a1bd460a596ecabf2bea30  ./Clitarchus_hookeri/trackList.json
+539d1638a45e6fedc458849fba4c55b6  ./Contarinia_nasturtii/trackList.json
+cdf7a504e62639905e9eef2da02bcc48  ./Copidosoma_floridanum/trackList.json
+6652eed44bf94b30925e372d667d71d9  ./Culex_quinquefasciatus/trackList.json
+b2b1020235e3a4d9760ac47101ccab16  ./Diabrotica_virgifera_training/trackList.json
+9f256861ad30e1e7b5611e5011ef8fc7  ./Diachasma_alloeum/trackList.json
+cb2f4c08bdfef3221af4494cd871829d  ./Diaphorina_citri_legacy/trackList.json
+cfbfbf417965f44d9dd84554140c9461  ./Diaphorina_citri/trackList.json
+6a9d5c49f1d2c484abcd93d2ae1d37d1  ./Drosophila_biarmipes/trackList.json
+9a2087a8f2857d30fdebc8cbcf573574  ./Drosophila_bipectinata/trackList.json
+f8f162b47a03985453d749ccedb397dd  ./Drosophila_elegans/trackList.json
+0b49e3b859e2ffa6d1ef780f99b46f69  ./Drosophila_eugracilis/trackList.json
+e0b0766cccfdf5c71f72f0da67bef53d  ./Drosophila_ficusphila/trackList.json
+11079a2dba35778d988fe688d36cea2f  ./Drosophila_kikkawai/trackList.json
+60ad31a27111c3022a907641ebfec25c  ./Drosophila_rhopaloa/trackList.json
+978f9ffdd632a3c04933817ae4bff4d3  ./Drosophila_takahashii/trackList.json
+f0f605b35e3aaa7186c21d8693f352c9  ./Dufourea_novaeangliae/trackList.json
+1a2ddc588852ddd4286e7566ec3f242f  ./Ephemera_danica/trackList.json
+f7d29c95e47ecb2369b1f8e6129a6445  ./Eufriesea_mexicana/trackList.json
+080948fa04277246551ed66e238d1146  ./Euglossa_dilemma/trackList.json
+52f161fdfc2a35820b4cb6c08455bc73  ./Eurytemora_affinis/trackList.json
+52f161fdfc2a35820b4cb6c08455bc73  ./Eurytemora_affinis_-_training/trackList.json
+92e9dff75e2272e36872b02a6bb95f4a  ./Fopius_arisanus/trackList.json
+f99d9d5a5028488e984d9b8fe58c3a13  ./Frankliniella_occidentalis/trackList.json
+03c1286764f2ad0750d10bdf5d2f38e9  ./Galleria_mellonella/trackList.json
+141c790749679047abe361c7cc089469  ./Gerris_buenoi/trackList.json
+09ad2e8ff09d6eb420154b4517a23e73  ./Habropoda_laboriosa/trackList.json
+d012eb29426be2e5a918da822a0fe2b7  ./Halyomorpha_halys/trackList.json
+3b9dca3a34dc4072c7ba0855a4497318  ./Heliothis_virescens/trackList.json
+2882efa5388188d26e7f89f06e2fb791  ./Holacanthella_duospinosa/trackList.json
+a97665d07614f660b1f747be8309ec2b  ./Homalodisca_vitripennis/trackList.json
+4cf0b8ffcbfbf5e0555d73e04ab95a93  ./Hyalella_azteca/trackList.json
+19e3530912066ad4e1b469e484b93d33  ./Ladona_fulva/trackList.json
+fbcc6de8af7fc0a956f399ce8a85a965  ./Laodelphax_striatellus/trackList.json
+526ab5166b1872b5fefee5bd7c736622  ./Lasioglossum_albipes/trackList.json
+9021eacb1f14cbca91b70662bc6ba17e  ./Latrodectus_hesperus/trackList.json
+65c7759983c4d4e91cfeb05823eb4dfe  ./Leptinotarsa_decemlineata/trackList.json
+574ba508607b7c009880f5fe1875899a  ./Leptinotarsa_decemlineata_training/trackList.json
+d91790069c2afaabfec8a0e809238563  ./Limnephilus_lunatus/trackList.json
+fa40a28fd30d1b6e8ffd846f7a05b003  ./Locusta_migratoria/trackList.json
+955cf3f655a5bd50c133deadc7a51eb4  ./Loxosceles_reclusa/trackList.json
+2d939d2e3442be94e508ad6092bf42bf  ./Lucilia_sericata/trackList.json
+9cb5d8a5b670b685345dd25685abc7cb  ./Mamestra_configurata/trackList.json
+3dd10441c590794d7bf02bfea9c2add2  ./Manduca_sexta/trackList.json
+47d0f2194d6e4dba5b9032ca5a2c4b5b  ./Mayetiola_destructor/trackList.json
+b222ccef9dc412134e5afae9b541c105  ./Medauroidea_extradentata/trackList.json
+2fddf7bc541d5bfdf78ad14ae147227f  ./Megachile_rotundata/trackList.json
+8d46d58dd25b68348a5086df2f554e3b  ./Melipona_quadrifasciata/trackList.json
+bb21ac7ca225785b36c49e829f9357f4  ./Microplitis_demolitor/trackList.json
+62554f4e3218fdfdad0c8e02ed81e913  ./Neodiprion_lecontei/trackList.json
+7def2f9009c9dd8218265ae2954b1c0d  ./Neodiprion_lecontei_training/trackList.json
+01026194909616737a04ebcc6c2a2116  ./Nicrophorus_vespilloides/trackList.json
+a5de3cb29aefe298a0b14437d6a89e86  ./Nylanderia_fulva/trackList.json
+f46b36c12516f8937057cecb48f1a128  ./Odontomachus_brunneus/trackList.json
+dcb533605d2eb82b2ca9f24283bcc4cc  ./Oncopeltus_fasciatus/trackList.json
+dcb533605d2eb82b2ca9f24283bcc4cc  ./Oncopeltus_fasciatus_training/trackList.json
+ee074162026de085b4a671cdc59f407e  ./Onthophagus_taurus/trackList.json
+caab301af2cd425ab1164df4b4e35d4e  ./Orussus_abietinus/trackList.json
+c57bcddbc207dec9cd8f6c020ca6b2a8  ./Osmia_lignaria/trackList.json
+f466aab927e02d783ae354d22d3942f7  ./Pachypsylla_venusta/trackList.json
+7180f884e6320b5ed4167f91336964e9  ./Parasteatoda_tepidariorum/trackList.json
+c74e3c45a013393264341db7318fb964  ./Photinus_pyralis/trackList.json
+9495feaf672b74ef52b7bc7cbdd653ac  ./Rhagoletis_zephyria/trackList.json
+fe95c6e7d92b1e21f7e3187045f4a18a  ./Rhipicephalus_microplus/trackList.json
+eaf0291609600c76a6b26555b07b9908  ./Rhyzopertha_dominica/trackList.json
+9123fcce320b3236232b637554ff606d  ./Tigriopus_californicus/trackList.json
+0b8afa7a3c2dd55563dcfe6b1a9a7a9f  ./Tribolium_castaneum/trackList.json
+f24abc91d64caecdfaf4ff55f5ada150  ./Tribolium_madens/trackList.json
+5405800b50e208b47b02a3e3a110ada9  ./Trichogramma_pretiosum/trackList.json
+a4c52c18667882d520f123047b797710  ./Varroa_destructor/trackList.json
+1fcc9148fe9120c53aa2fa6e48f36431  ./Varroa_jacobsoni/trackList.json
+2525424cc8dce29fc94c08bc730b1889  ./Venturia_canescens/trackList.json
diff --git a/organisms/stage/stage-v2/organism_list.mod b/organisms/stage/stage-v2/organism_list.mod
new file mode 100644
index 0000000..c4ff49b
--- /dev/null
+++ b/organisms/stage/stage-v2/organism_list.mod
@@ -0,0 +1,139 @@
+Aethina_tumida|/app/data/other_species/aettum/jbrowse/data
+Agrilus_planipennis|/app/data/BCM_i5k_pilot/agrpla/jbrowse/data
+Amyelois_transitella|/app/data/other_species/amytra/jbrowse/data
+Anoplophora_glabripennis|/app/data/BCM_i5k_pilot/anogla/BCM/jbrowse/data
+Apis_mellifera|/app/data/other_species/apimel/Amel_4.5/jbrowse/data/
+Athalia_rosae|/app/data/BCM_i5k_pilot/athros/BCM/jbrowse/data
+Bactrocera_oleae|/app/data/other_species/bacole/jbrowse/data
+Bactrocera_dorsalis|/app/data/other_species/bacdor/jbrowse/data
+Bactrocera_cucurbitae|/app/data/other_species/baccuc/jbrowse/data
+Bemisia_tabaci|/app/data/other_species/bemtab/jbrowse/data
+Blattella_germanica|/app/data/BCM_i5k_pilot/blager/BCM/jbrowse/data
+Bombus_terrestris|/app/data/other_species/bomter/Bter_1.0/jbrowse/data
+Bombus_impatiens|/app/data/other_species/bomimp/BIMP_2.1/jbrowse/data
+Bradysia_coprophila|/app/data/other_species/bracop/BU_Bcop_v1/jbrowse/data
+Catajapyx_aquilonaris|/app/data/BCM_i5k_pilot/cataqu/jbrowse/data
+Centruroides_sculpturatus|/app/data/BCM_i5k_pilot/censcu/jbrowse/data
+Cephus_cinctus|/app/data/other_species/cepcin/Ccin1/jbrowse/data/
+Ceratitis_capitata|/app/data/BCM_i5k_pilot/cercap/jbrowse/data
+Chelonus_insularis|/app/data/other_species/cheins/ASM1335770v1/jbrowse/data
+Cimex_lectularius|/app/data/BCM_i5k_pilot/cimlec/BCM/jbrowse/data
+Clitarchus_hookeri|/app/data/other_species/clihoo/jbrowse/data
+Contarinia_nasturtii|/app/data/other_species/connas/AAFC_CNas_1.1/jbrowse/data
+Copidosoma_floridanum|/app/data/BCM_i5k_pilot/copflo/jbrowse/data
+Culex_quinquefasciatus|/app/data/other_species/culqui/VPISU_Cqui_1.0_pri_paternal/jbrowse/data
+Diabrotica_virgifera_training|/app/data/other_species/diavir/Dvir_v2.0_RefSeq/jbrowse/data
+Diachasma_alloeum|/app/data/other_species/diaall/Dall2.0/jbrowse/data
+Diaphorina_citri_legacy|/app/data/other_species/diacit_legacy/jbrowse/data
+Diaphorina_citri|/app/data/other_species/diacit/jbrowse/data
+Drosophila_elegans|/app/data/other_species/droele/ASM1815250v1/jbrowse/data
+Drosophila_rhopaloa|/app/data/modencode/drorho/Drho_2.0/jbrowse/data
+Drosophila_ficusphila|/app/data/other_species/drofic/ASM1815226v1/jbrowse/data
+Drosophila_kikkawai|/app/data/other_species/drokik/ASM1815253v1/jbrowse/data
+Drosophila_takahashii|/app/data/modencode/drotak/Dtak_2.0/jbrowse/data
+Drosophila_eugracilis|/app/data/other_species/droeug/ASM1815383v1/jbrowse/data
+Drosophila_bipectinata|/app/data/other_species/drobip/ASM1815384v1/jbrowse/data
+Drosophila_biarmipes|/app/data/modencode/drobia/Dbia_2.0/jbrowse/data
+Dufourea_novaeangliae|/app/data/other_species/dufnov/jbrowse/data
+Ephemera_danica|/app/data/BCM_i5k_pilot/ephdan/Edan_2.0/jbrowse/data/
+Eufriesea_mexicana|/app/data/other_species/eufmex/ASM148370v1/jbrowse/data
+Euglossa_dilemma|/app/data/other_species/eugdil/jbrowse/data
+Eurytemora_affinis|/app/data/BCM_i5k_pilot/euraff/jbrowse/data
+Eurytemora_affinis|/app/data/BCM_i5k_pilot/euraff/jbrowse/data
+Eurytemora_affinis_-_training|/app/data/BCM_i5k_pilot/euraff/jbrowse/data
+Fopius_arisanus|/app/data/other_species/fopari/jbrowse/data
+Frankliniella_occidentalis|/app/data/BCM_i5k_pilot/fraocc/Focc_3.0/jbrowse/data
+Galleria_mellonella|/app/data/other_species/galmel/ASM364042v2/jbrowse/data
+Gerris_buenoi|/app/data/BCM_i5k_pilot/gerbue/jbrowse/data/
+Habropoda_laboriosa|/app/data/other_species/hablab/jbrowse/data
+Halyomorpha_halys|/app/data/BCM_i5k_pilot/halhal/Hhal_1.1/jbrowse/data
+Heliothis_virescens|/app/data/other_species/helvir/jbrowse/data/
+Holacanthella_duospinosa|/app/data/other_species/holduo/ASM273828v1/jbrowse/data
+Homalodisca_vitripennis|/app/data/BCM_i5k_pilot/homvit/jbrowse/data
+Hyalella_azteca|/app/data/BCM_i5k_pilot/hyaazt/Hazt_2.0.1/jbrowse/data
+Ladona_fulva|/app/data/other_species/ladful/Lful_2.0/jbrowse/data
+Laodelphax_striatellus|/app/data/other_species/laostr/ASM333518v2/jbrowse/data
+Lasioglossum_albipes|/app/data/other_species/lasalb/jbrowse/data
+Latrodectus_hesperus|/app/data/BCM_i5k_pilot/lathes/GCA_000697925.1/jbrowse/data
+Leptinotarsa_decemlineata|/app/data/BCM_i5k_pilot/lepdec/Ldec_2.0/jbrowse/data
+Leptinotarsa_decemlineata_training|/app/data/BCM_i5k_pilot/lepdec/jbrowse/data
+Limnephilus_lunatus|/app/data/BCM_i5k_pilot/limlun/jbrowse/data
+Locusta_migratoria|/app/data/other_species/locmig/jbrowse/data/
+Loxosceles_reclusa|/app/data/BCM_i5k_pilot/loxrec/GCA_001188405.1/jbrowse/data
+Lucilia_sericata|/app/data/other_species/lucser/ASM1558622v1/jbrowse/data
+Manduca_sexta|/app/data/other_species/mansex/JHU_Msex_v1.0/jbrowse/data
+Mayetiola_destructor|/app/data/other_species/maydes/jbrowse/data
+Medauroidea_extradentata|/app/data/other_species/medext/GCA_003012365.1/jbrowse/data
+Megachile_rotundata|/app/data/other_species/megrot/jbrowse/data
+Melipona_quadrifasciata|/app/data/other_species/melqua/jbrowse/data
+Microplitis_demolitor|/app/data/other_species/micdem/jbrowse/data
+Neodiprion_lecontei|/app/data/other_species/neolec/Nlec1.1/jbrowse/data
+Neodiprion_lecontei_training|/app/data/other_species/neolec/jbrowse/data
+Nicrophorus_vespilloides|/app/data/other_species/nicves/jbrowse/data
+Nylanderia_fulva|/app/data/other_species/nylful/TAMU_Nfulva_1.0/jbrowse/data
+Odontomachus_brunneus|/app/data/other_species/odobru/Obru_v1/jbrowse/data
+Oncopeltus_fasciatus_training|/app/data/BCM_i5k_pilot/oncfas/jbrowse/data
+Oncopeltus_fasciatus|/app/data/BCM_i5k_pilot/oncfas/jbrowse/data
+33_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+2_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+10_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+28_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+34_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+29_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+30_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+39_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+31_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+35_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+40_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+30_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+39_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+31_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+35_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+40_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+36_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+37_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+18_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+19_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+20_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+22_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+25_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+38_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+7_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+3_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+4_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+Onthophagus_taurus|/app/data/BCM_i5k_pilot/onttau/jbrowse/data
+8_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+5_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+6_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+9_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+13_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+12_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+15_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+14_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+16_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+17_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+1_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+11_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+32_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+21_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+23_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+24_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+26_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+27_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+Orussus_abietinus|/app/data/BCM_i5k_pilot/oruabi/BCM/jbrowse/data
+Osmia_lignaria|/app/data/other_species/osmlig/USDA_OLig_1.0/jbrowse/data
+Pachypsylla_venusta|/app/data/BCM_i5k_pilot/pacven/jbrowse/data
+Parasteatoda_tepidariorum|/app/data/BCM_i5k_pilot/partep/jbrowse/data
+Photinus_pyralis|/app/data/other_species/phopyr/Ppyr1.3/jbrowse/data
+Rhagoletis_zephyria|/app/data/other_species/rhazep/jbrowse/data
+Rhipicephalus_microplus|/app/data/other_species/rhimic/ASM1333972v1/jbrowse/data
+Rhyzopertha_dominica|/app/data/other_species/rhydom/RdoDt3_tmp/jbrowse/data
+Saccharomyceseubayanus|/app/data/other_species/saceub/SEUB3.0/jbrowse/data
+Tigriopus_californicus|/app/data/other_species/tigcal/jbrowse/data
+Tribolium_castaneum|/app/data/other_species/tricas/jbrowse/data
+Tribolium_madens|/app/data/other_species/trimad/Tmad_KSU_1.1/jbrowse/data
+Trichogramma_pretiosum|/app/data/BCM_i5k_pilot/tripre/jbrowse/data
+Varroa_jacobsoni|/app/data/other_species/varjac/vjacob_1.0/jbrowse/data
+Varroa_destructor|/app/data/other_species/vardes/Vdes_3.0/jbrowse/data
+Venturia_canescens|/app/data/other_species/vencan/ASM1945775v1/jbrowse/data
+Mamestra_configurata|/app/data/other_species/mamcon/GCA_002192655.1/jbrowse/data
diff --git a/organisms/stage/stage-v2/organism_list.txt b/organisms/stage/stage-v2/organism_list.txt
new file mode 100644
index 0000000..2068b28
--- /dev/null
+++ b/organisms/stage/stage-v2/organism_list.txt
@@ -0,0 +1,139 @@
+ Aethina_tumida                     | /app/data/other_species/aettum/jbrowse/data
+ Agrilus_planipennis                | /app/data/BCM_i5k_pilot/agrpla/jbrowse/data
+ Amyelois_transitella               | /app/data/other_species/amytra/jbrowse/data
+ Anoplophora_glabripennis           | /app/data/BCM_i5k_pilot/anogla/BCM/jbrowse/data
+ Apis_mellifera                     | /app/data/other_species/apimel/Amel_4.5/jbrowse/data/
+ Athalia_rosae                      | /app/data/BCM_i5k_pilot/athros/BCM/jbrowse/data
+ Bactrocera_oleae                   | /app/data/other_species/bacole/jbrowse/data
+ Bactrocera_dorsalis                | /app/data/other_species/bacdor/jbrowse/data
+ Bactrocera_cucurbitae              | /app/data/other_species/baccuc/jbrowse/data
+ Bemisia_tabaci                     | /app/data/other_species/bemtab/jbrowse/data
+ Blattella_germanica                | /app/data/BCM_i5k_pilot/blager/BCM/jbrowse/data
+ Bombus_terrestris                  | /app/data/other_species/bomter/Bter_1.0/jbrowse/data
+ Bombus_impatiens                   | /app/data/other_species/bomimp/BIMP_2.1/jbrowse/data
+ Bradysia_coprophila                | /app/data/other_species/bracop/BU_Bcop_v1/jbrowse/data
+ Catajapyx_aquilonaris              | /app/data/BCM_i5k_pilot/cataqu/jbrowse/data
+ Centruroides_sculpturatus          | /app/data/BCM_i5k_pilot/censcu/jbrowse/data
+ Cephus_cinctus                     | /app/data/other_species/cepcin/Ccin1/jbrowse/data/
+ Ceratitis_capitata                 | /app/data/BCM_i5k_pilot/cercap/jbrowse/data
+ Chelonus_insularis                 | /app/data/other_species/cheins/ASM1335770v1/jbrowse/data
+ Cimex_lectularius                  | /app/data/BCM_i5k_pilot/cimlec/BCM/jbrowse/data
+ Clitarchus_hookeri                 | /app/data/other_species/clihoo/jbrowse/data
+ Contarinia_nasturtii               | /app/data/other_species/connas/AAFC_CNas_1.1/jbrowse/data
+ Copidosoma_floridanum              | /app/data/BCM_i5k_pilot/copflo/jbrowse/data
+ Culex_quinquefasciatus             | /app/data/other_species/culqui/VPISU_Cqui_1.0_pri_paternal/jbrowse/data
+ Diabrotica_virgifera_training      | /app/data/other_species/diavir/Dvir_v2.0_RefSeq/jbrowse/data
+ Diachasma_alloeum                  | /app/data/other_species/diaall/Dall2.0/jbrowse/data
+ Diaphorina_citri_legacy            | /app/data/other_species/diacit_legacy/jbrowse/data
+ Diaphorina_citri                   | /app/data/other_species/diacit/jbrowse/data
+ Drosophila_elegans                 | /app/data/other_species/droele/ASM1815250v1/jbrowse/data
+ Drosophila_rhopaloa                | /app/data/modencode/drorho/Drho_2.0/jbrowse/data
+ Drosophila_ficusphila              | /app/data/other_species/drofic/ASM1815226v1/jbrowse/data
+ Drosophila_kikkawai                | /app/data/other_species/drokik/ASM1815253v1/jbrowse/data
+ Drosophila_takahashii              | /app/data/modencode/drotak/Dtak_2.0/jbrowse/data
+ Drosophila_eugracilis              | /app/data/other_species/droeug/ASM1815383v1/jbrowse/data
+ Drosophila_bipectinata             | /app/data/other_species/drobip/ASM1815384v1/jbrowse/data
+ Drosophila_biarmipes               | /app/data/modencode/drobia/Dbia_2.0/jbrowse/data
+ Dufourea_novaeangliae              | /app/data/other_species/dufnov/jbrowse/data
+ Ephemera_danica                    | /app/data/BCM_i5k_pilot/ephdan/Edan_2.0/jbrowse/data/
+ Eufriesea_mexicana                 | /app/data/other_species/eufmex/ASM148370v1/jbrowse/data
+ Euglossa_dilemma                   | /app/data/other_species/eugdil/jbrowse/data
+ Eurytemora_affinis                 | /app/data/BCM_i5k_pilot/euraff/jbrowse/data
+ Eurytemora_affinis                 | /app/data/BCM_i5k_pilot/euraff/jbrowse/data
+ Eurytemora_affinis_-_training      | /app/data/BCM_i5k_pilot/euraff/jbrowse/data
+ Fopius_arisanus                    | /app/data/other_species/fopari/jbrowse/data
+ Frankliniella_occidentalis         | /app/data/BCM_i5k_pilot/fraocc/Focc_3.0/jbrowse/data
+ Galleria_mellonella                | /app/data/other_species/galmel/ASM364042v2/jbrowse/data
+ Gerris_buenoi                      | /app/data/BCM_i5k_pilot/gerbue/jbrowse/data/
+ Habropoda_laboriosa                | /app/data/other_species/hablab/jbrowse/data
+ Halyomorpha_halys                  | /app/data/BCM_i5k_pilot/halhal/Hhal_1.1/jbrowse/data
+ Heliothis_virescens                | /app/data/other_species/helvir/jbrowse/data/
+ Holacanthella_duospinosa           | /app/data/other_species/holduo/ASM273828v1/jbrowse/data
+ Homalodisca_vitripennis            | /app/data/BCM_i5k_pilot/homvit/jbrowse/data
+ Hyalella_azteca                    | /app/data/BCM_i5k_pilot/hyaazt/Hazt_2.0.1/jbrowse/data
+ Ladona_fulva                       | /app/data/other_species/ladful/Lful_2.0/jbrowse/data
+ Laodelphax_striatellus             | /app/data/other_species/laostr/ASM333518v2/jbrowse/data
+ Lasioglossum_albipes               | /app/data/other_species/lasalb/jbrowse/data
+ Latrodectus_hesperus               | /app/data/BCM_i5k_pilot/lathes/GCA_000697925.1/jbrowse/data
+ Leptinotarsa_decemlineata          | /app/data/BCM_i5k_pilot/lepdec/Ldec_2.0/jbrowse/data
+ Leptinotarsa_decemlineata_training | /app/data/BCM_i5k_pilot/lepdec/jbrowse/data
+ Limnephilus_lunatus                | /app/data/BCM_i5k_pilot/limlun/jbrowse/data
+ Locusta_migratoria                 | /app/data/other_species/locmig/jbrowse/data/
+ Loxosceles_reclusa                 | /app/data/BCM_i5k_pilot/loxrec/GCA_001188405.1/jbrowse/data
+ Lucilia_sericata                   | /app/data/other_species/lucser/ASM1558622v1/jbrowse/data
+ Manduca_sexta                      | /app/data/other_species/mansex/JHU_Msex_v1.0/jbrowse/data
+ Mayetiola_destructor               | /app/data/other_species/maydes/jbrowse/data
+ Medauroidea_extradentata           | /app/data/other_species/medext/GCA_003012365.1/jbrowse/data
+ Megachile_rotundata                | /app/data/other_species/megrot/jbrowse/data
+ Melipona_quadrifasciata            | /app/data/other_species/melqua/jbrowse/data
+ Microplitis_demolitor              | /app/data/other_species/micdem/jbrowse/data
+ Neodiprion_lecontei                | /app/data/other_species/neolec/Nlec1.1/jbrowse/data
+ Neodiprion_lecontei_training       | /app/data/other_species/neolec/jbrowse/data
+ Nicrophorus_vespilloides           | /app/data/other_species/nicves/jbrowse/data
+ Nylanderia_fulva                   | /app/data/other_species/nylful/TAMU_Nfulva_1.0/jbrowse/data
+ Odontomachus_brunneus              | /app/data/other_species/odobru/Obru_v1/jbrowse/data
+ Oncopeltus_fasciatus_training      | /app/data/BCM_i5k_pilot/oncfas/jbrowse/data
+ Oncopeltus_fasciatus               | /app/data/BCM_i5k_pilot/oncfas/jbrowse/data
+ 33_-_Onthophagus_taurus_training   | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+ 2_-_Onthophagus_taurus_training    | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+ 10_-_Onthophagus_taurus_training   | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+ 28_-_Onthophagus_taurus_training   | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+ 34_-_Onthophagus_taurus_training   | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+ 29_-_Onthophagus_taurus_training   | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+ 30_-_Onthophagus_taurus_training   | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+ 39_-_Onthophagus_taurus_training   | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+ 31_-_Onthophagus_taurus_training   | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+ 35_-_Onthophagus_taurus_training   | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+ 40_-_Onthophagus_taurus_training   | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+ 30_-_Onthophagus_taurus_training   | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+ 39_-_Onthophagus_taurus_training   | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+ 31_-_Onthophagus_taurus_training   | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+ 35_-_Onthophagus_taurus_training   | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+ 40_-_Onthophagus_taurus_training   | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+ 36_-_Onthophagus_taurus_training   | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+ 37_-_Onthophagus_taurus_training   | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+ 18_-_Onthophagus_taurus_training   | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+ 19_-_Onthophagus_taurus_training   | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+ 20_-_Onthophagus_taurus_training   | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+ 22_-_Onthophagus_taurus_training   | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+ 25_-_Onthophagus_taurus_training   | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+ 38_-_Onthophagus_taurus_training   | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+ 7_-_Onthophagus_taurus_training    | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+ 3_-_Onthophagus_taurus_training    | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+ 4_-_Onthophagus_taurus_training    | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+ Onthophagus_taurus                 | /app/data/BCM_i5k_pilot/onttau/jbrowse/data
+ 8_-_Onthophagus_taurus_training    | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+ 5_-_Onthophagus_taurus_training    | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+ 6_-_Onthophagus_taurus_training    | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+ 9_-_Onthophagus_taurus_training    | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+ 13_-_Onthophagus_taurus_training   | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+ 12_-_Onthophagus_taurus_training   | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+ 15_-_Onthophagus_taurus_training   | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+ 14_-_Onthophagus_taurus_training   | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+ 16_-_Onthophagus_taurus_training   | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+ 17_-_Onthophagus_taurus_training   | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+ 1_-_Onthophagus_taurus_training    | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+ 11_-_Onthophagus_taurus_training   | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+ 32_-_Onthophagus_taurus_training   | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+ 21_-_Onthophagus_taurus_training   | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+ 23_-_Onthophagus_taurus_training   | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+ 24_-_Onthophagus_taurus_training   | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+ 26_-_Onthophagus_taurus_training   | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+ 27_-_Onthophagus_taurus_training   | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+ Orussus_abietinus                  | /app/data/BCM_i5k_pilot/oruabi/BCM/jbrowse/data
+ Osmia_lignaria                     | /app/data/other_species/osmlig/USDA_OLig_1.0/jbrowse/data
+ Pachypsylla_venusta                | /app/data/BCM_i5k_pilot/pacven/jbrowse/data
+ Parasteatoda_tepidariorum          | /app/data/BCM_i5k_pilot/partep/jbrowse/data
+ Photinus_pyralis                   | /app/data/other_species/phopyr/Ppyr1.3/jbrowse/data
+ Rhagoletis_zephyria                | /app/data/other_species/rhazep/jbrowse/data
+ Rhipicephalus_microplus            | /app/data/other_species/rhimic/ASM1333972v1/jbrowse/data
+ Rhyzopertha_dominica               | /app/data/other_species/rhydom/RdoDt3_tmp/jbrowse/data
+ Saccharomyces eubayanus            | /app/data/other_species/saceub/SEUB3.0/jbrowse/data
+ Tigriopus_californicus             | /app/data/other_species/tigcal/jbrowse/data
+ Tribolium_castaneum                | /app/data/other_species/tricas/jbrowse/data
+ Tribolium_madens                   | /app/data/other_species/trimad/Tmad_KSU_1.1/jbrowse/data
+ Trichogramma_pretiosum             | /app/data/BCM_i5k_pilot/tripre/jbrowse/data
+ Varroa_jacobsoni                   | /app/data/other_species/varjac/vjacob_1.0/jbrowse/data
+ Varroa_destructor                  | /app/data/other_species/vardes/Vdes_3.0/jbrowse/data
+ Venturia_canescens                 | /app/data/other_species/vencan/ASM1945775v1/jbrowse/data
+ Mamestra_configurata               | /app/data/other_species/mamcon/GCA_002192655.1/jbrowse/data
diff --git a/scripts/stage/., b/scripts/stage/.,
new file mode 100644
index 0000000..d8f5d09
--- /dev/null
+++ b/scripts/stage/.,
@@ -0,0 +1,140 @@
+Saccharomyceseubayanus|/app/data/other_species/saceub/SEUB3.0/jbrowse/data
+Neodiprion_fabricii|/app/data/other_species/neofab/iyNeoFabr1.1/jbrowse/data
+Neodiprion_pinetum|/app/data/other_species/neopin/iyNeoPine1.1/jbrowse/data
+Photinus_pyralis|/app/data/other_species/phopyr/Ppyr1.3/jbrowse/data
+Venturia_canescens|/app/data/other_species/vencan/ASM1945775v1/jbrowse/data
+Helicoverpa_zea|/app/data/other_species/helzea/ilHelZeax1.1/jbrowse/data
+Manduca_sexta|/app/data/other_species/mansex/JHU_Msex_v1.0/jbrowse/data
+Drosophila_elegans|/app/data/other_species/droele/ASM1815250v1/jbrowse/data
+Diabrotica_virgifera_training|/app/data/other_species/diavir/Dvir_v2.0_RefSeq/jbrowse/data
+Drosophila_bipectinata|/app/data/other_species/drobip/ASM1815384v1/jbrowse/data
+Bradysia_coprophila|/app/data/other_species/bracop/BU_Bcop_v1/jbrowse/data
+Drosophila_eugracilis|/app/data/other_species/droeug/ASM1815383v1/jbrowse/data
+Lucilia_sericata|/app/data/other_species/lucser/ASM1558622v1/jbrowse/data
+Culex_quinquefasciatus|/app/data/other_species/culqui/VPISU_Cqui_1.0_pri_paternal/jbrowse/data
+Diprion_similis|/app/data//other_species/dipsim/iyDipSimi1.1/jbrowse/data
+Drosophila_kikkawai|/app/data/other_species/drokik/ASM1815253v1/jbrowse/data
+Drosophila_ficusphila|/app/data/other_species/drofic/ASM1815226v1/jbrowse/data
+Ladona_fulva|/app/data/other_species/ladful/Lful_2.0/jbrowse/data
+Rhipicephalus_microplus|/app/data/other_species/rhimic/ASM1333972v1/jbrowse/data
+Tribolium_madens|/app/data/other_species/trimad/Tmad_KSU_1.1/jbrowse/data
+Drosophila_rhopaloa|/app/data/other_species/drorho/ASM1815211v1/jbrowse/data
+Neodiprion_virginiana|/app/data/other_species/neovir/iyNeoVirg1.1/jbrowse/data
+Drosophila_takahashii|/app/data/other_species/drotak/ASM1815269v1/jbrowse/data
+Schistocerca_americana|/app/data/other_species/schame/iqSchAmer2.1/jbrowse/data
+Schistocercapiceifrons|/app/data/other_species/schpic/iqSchPice1.1/jbrowse/data/
+Hyalella_azteca|/app/data/BCM_i5k_pilot/hyaazt/Hazt_2.0.1/jbrowse/data
+Aethina_tumida|/app/data/other_species/aettum/jbrowse/data
+Agrilus_planipennis|/app/data/BCM_i5k_pilot/agrpla/jbrowse/data
+Ceratitis_capitata|/app/data/BCM_i5k_pilot/cercap/jbrowse/data
+Amyelois_transitella|/app/data/other_species/amytra/jbrowse/data
+Bactrocera_cucurbitae|/app/data/other_species/baccuc/jbrowse/data
+Bactrocera_dorsalis|/app/data/other_species/bacdor/jbrowse/data
+Bactrocera_oleae|/app/data/other_species/bacole/jbrowse/data
+Copidosoma_floridanum|/app/data/BCM_i5k_pilot/copflo/jbrowse/data
+Catajapyx_aquilonaris|/app/data/BCM_i5k_pilot/cataqu/jbrowse/data
+Oncopeltus_fasciatus|/app/data/BCM_i5k_pilot/oncfas/jbrowse/data
+Eufriesea_mexicana|/app/data/other_species/eufmex/ASM148370v1/jbrowse/data
+Dufourea_novaeangliae|/app/data/other_species/dufnov/jbrowse/data
+Fopius_arisanus|/app/data/other_species/fopari/jbrowse/data
+Eurytemora_affinis|/app/data/BCM_i5k_pilot/euraff/jbrowse/data
+Habropoda_laboriosa|/app/data/other_species/hablab/jbrowse/data
+Homalodisca_vitripennis|/app/data/BCM_i5k_pilot/homvit/jbrowse/data
+Lasioglossum_albipes|/app/data/other_species/lasalb/jbrowse/data
+Onthophagus_taurus|/app/data/BCM_i5k_pilot/onttau/jbrowse/data
+Varroa_destructor|/app/data/other_species/vardes/Vdes_3.0/jbrowse/data
+Gerris_buenoi|/app/data/BCM_i5k_pilot/gerbue/jbrowse/data/
+Athalia_rosae|/app/data/BCM_i5k_pilot/athros/BCM/jbrowse/data
+Orussus_abietinus|/app/data/BCM_i5k_pilot/oruabi/BCM/jbrowse/data
+Blattella_germanica|/app/data/BCM_i5k_pilot/blager/BCM/jbrowse/data
+Anoplophora_glabripennis|/app/data/BCM_i5k_pilot/anogla/BCM/jbrowse/data
+Cimex_lectularius|/app/data/BCM_i5k_pilot/cimlec/BCM/jbrowse/data
+Eurytemora_affinis_-_training|/app/data/BCM_i5k_pilot/euraff/jbrowse/data
+Limnephilus_lunatus|/app/data/BCM_i5k_pilot/limlun/jbrowse/data
+Diaphorina_citri_legacy|/app/data/other_species/diacit_legacy/jbrowse/data
+Mayetiola_destructor|/app/data/other_species/maydes/jbrowse/data
+Megachile_rotundata|/app/data/other_species/megrot/jbrowse/data
+Pachypsylla_venusta|/app/data/BCM_i5k_pilot/pacven/jbrowse/data
+Melipona_quadrifasciata|/app/data/other_species/melqua/jbrowse/data
+Parasteatoda_tepidariorum|/app/data/BCM_i5k_pilot/partep/jbrowse/data
+Nicrophorus_vespilloides|/app/data/other_species/nicves/jbrowse/data
+Leptinotarsa_decemlineata_training|/app/data/BCM_i5k_pilot/lepdec/jbrowse/data
+Rhagoletis_zephyria|/app/data/other_species/rhazep/jbrowse/data
+Tigriopus_californicus|/app/data/other_species/tigcal/jbrowse/data
+Tribolium_castaneum|/app/data/other_species/tricas/jbrowse/data
+Trichogramma_pretiosum|/app/data/BCM_i5k_pilot/tripre/jbrowse/data
+Oncopeltus_fasciatus_training|/app/data/BCM_i5k_pilot/oncfas/jbrowse/data
+Neodiprion_lecontei_training|/app/data/other_species/neolec/jbrowse/data
+Clitarchus_hookeri|/app/data/other_species/clihoo/jbrowse/data
+Microplitis_demolitor|/app/data/other_species/micdem/jbrowse/data
+Drosophila_biarmipes|/app/data/modencode/drobia/Dbia_2.0/jbrowse/data
+Holacanthella_duospinosa|/app/data/other_species/holduo/ASM273828v1/jbrowse/data
+Leptinotarsa_decemlineata|/app/data/BCM_i5k_pilot/lepdec/Ldec_2.0/jbrowse/data
+Laodelphax_striatellus|/app/data/other_species/laostr/ASM333518v2/jbrowse/data
+10_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+2_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+Diaphorina_citri|/app/data/other_species/diacit/jbrowse/data
+7_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+Centruroides_sculpturatus|/app/data/BCM_i5k_pilot/censcu/jbrowse/data
+Medauroidea_extradentata|/app/data/other_species/medext/GCA_003012365.1/jbrowse/data
+Nylanderia_fulva|/app/data/other_species/nylful/TAMU_Nfulva_1.0/jbrowse/data
+Frankliniella_occidentalis|/app/data/BCM_i5k_pilot/fraocc/Focc_3.0/jbrowse/data
+Loxosceles_reclusa|/app/data/BCM_i5k_pilot/loxrec/GCA_001188405.1/jbrowse/data
+Euglossa_dilemma|/app/data/other_species/eugdil/jbrowse/data
+Varroa_jacobsoni|/app/data/other_species/varjac/vjacob_1.0/jbrowse/data
+Halyomorpha_halys|/app/data/BCM_i5k_pilot/halhal/Hhal_1.1/jbrowse/data
+Bemisia_tabaci|/app/data/other_species/bemtab/jbrowse/data
+Galleria_mellonella|/app/data/other_species/galmel/ASM364042v2/jbrowse/data
+Latrodectus_hesperus|/app/data/BCM_i5k_pilot/lathes/GCA_000697925.1/jbrowse/data
+Heliothis_virescens|/app/data/other_species/helvir/jbrowse/data/
+Locusta_migratoria|/app/data/other_species/locmig/jbrowse/data/
+Contarinia_nasturtii|/app/data/other_species/connas/AAFC_CNas_1.1/jbrowse/data
+Ephemera_danica|/app/data/BCM_i5k_pilot/ephdan/Edan_2.0/jbrowse/data/
+Cephus_cinctus|/app/data/other_species/cepcin/Ccin1/jbrowse/data/
+Odontomachus_brunneus|/app/data/other_species/odobru/Obru_v1/jbrowse/data
+Osmia_lignaria|/app/data/other_species/osmlig/USDA_OLig_1.0/jbrowse/data
+3_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+4_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+Bombus_impatiens|/app/data/other_species/bomimp/BIMP_2.1/jbrowse/data
+Mamestra_configurata|/app/data/other_species/mamcon/GCA_002192655.1/jbrowse/data
+Bombus_terrestris|/app/data/other_species/bomter/Bter_1.0/jbrowse/data
+Neodiprion_lecontei|/app/data/other_species/neolec/Nlec1.1/jbrowse/data
+Apis_mellifera|/app/data/other_species/apimel/Amel_4.5/jbrowse/data/
+Rhyzopertha_dominica|/app/data/other_species/rhydom/RdoDt3_tmp/jbrowse/data
+Diachasma_alloeum|/app/data/other_species/diaall/Dall2.0/jbrowse/data
+Chelonus_insularis|/app/data/other_species/cheins/ASM1335770v1/jbrowse/data
+8_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+5_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+6_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+9_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+13_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+12_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+15_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+14_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+16_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+17_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+1_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+11_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+32_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+21_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+23_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+24_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+26_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+27_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+28_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+34_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+29_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+30_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+39_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+31_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+35_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+40_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+36_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+37_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+18_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+19_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+20_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+22_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+25_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+38_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+33_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
diff --git a/scripts/stage/README b/scripts/stage/README
index cf2ce78..080c430 100644
--- a/scripts/stage/README
+++ b/scripts/stage/README
@@ -5,7 +5,7 @@ select common_name, directory from organism ORDER by common_name;
 psql-U postgres -d webapollo_2 -c 'select common_name,directory from organism ORDER by common_name;'>organism_list.txt
 
 #makeaworkingfile
-cporganism_list.txtorganism_list.txt2
+cp organism_list.txtorganism_list.txt2
 
 
 
diff --git a/scripts/stage/may_20_2022_organism_list.txt b/scripts/stage/may_20_2022_organism_list.txt
new file mode 100644
index 0000000..d8f5d09
--- /dev/null
+++ b/scripts/stage/may_20_2022_organism_list.txt
@@ -0,0 +1,140 @@
+Saccharomyceseubayanus|/app/data/other_species/saceub/SEUB3.0/jbrowse/data
+Neodiprion_fabricii|/app/data/other_species/neofab/iyNeoFabr1.1/jbrowse/data
+Neodiprion_pinetum|/app/data/other_species/neopin/iyNeoPine1.1/jbrowse/data
+Photinus_pyralis|/app/data/other_species/phopyr/Ppyr1.3/jbrowse/data
+Venturia_canescens|/app/data/other_species/vencan/ASM1945775v1/jbrowse/data
+Helicoverpa_zea|/app/data/other_species/helzea/ilHelZeax1.1/jbrowse/data
+Manduca_sexta|/app/data/other_species/mansex/JHU_Msex_v1.0/jbrowse/data
+Drosophila_elegans|/app/data/other_species/droele/ASM1815250v1/jbrowse/data
+Diabrotica_virgifera_training|/app/data/other_species/diavir/Dvir_v2.0_RefSeq/jbrowse/data
+Drosophila_bipectinata|/app/data/other_species/drobip/ASM1815384v1/jbrowse/data
+Bradysia_coprophila|/app/data/other_species/bracop/BU_Bcop_v1/jbrowse/data
+Drosophila_eugracilis|/app/data/other_species/droeug/ASM1815383v1/jbrowse/data
+Lucilia_sericata|/app/data/other_species/lucser/ASM1558622v1/jbrowse/data
+Culex_quinquefasciatus|/app/data/other_species/culqui/VPISU_Cqui_1.0_pri_paternal/jbrowse/data
+Diprion_similis|/app/data//other_species/dipsim/iyDipSimi1.1/jbrowse/data
+Drosophila_kikkawai|/app/data/other_species/drokik/ASM1815253v1/jbrowse/data
+Drosophila_ficusphila|/app/data/other_species/drofic/ASM1815226v1/jbrowse/data
+Ladona_fulva|/app/data/other_species/ladful/Lful_2.0/jbrowse/data
+Rhipicephalus_microplus|/app/data/other_species/rhimic/ASM1333972v1/jbrowse/data
+Tribolium_madens|/app/data/other_species/trimad/Tmad_KSU_1.1/jbrowse/data
+Drosophila_rhopaloa|/app/data/other_species/drorho/ASM1815211v1/jbrowse/data
+Neodiprion_virginiana|/app/data/other_species/neovir/iyNeoVirg1.1/jbrowse/data
+Drosophila_takahashii|/app/data/other_species/drotak/ASM1815269v1/jbrowse/data
+Schistocerca_americana|/app/data/other_species/schame/iqSchAmer2.1/jbrowse/data
+Schistocercapiceifrons|/app/data/other_species/schpic/iqSchPice1.1/jbrowse/data/
+Hyalella_azteca|/app/data/BCM_i5k_pilot/hyaazt/Hazt_2.0.1/jbrowse/data
+Aethina_tumida|/app/data/other_species/aettum/jbrowse/data
+Agrilus_planipennis|/app/data/BCM_i5k_pilot/agrpla/jbrowse/data
+Ceratitis_capitata|/app/data/BCM_i5k_pilot/cercap/jbrowse/data
+Amyelois_transitella|/app/data/other_species/amytra/jbrowse/data
+Bactrocera_cucurbitae|/app/data/other_species/baccuc/jbrowse/data
+Bactrocera_dorsalis|/app/data/other_species/bacdor/jbrowse/data
+Bactrocera_oleae|/app/data/other_species/bacole/jbrowse/data
+Copidosoma_floridanum|/app/data/BCM_i5k_pilot/copflo/jbrowse/data
+Catajapyx_aquilonaris|/app/data/BCM_i5k_pilot/cataqu/jbrowse/data
+Oncopeltus_fasciatus|/app/data/BCM_i5k_pilot/oncfas/jbrowse/data
+Eufriesea_mexicana|/app/data/other_species/eufmex/ASM148370v1/jbrowse/data
+Dufourea_novaeangliae|/app/data/other_species/dufnov/jbrowse/data
+Fopius_arisanus|/app/data/other_species/fopari/jbrowse/data
+Eurytemora_affinis|/app/data/BCM_i5k_pilot/euraff/jbrowse/data
+Habropoda_laboriosa|/app/data/other_species/hablab/jbrowse/data
+Homalodisca_vitripennis|/app/data/BCM_i5k_pilot/homvit/jbrowse/data
+Lasioglossum_albipes|/app/data/other_species/lasalb/jbrowse/data
+Onthophagus_taurus|/app/data/BCM_i5k_pilot/onttau/jbrowse/data
+Varroa_destructor|/app/data/other_species/vardes/Vdes_3.0/jbrowse/data
+Gerris_buenoi|/app/data/BCM_i5k_pilot/gerbue/jbrowse/data/
+Athalia_rosae|/app/data/BCM_i5k_pilot/athros/BCM/jbrowse/data
+Orussus_abietinus|/app/data/BCM_i5k_pilot/oruabi/BCM/jbrowse/data
+Blattella_germanica|/app/data/BCM_i5k_pilot/blager/BCM/jbrowse/data
+Anoplophora_glabripennis|/app/data/BCM_i5k_pilot/anogla/BCM/jbrowse/data
+Cimex_lectularius|/app/data/BCM_i5k_pilot/cimlec/BCM/jbrowse/data
+Eurytemora_affinis_-_training|/app/data/BCM_i5k_pilot/euraff/jbrowse/data
+Limnephilus_lunatus|/app/data/BCM_i5k_pilot/limlun/jbrowse/data
+Diaphorina_citri_legacy|/app/data/other_species/diacit_legacy/jbrowse/data
+Mayetiola_destructor|/app/data/other_species/maydes/jbrowse/data
+Megachile_rotundata|/app/data/other_species/megrot/jbrowse/data
+Pachypsylla_venusta|/app/data/BCM_i5k_pilot/pacven/jbrowse/data
+Melipona_quadrifasciata|/app/data/other_species/melqua/jbrowse/data
+Parasteatoda_tepidariorum|/app/data/BCM_i5k_pilot/partep/jbrowse/data
+Nicrophorus_vespilloides|/app/data/other_species/nicves/jbrowse/data
+Leptinotarsa_decemlineata_training|/app/data/BCM_i5k_pilot/lepdec/jbrowse/data
+Rhagoletis_zephyria|/app/data/other_species/rhazep/jbrowse/data
+Tigriopus_californicus|/app/data/other_species/tigcal/jbrowse/data
+Tribolium_castaneum|/app/data/other_species/tricas/jbrowse/data
+Trichogramma_pretiosum|/app/data/BCM_i5k_pilot/tripre/jbrowse/data
+Oncopeltus_fasciatus_training|/app/data/BCM_i5k_pilot/oncfas/jbrowse/data
+Neodiprion_lecontei_training|/app/data/other_species/neolec/jbrowse/data
+Clitarchus_hookeri|/app/data/other_species/clihoo/jbrowse/data
+Microplitis_demolitor|/app/data/other_species/micdem/jbrowse/data
+Drosophila_biarmipes|/app/data/modencode/drobia/Dbia_2.0/jbrowse/data
+Holacanthella_duospinosa|/app/data/other_species/holduo/ASM273828v1/jbrowse/data
+Leptinotarsa_decemlineata|/app/data/BCM_i5k_pilot/lepdec/Ldec_2.0/jbrowse/data
+Laodelphax_striatellus|/app/data/other_species/laostr/ASM333518v2/jbrowse/data
+10_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+2_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+Diaphorina_citri|/app/data/other_species/diacit/jbrowse/data
+7_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+Centruroides_sculpturatus|/app/data/BCM_i5k_pilot/censcu/jbrowse/data
+Medauroidea_extradentata|/app/data/other_species/medext/GCA_003012365.1/jbrowse/data
+Nylanderia_fulva|/app/data/other_species/nylful/TAMU_Nfulva_1.0/jbrowse/data
+Frankliniella_occidentalis|/app/data/BCM_i5k_pilot/fraocc/Focc_3.0/jbrowse/data
+Loxosceles_reclusa|/app/data/BCM_i5k_pilot/loxrec/GCA_001188405.1/jbrowse/data
+Euglossa_dilemma|/app/data/other_species/eugdil/jbrowse/data
+Varroa_jacobsoni|/app/data/other_species/varjac/vjacob_1.0/jbrowse/data
+Halyomorpha_halys|/app/data/BCM_i5k_pilot/halhal/Hhal_1.1/jbrowse/data
+Bemisia_tabaci|/app/data/other_species/bemtab/jbrowse/data
+Galleria_mellonella|/app/data/other_species/galmel/ASM364042v2/jbrowse/data
+Latrodectus_hesperus|/app/data/BCM_i5k_pilot/lathes/GCA_000697925.1/jbrowse/data
+Heliothis_virescens|/app/data/other_species/helvir/jbrowse/data/
+Locusta_migratoria|/app/data/other_species/locmig/jbrowse/data/
+Contarinia_nasturtii|/app/data/other_species/connas/AAFC_CNas_1.1/jbrowse/data
+Ephemera_danica|/app/data/BCM_i5k_pilot/ephdan/Edan_2.0/jbrowse/data/
+Cephus_cinctus|/app/data/other_species/cepcin/Ccin1/jbrowse/data/
+Odontomachus_brunneus|/app/data/other_species/odobru/Obru_v1/jbrowse/data
+Osmia_lignaria|/app/data/other_species/osmlig/USDA_OLig_1.0/jbrowse/data
+3_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+4_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+Bombus_impatiens|/app/data/other_species/bomimp/BIMP_2.1/jbrowse/data
+Mamestra_configurata|/app/data/other_species/mamcon/GCA_002192655.1/jbrowse/data
+Bombus_terrestris|/app/data/other_species/bomter/Bter_1.0/jbrowse/data
+Neodiprion_lecontei|/app/data/other_species/neolec/Nlec1.1/jbrowse/data
+Apis_mellifera|/app/data/other_species/apimel/Amel_4.5/jbrowse/data/
+Rhyzopertha_dominica|/app/data/other_species/rhydom/RdoDt3_tmp/jbrowse/data
+Diachasma_alloeum|/app/data/other_species/diaall/Dall2.0/jbrowse/data
+Chelonus_insularis|/app/data/other_species/cheins/ASM1335770v1/jbrowse/data
+8_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+5_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+6_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+9_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+13_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+12_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+15_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+14_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+16_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+17_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+1_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+11_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+32_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+21_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+23_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+24_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+26_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+27_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+28_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+34_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+29_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+30_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+39_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+31_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+35_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+40_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+36_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+37_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+18_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+19_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+20_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+22_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+25_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+38_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
+33_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
diff --git a/scripts/stage/move_conf_files_back.sh b/scripts/stage/move_conf_files_back.sh
index f25d46b..6bdd5be 100644
--- a/scripts/stage/move_conf_files_back.sh
+++ b/scripts/stage/move_conf_files_back.sh
@@ -1,256 +1,280 @@
+cp ../../working/stage/Saccharomyceseubayanus/* /app/data/other_species/saceub/SEUB3.0/jbrowse/data/; 
+cp ../../css/custom.css /app/data/other_species/saceub/SEUB3.0/jbrowse/data/; 
+cp ../../working/stage/Neodiprion_fabricii/* /app/data/other_species/neofab/iyNeoFabr1.1/jbrowse/data/; 
+cp ../../css/custom.css /app/data/other_species/neofab/iyNeoFabr1.1/jbrowse/data/; 
+cp ../../working/stage/Neodiprion_pinetum/* /app/data/other_species/neopin/iyNeoPine1.1/jbrowse/data/; 
+cp ../../css/custom.css /app/data/other_species/neopin/iyNeoPine1.1/jbrowse/data/; 
+cp ../../working/stage/Photinus_pyralis/* /app/data/other_species/phopyr/Ppyr1.3/jbrowse/data/; 
+cp ../../css/custom.css /app/data/other_species/phopyr/Ppyr1.3/jbrowse/data/; 
+cp ../../working/stage/Venturia_canescens/* /app/data/other_species/vencan/ASM1945775v1/jbrowse/data/; 
+cp ../../css/custom.css /app/data/other_species/vencan/ASM1945775v1/jbrowse/data/; 
+cp ../../working/stage/Helicoverpa_zea/* /app/data/other_species/helzea/ilHelZeax1.1/jbrowse/data/; 
+cp ../../css/custom.css /app/data/other_species/helzea/ilHelZeax1.1/jbrowse/data/; 
+cp ../../working/stage/Manduca_sexta/* /app/data/other_species/mansex/JHU_Msex_v1.0/jbrowse/data/; 
+cp ../../css/custom.css /app/data/other_species/mansex/JHU_Msex_v1.0/jbrowse/data/; 
+cp ../../working/stage/Drosophila_elegans/* /app/data/other_species/droele/ASM1815250v1/jbrowse/data/; 
+cp ../../css/custom.css /app/data/other_species/droele/ASM1815250v1/jbrowse/data/; 
+cp ../../working/stage/Diabrotica_virgifera_training/* /app/data/other_species/diavir/Dvir_v2.0_RefSeq/jbrowse/data/; 
+cp ../../css/custom.css /app/data/other_species/diavir/Dvir_v2.0_RefSeq/jbrowse/data/; 
+cp ../../working/stage/Drosophila_bipectinata/* /app/data/other_species/drobip/ASM1815384v1/jbrowse/data/; 
+cp ../../css/custom.css /app/data/other_species/drobip/ASM1815384v1/jbrowse/data/; 
+cp ../../working/stage/Bradysia_coprophila/* /app/data/other_species/bracop/BU_Bcop_v1/jbrowse/data/; 
+cp ../../css/custom.css /app/data/other_species/bracop/BU_Bcop_v1/jbrowse/data/; 
+cp ../../working/stage/Drosophila_eugracilis/* /app/data/other_species/droeug/ASM1815383v1/jbrowse/data/; 
+cp ../../css/custom.css /app/data/other_species/droeug/ASM1815383v1/jbrowse/data/; 
+cp ../../working/stage/Lucilia_sericata/* /app/data/other_species/lucser/ASM1558622v1/jbrowse/data/; 
+cp ../../css/custom.css /app/data/other_species/lucser/ASM1558622v1/jbrowse/data/; 
+cp ../../working/stage/Culex_quinquefasciatus/* /app/data/other_species/culqui/VPISU_Cqui_1.0_pri_paternal/jbrowse/data/; 
+cp ../../css/custom.css /app/data/other_species/culqui/VPISU_Cqui_1.0_pri_paternal/jbrowse/data/; 
+cp ../../working/stage/Diprion_similis/* /app/data//other_species/dipsim/iyDipSimi1.1/jbrowse/data/; 
+cp ../../css/custom.css /app/data//other_species/dipsim/iyDipSimi1.1/jbrowse/data/; 
+cp ../../working/stage/Drosophila_kikkawai/* /app/data/other_species/drokik/ASM1815253v1/jbrowse/data/; 
+cp ../../css/custom.css /app/data/other_species/drokik/ASM1815253v1/jbrowse/data/; 
+cp ../../working/stage/Drosophila_ficusphila/* /app/data/other_species/drofic/ASM1815226v1/jbrowse/data/; 
+cp ../../css/custom.css /app/data/other_species/drofic/ASM1815226v1/jbrowse/data/; 
+cp ../../working/stage/Ladona_fulva/* /app/data/other_species/ladful/Lful_2.0/jbrowse/data/; 
+cp ../../css/custom.css /app/data/other_species/ladful/Lful_2.0/jbrowse/data/; 
+cp ../../working/stage/Rhipicephalus_microplus/* /app/data/other_species/rhimic/ASM1333972v1/jbrowse/data/; 
+cp ../../css/custom.css /app/data/other_species/rhimic/ASM1333972v1/jbrowse/data/; 
+cp ../../working/stage/Tribolium_madens/* /app/data/other_species/trimad/Tmad_KSU_1.1/jbrowse/data/; 
+cp ../../css/custom.css /app/data/other_species/trimad/Tmad_KSU_1.1/jbrowse/data/; 
+cp ../../working/stage/Drosophila_rhopaloa/* /app/data/other_species/drorho/ASM1815211v1/jbrowse/data/; 
+cp ../../css/custom.css /app/data/other_species/drorho/ASM1815211v1/jbrowse/data/; 
+cp ../../working/stage/Neodiprion_virginiana/* /app/data/other_species/neovir/iyNeoVirg1.1/jbrowse/data/; 
+cp ../../css/custom.css /app/data/other_species/neovir/iyNeoVirg1.1/jbrowse/data/; 
+cp ../../working/stage/Drosophila_takahashii/* /app/data/other_species/drotak/ASM1815269v1/jbrowse/data/; 
+cp ../../css/custom.css /app/data/other_species/drotak/ASM1815269v1/jbrowse/data/; 
+cp ../../working/stage/Schistocerca_americana/* /app/data/other_species/schame/iqSchAmer2.1/jbrowse/data/; 
+cp ../../css/custom.css /app/data/other_species/schame/iqSchAmer2.1/jbrowse/data/; 
+cp ../../working/stage/Schistocercapiceifrons/* /app/data/other_species/schpic/iqSchPice1.1/jbrowse/data//; 
+cp ../../css/custom.css /app/data/other_species/schpic/iqSchPice1.1/jbrowse/data//; 
+cp ../../working/stage/Hyalella_azteca/* /app/data/BCM_i5k_pilot/hyaazt/Hazt_2.0.1/jbrowse/data/; 
+cp ../../css/custom.css /app/data/BCM_i5k_pilot/hyaazt/Hazt_2.0.1/jbrowse/data/; 
+cp ../../working/stage/Aethina_tumida/* /app/data/other_species/aettum/jbrowse/data/; 
+cp ../../css/custom.css /app/data/other_species/aettum/jbrowse/data/; 
+cp ../../working/stage/Agrilus_planipennis/* /app/data/BCM_i5k_pilot/agrpla/jbrowse/data/; 
+cp ../../css/custom.css /app/data/BCM_i5k_pilot/agrpla/jbrowse/data/; 
+cp ../../working/stage/Ceratitis_capitata/* /app/data/BCM_i5k_pilot/cercap/jbrowse/data/; 
+cp ../../css/custom.css /app/data/BCM_i5k_pilot/cercap/jbrowse/data/; 
+cp ../../working/stage/Amyelois_transitella/* /app/data/other_species/amytra/jbrowse/data/; 
+cp ../../css/custom.css /app/data/other_species/amytra/jbrowse/data/; 
+cp ../../working/stage/Bactrocera_cucurbitae/* /app/data/other_species/baccuc/jbrowse/data/; 
+cp ../../css/custom.css /app/data/other_species/baccuc/jbrowse/data/; 
+cp ../../working/stage/Bactrocera_dorsalis/* /app/data/other_species/bacdor/jbrowse/data/; 
+cp ../../css/custom.css /app/data/other_species/bacdor/jbrowse/data/; 
+cp ../../working/stage/Bactrocera_oleae/* /app/data/other_species/bacole/jbrowse/data/; 
+cp ../../css/custom.css /app/data/other_species/bacole/jbrowse/data/; 
+cp ../../working/stage/Copidosoma_floridanum/* /app/data/BCM_i5k_pilot/copflo/jbrowse/data/; 
+cp ../../css/custom.css /app/data/BCM_i5k_pilot/copflo/jbrowse/data/; 
+cp ../../working/stage/Catajapyx_aquilonaris/* /app/data/BCM_i5k_pilot/cataqu/jbrowse/data/; 
+cp ../../css/custom.css /app/data/BCM_i5k_pilot/cataqu/jbrowse/data/; 
+cp ../../working/stage/Oncopeltus_fasciatus/* /app/data/BCM_i5k_pilot/oncfas/jbrowse/data/; 
+cp ../../css/custom.css /app/data/BCM_i5k_pilot/oncfas/jbrowse/data/; 
+cp ../../working/stage/Eufriesea_mexicana/* /app/data/other_species/eufmex/ASM148370v1/jbrowse/data/; 
+cp ../../css/custom.css /app/data/other_species/eufmex/ASM148370v1/jbrowse/data/; 
+cp ../../working/stage/Dufourea_novaeangliae/* /app/data/other_species/dufnov/jbrowse/data/; 
+cp ../../css/custom.css /app/data/other_species/dufnov/jbrowse/data/; 
+cp ../../working/stage/Fopius_arisanus/* /app/data/other_species/fopari/jbrowse/data/; 
+cp ../../css/custom.css /app/data/other_species/fopari/jbrowse/data/; 
+cp ../../working/stage/Eurytemora_affinis/* /app/data/BCM_i5k_pilot/euraff/jbrowse/data/; 
+cp ../../css/custom.css /app/data/BCM_i5k_pilot/euraff/jbrowse/data/; 
+cp ../../working/stage/Habropoda_laboriosa/* /app/data/other_species/hablab/jbrowse/data/; 
+cp ../../css/custom.css /app/data/other_species/hablab/jbrowse/data/; 
+cp ../../working/stage/Homalodisca_vitripennis/* /app/data/BCM_i5k_pilot/homvit/jbrowse/data/; 
+cp ../../css/custom.css /app/data/BCM_i5k_pilot/homvit/jbrowse/data/; 
+cp ../../working/stage/Lasioglossum_albipes/* /app/data/other_species/lasalb/jbrowse/data/; 
+cp ../../css/custom.css /app/data/other_species/lasalb/jbrowse/data/; 
+cp ../../working/stage/Onthophagus_taurus/* /app/data/BCM_i5k_pilot/onttau/jbrowse/data/; 
+cp ../../css/custom.css /app/data/BCM_i5k_pilot/onttau/jbrowse/data/; 
+cp ../../working/stage/Varroa_destructor/* /app/data/other_species/vardes/Vdes_3.0/jbrowse/data/; 
+cp ../../css/custom.css /app/data/other_species/vardes/Vdes_3.0/jbrowse/data/; 
+cp ../../working/stage/Gerris_buenoi/* /app/data/BCM_i5k_pilot/gerbue/jbrowse/data//; 
+cp ../../css/custom.css /app/data/BCM_i5k_pilot/gerbue/jbrowse/data//; 
+cp ../../working/stage/Athalia_rosae/* /app/data/BCM_i5k_pilot/athros/BCM/jbrowse/data/; 
+cp ../../css/custom.css /app/data/BCM_i5k_pilot/athros/BCM/jbrowse/data/; 
+cp ../../working/stage/Orussus_abietinus/* /app/data/BCM_i5k_pilot/oruabi/BCM/jbrowse/data/; 
+cp ../../css/custom.css /app/data/BCM_i5k_pilot/oruabi/BCM/jbrowse/data/; 
+cp ../../working/stage/Blattella_germanica/* /app/data/BCM_i5k_pilot/blager/BCM/jbrowse/data/; 
+cp ../../css/custom.css /app/data/BCM_i5k_pilot/blager/BCM/jbrowse/data/; 
+cp ../../working/stage/Anoplophora_glabripennis/* /app/data/BCM_i5k_pilot/anogla/BCM/jbrowse/data/; 
+cp ../../css/custom.css /app/data/BCM_i5k_pilot/anogla/BCM/jbrowse/data/; 
+cp ../../working/stage/Cimex_lectularius/* /app/data/BCM_i5k_pilot/cimlec/BCM/jbrowse/data/; 
+cp ../../css/custom.css /app/data/BCM_i5k_pilot/cimlec/BCM/jbrowse/data/; 
+cp ../../working/stage/Eurytemora_affinis_-_training/* /app/data/BCM_i5k_pilot/euraff/jbrowse/data/; 
+cp ../../css/custom.css /app/data/BCM_i5k_pilot/euraff/jbrowse/data/; 
+cp ../../working/stage/Limnephilus_lunatus/* /app/data/BCM_i5k_pilot/limlun/jbrowse/data/; 
+cp ../../css/custom.css /app/data/BCM_i5k_pilot/limlun/jbrowse/data/; 
+cp ../../working/stage/Diaphorina_citri_legacy/* /app/data/other_species/diacit_legacy/jbrowse/data/; 
+cp ../../css/custom.css /app/data/other_species/diacit_legacy/jbrowse/data/; 
+cp ../../working/stage/Mayetiola_destructor/* /app/data/other_species/maydes/jbrowse/data/; 
+cp ../../css/custom.css /app/data/other_species/maydes/jbrowse/data/; 
+cp ../../working/stage/Megachile_rotundata/* /app/data/other_species/megrot/jbrowse/data/; 
+cp ../../css/custom.css /app/data/other_species/megrot/jbrowse/data/; 
+cp ../../working/stage/Pachypsylla_venusta/* /app/data/BCM_i5k_pilot/pacven/jbrowse/data/; 
+cp ../../css/custom.css /app/data/BCM_i5k_pilot/pacven/jbrowse/data/; 
+cp ../../working/stage/Melipona_quadrifasciata/* /app/data/other_species/melqua/jbrowse/data/; 
+cp ../../css/custom.css /app/data/other_species/melqua/jbrowse/data/; 
+cp ../../working/stage/Parasteatoda_tepidariorum/* /app/data/BCM_i5k_pilot/partep/jbrowse/data/; 
+cp ../../css/custom.css /app/data/BCM_i5k_pilot/partep/jbrowse/data/; 
+cp ../../working/stage/Nicrophorus_vespilloides/* /app/data/other_species/nicves/jbrowse/data/; 
+cp ../../css/custom.css /app/data/other_species/nicves/jbrowse/data/; 
+cp ../../working/stage/Leptinotarsa_decemlineata_training/* /app/data/BCM_i5k_pilot/lepdec/jbrowse/data/; 
+cp ../../css/custom.css /app/data/BCM_i5k_pilot/lepdec/jbrowse/data/; 
+cp ../../working/stage/Rhagoletis_zephyria/* /app/data/other_species/rhazep/jbrowse/data/; 
+cp ../../css/custom.css /app/data/other_species/rhazep/jbrowse/data/; 
+cp ../../working/stage/Tigriopus_californicus/* /app/data/other_species/tigcal/jbrowse/data/; 
+cp ../../css/custom.css /app/data/other_species/tigcal/jbrowse/data/; 
+cp ../../working/stage/Tribolium_castaneum/* /app/data/other_species/tricas/jbrowse/data/; 
+cp ../../css/custom.css /app/data/other_species/tricas/jbrowse/data/; 
+cp ../../working/stage/Trichogramma_pretiosum/* /app/data/BCM_i5k_pilot/tripre/jbrowse/data/; 
+cp ../../css/custom.css /app/data/BCM_i5k_pilot/tripre/jbrowse/data/; 
+cp ../../working/stage/Oncopeltus_fasciatus_training/* /app/data/BCM_i5k_pilot/oncfas/jbrowse/data/; 
+cp ../../css/custom.css /app/data/BCM_i5k_pilot/oncfas/jbrowse/data/; 
+cp ../../working/stage/Neodiprion_lecontei_training/* /app/data/other_species/neolec/jbrowse/data/; 
+cp ../../css/custom.css /app/data/other_species/neolec/jbrowse/data/; 
+cp ../../working/stage/Clitarchus_hookeri/* /app/data/other_species/clihoo/jbrowse/data/; 
+cp ../../css/custom.css /app/data/other_species/clihoo/jbrowse/data/; 
+cp ../../working/stage/Microplitis_demolitor/* /app/data/other_species/micdem/jbrowse/data/; 
+cp ../../css/custom.css /app/data/other_species/micdem/jbrowse/data/; 
+cp ../../working/stage/Drosophila_biarmipes/* /app/data/modencode/drobia/Dbia_2.0/jbrowse/data/; 
+cp ../../css/custom.css /app/data/modencode/drobia/Dbia_2.0/jbrowse/data/; 
+cp ../../working/stage/Holacanthella_duospinosa/* /app/data/other_species/holduo/ASM273828v1/jbrowse/data/; 
+cp ../../css/custom.css /app/data/other_species/holduo/ASM273828v1/jbrowse/data/; 
+cp ../../working/stage/Leptinotarsa_decemlineata/* /app/data/BCM_i5k_pilot/lepdec/Ldec_2.0/jbrowse/data/; 
+cp ../../css/custom.css /app/data/BCM_i5k_pilot/lepdec/Ldec_2.0/jbrowse/data/; 
+cp ../../working/stage/Laodelphax_striatellus/* /app/data/other_species/laostr/ASM333518v2/jbrowse/data/; 
+cp ../../css/custom.css /app/data/other_species/laostr/ASM333518v2/jbrowse/data/; 
 cp ../../working/stage/10_-_Onthophagus_taurus_training/* /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
 cp ../../css/custom.css /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
-cp ../../working/stage/11_-_Onthophagus_taurus_training/* /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
+cp ../../working/stage/2_-_Onthophagus_taurus_training/* /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
 cp ../../css/custom.css /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
-cp ../../working/stage/12_-_Onthophagus_taurus_training/* /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
+cp ../../working/stage/Diaphorina_citri/* /app/data/other_species/diacit/jbrowse/data/; 
+cp ../../css/custom.css /app/data/other_species/diacit/jbrowse/data/; 
+cp ../../working/stage/7_-_Onthophagus_taurus_training/* /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
+cp ../../css/custom.css /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
+cp ../../working/stage/Centruroides_sculpturatus/* /app/data/BCM_i5k_pilot/censcu/jbrowse/data/; 
+cp ../../css/custom.css /app/data/BCM_i5k_pilot/censcu/jbrowse/data/; 
+cp ../../working/stage/Medauroidea_extradentata/* /app/data/other_species/medext/GCA_003012365.1/jbrowse/data/; 
+cp ../../css/custom.css /app/data/other_species/medext/GCA_003012365.1/jbrowse/data/; 
+cp ../../working/stage/Nylanderia_fulva/* /app/data/other_species/nylful/TAMU_Nfulva_1.0/jbrowse/data/; 
+cp ../../css/custom.css /app/data/other_species/nylful/TAMU_Nfulva_1.0/jbrowse/data/; 
+cp ../../working/stage/Frankliniella_occidentalis/* /app/data/BCM_i5k_pilot/fraocc/Focc_3.0/jbrowse/data/; 
+cp ../../css/custom.css /app/data/BCM_i5k_pilot/fraocc/Focc_3.0/jbrowse/data/; 
+cp ../../working/stage/Loxosceles_reclusa/* /app/data/BCM_i5k_pilot/loxrec/GCA_001188405.1/jbrowse/data/; 
+cp ../../css/custom.css /app/data/BCM_i5k_pilot/loxrec/GCA_001188405.1/jbrowse/data/; 
+cp ../../working/stage/Euglossa_dilemma/* /app/data/other_species/eugdil/jbrowse/data/; 
+cp ../../css/custom.css /app/data/other_species/eugdil/jbrowse/data/; 
+cp ../../working/stage/Varroa_jacobsoni/* /app/data/other_species/varjac/vjacob_1.0/jbrowse/data/; 
+cp ../../css/custom.css /app/data/other_species/varjac/vjacob_1.0/jbrowse/data/; 
+cp ../../working/stage/Halyomorpha_halys/* /app/data/BCM_i5k_pilot/halhal/Hhal_1.1/jbrowse/data/; 
+cp ../../css/custom.css /app/data/BCM_i5k_pilot/halhal/Hhal_1.1/jbrowse/data/; 
+cp ../../working/stage/Bemisia_tabaci/* /app/data/other_species/bemtab/jbrowse/data/; 
+cp ../../css/custom.css /app/data/other_species/bemtab/jbrowse/data/; 
+cp ../../working/stage/Galleria_mellonella/* /app/data/other_species/galmel/ASM364042v2/jbrowse/data/; 
+cp ../../css/custom.css /app/data/other_species/galmel/ASM364042v2/jbrowse/data/; 
+cp ../../working/stage/Latrodectus_hesperus/* /app/data/BCM_i5k_pilot/lathes/GCA_000697925.1/jbrowse/data/; 
+cp ../../css/custom.css /app/data/BCM_i5k_pilot/lathes/GCA_000697925.1/jbrowse/data/; 
+cp ../../working/stage/Heliothis_virescens/* /app/data/other_species/helvir/jbrowse/data//; 
+cp ../../css/custom.css /app/data/other_species/helvir/jbrowse/data//; 
+cp ../../working/stage/Locusta_migratoria/* /app/data/other_species/locmig/jbrowse/data//; 
+cp ../../css/custom.css /app/data/other_species/locmig/jbrowse/data//; 
+cp ../../working/stage/Contarinia_nasturtii/* /app/data/other_species/connas/AAFC_CNas_1.1/jbrowse/data/; 
+cp ../../css/custom.css /app/data/other_species/connas/AAFC_CNas_1.1/jbrowse/data/; 
+cp ../../working/stage/Ephemera_danica/* /app/data/BCM_i5k_pilot/ephdan/Edan_2.0/jbrowse/data//; 
+cp ../../css/custom.css /app/data/BCM_i5k_pilot/ephdan/Edan_2.0/jbrowse/data//; 
+cp ../../working/stage/Cephus_cinctus/* /app/data/other_species/cepcin/Ccin1/jbrowse/data//; 
+cp ../../css/custom.css /app/data/other_species/cepcin/Ccin1/jbrowse/data//; 
+cp ../../working/stage/Odontomachus_brunneus/* /app/data/other_species/odobru/Obru_v1/jbrowse/data/; 
+cp ../../css/custom.css /app/data/other_species/odobru/Obru_v1/jbrowse/data/; 
+cp ../../working/stage/Osmia_lignaria/* /app/data/other_species/osmlig/USDA_OLig_1.0/jbrowse/data/; 
+cp ../../css/custom.css /app/data/other_species/osmlig/USDA_OLig_1.0/jbrowse/data/; 
+cp ../../working/stage/3_-_Onthophagus_taurus_training/* /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
+cp ../../css/custom.css /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
+cp ../../working/stage/4_-_Onthophagus_taurus_training/* /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
+cp ../../css/custom.css /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
+cp ../../working/stage/Bombus_impatiens/* /app/data/other_species/bomimp/BIMP_2.1/jbrowse/data/; 
+cp ../../css/custom.css /app/data/other_species/bomimp/BIMP_2.1/jbrowse/data/; 
+cp ../../working/stage/Mamestra_configurata/* /app/data/other_species/mamcon/GCA_002192655.1/jbrowse/data/; 
+cp ../../css/custom.css /app/data/other_species/mamcon/GCA_002192655.1/jbrowse/data/; 
+cp ../../working/stage/Bombus_terrestris/* /app/data/other_species/bomter/Bter_1.0/jbrowse/data/; 
+cp ../../css/custom.css /app/data/other_species/bomter/Bter_1.0/jbrowse/data/; 
+cp ../../working/stage/Neodiprion_lecontei/* /app/data/other_species/neolec/Nlec1.1/jbrowse/data/; 
+cp ../../css/custom.css /app/data/other_species/neolec/Nlec1.1/jbrowse/data/; 
+cp ../../working/stage/Apis_mellifera/* /app/data/other_species/apimel/Amel_4.5/jbrowse/data//; 
+cp ../../css/custom.css /app/data/other_species/apimel/Amel_4.5/jbrowse/data//; 
+cp ../../working/stage/Rhyzopertha_dominica/* /app/data/other_species/rhydom/RdoDt3_tmp/jbrowse/data/; 
+cp ../../css/custom.css /app/data/other_species/rhydom/RdoDt3_tmp/jbrowse/data/; 
+cp ../../working/stage/Diachasma_alloeum/* /app/data/other_species/diaall/Dall2.0/jbrowse/data/; 
+cp ../../css/custom.css /app/data/other_species/diaall/Dall2.0/jbrowse/data/; 
+cp ../../working/stage/Chelonus_insularis/* /app/data/other_species/cheins/ASM1335770v1/jbrowse/data/; 
+cp ../../css/custom.css /app/data/other_species/cheins/ASM1335770v1/jbrowse/data/; 
+cp ../../working/stage/8_-_Onthophagus_taurus_training/* /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
+cp ../../css/custom.css /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
+cp ../../working/stage/5_-_Onthophagus_taurus_training/* /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
+cp ../../css/custom.css /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
+cp ../../working/stage/6_-_Onthophagus_taurus_training/* /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
+cp ../../css/custom.css /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
+cp ../../working/stage/9_-_Onthophagus_taurus_training/* /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
 cp ../../css/custom.css /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
 cp ../../working/stage/13_-_Onthophagus_taurus_training/* /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
 cp ../../css/custom.css /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
-cp ../../working/stage/14_-_Onthophagus_taurus_training/* /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
+cp ../../working/stage/12_-_Onthophagus_taurus_training/* /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
 cp ../../css/custom.css /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
 cp ../../working/stage/15_-_Onthophagus_taurus_training/* /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
 cp ../../css/custom.css /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
+cp ../../working/stage/14_-_Onthophagus_taurus_training/* /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
+cp ../../css/custom.css /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
 cp ../../working/stage/16_-_Onthophagus_taurus_training/* /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
 cp ../../css/custom.css /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
 cp ../../working/stage/17_-_Onthophagus_taurus_training/* /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
 cp ../../css/custom.css /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
-cp ../../working/stage/18_-_Onthophagus_taurus_training/* /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
-cp ../../css/custom.css /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
-cp ../../working/stage/19_-_Onthophagus_taurus_training/* /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
-cp ../../css/custom.css /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
 cp ../../working/stage/1_-_Onthophagus_taurus_training/* /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
 cp ../../css/custom.css /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
-cp ../../working/stage/20_-_Onthophagus_taurus_training/* /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
+cp ../../working/stage/11_-_Onthophagus_taurus_training/* /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
 cp ../../css/custom.css /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
-cp ../../working/stage/21_-_Onthophagus_taurus_training/* /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
+cp ../../working/stage/32_-_Onthophagus_taurus_training/* /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
 cp ../../css/custom.css /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
-cp ../../working/stage/22_-_Onthophagus_taurus_training/* /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
+cp ../../working/stage/21_-_Onthophagus_taurus_training/* /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
 cp ../../css/custom.css /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
 cp ../../working/stage/23_-_Onthophagus_taurus_training/* /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
 cp ../../css/custom.css /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
 cp ../../working/stage/24_-_Onthophagus_taurus_training/* /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
 cp ../../css/custom.css /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
-cp ../../working/stage/25_-_Onthophagus_taurus_training/* /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
-cp ../../css/custom.css /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
 cp ../../working/stage/26_-_Onthophagus_taurus_training/* /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
 cp ../../css/custom.css /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
 cp ../../working/stage/27_-_Onthophagus_taurus_training/* /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
 cp ../../css/custom.css /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
 cp ../../working/stage/28_-_Onthophagus_taurus_training/* /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
 cp ../../css/custom.css /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
-cp ../../working/stage/29_-_Onthophagus_taurus_training/* /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
+cp ../../working/stage/34_-_Onthophagus_taurus_training/* /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
 cp ../../css/custom.css /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
-cp ../../working/stage/2_-_Onthophagus_taurus_training/* /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
+cp ../../working/stage/29_-_Onthophagus_taurus_training/* /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
 cp ../../css/custom.css /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
 cp ../../working/stage/30_-_Onthophagus_taurus_training/* /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
 cp ../../css/custom.css /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
-cp ../../working/stage/31_-_Onthophagus_taurus_training/* /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
-cp ../../css/custom.css /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
-cp ../../working/stage/32_-_Onthophagus_taurus_training/* /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
-cp ../../css/custom.css /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
-cp ../../working/stage/33_-_Onthophagus_taurus_training/* /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
+cp ../../working/stage/39_-_Onthophagus_taurus_training/* /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
 cp ../../css/custom.css /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
-cp ../../working/stage/34_-_Onthophagus_taurus_training/* /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
+cp ../../working/stage/31_-_Onthophagus_taurus_training/* /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
 cp ../../css/custom.css /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
 cp ../../working/stage/35_-_Onthophagus_taurus_training/* /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
 cp ../../css/custom.css /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
+cp ../../working/stage/40_-_Onthophagus_taurus_training/* /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
+cp ../../css/custom.css /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
 cp ../../working/stage/36_-_Onthophagus_taurus_training/* /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
 cp ../../css/custom.css /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
 cp ../../working/stage/37_-_Onthophagus_taurus_training/* /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
 cp ../../css/custom.css /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
-cp ../../working/stage/38_-_Onthophagus_taurus_training/* /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
-cp ../../css/custom.css /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
-cp ../../working/stage/39_-_Onthophagus_taurus_training/* /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
-cp ../../css/custom.css /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
-cp ../../working/stage/3_-_Onthophagus_taurus_training/* /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
-cp ../../css/custom.css /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
-cp ../../working/stage/40_-_Onthophagus_taurus_training/* /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
+cp ../../working/stage/18_-_Onthophagus_taurus_training/* /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
 cp ../../css/custom.css /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
-cp ../../working/stage/4_-_Onthophagus_taurus_training/* /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
+cp ../../working/stage/19_-_Onthophagus_taurus_training/* /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
 cp ../../css/custom.css /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
-cp ../../working/stage/5_-_Onthophagus_taurus_training/* /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
+cp ../../working/stage/20_-_Onthophagus_taurus_training/* /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
 cp ../../css/custom.css /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
-cp ../../working/stage/6_-_Onthophagus_taurus_training/* /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
+cp ../../working/stage/22_-_Onthophagus_taurus_training/* /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
 cp ../../css/custom.css /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
-cp ../../working/stage/7_-_Onthophagus_taurus_training/* /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
+cp ../../working/stage/25_-_Onthophagus_taurus_training/* /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
 cp ../../css/custom.css /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
-cp ../../working/stage/8_-_Onthophagus_taurus_training/* /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
+cp ../../working/stage/38_-_Onthophagus_taurus_training/* /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
 cp ../../css/custom.css /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
-cp ../../working/stage/9_-_Onthophagus_taurus_training/* /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
+cp ../../working/stage/33_-_Onthophagus_taurus_training/* /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
 cp ../../css/custom.css /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; 
-cp ../../working/stage/Aethina_tumida/* /app/data/other_species/aettum/jbrowse/data/; 
-cp ../../css/custom.css /app/data/other_species/aettum/jbrowse/data/; 
-cp ../../working/stage/Agrilus_planipennis/* /app/data/BCM_i5k_pilot/agrpla/jbrowse/data/; 
-cp ../../css/custom.css /app/data/BCM_i5k_pilot/agrpla/jbrowse/data/; 
-cp ../../working/stage/Amyelois_transitella/* /app/data/other_species/amytra/jbrowse/data/; 
-cp ../../css/custom.css /app/data/other_species/amytra/jbrowse/data/; 
-cp ../../working/stage/Anoplophora_glabripennis/* /app/data/BCM_i5k_pilot/anogla/BCM/jbrowse/data/; 
-cp ../../css/custom.css /app/data/BCM_i5k_pilot/anogla/BCM/jbrowse/data/; 
-cp ../../working/stage/Apis_mellifera/* /app/data/other_species/apimel/Amel_4.5/jbrowse/data//; 
-cp ../../css/custom.css /app/data/other_species/apimel/Amel_4.5/jbrowse/data//; 
-cp ../../working/stage/Athalia_rosae/* /app/data/BCM_i5k_pilot/athros/BCM/jbrowse/data/; 
-cp ../../css/custom.css /app/data/BCM_i5k_pilot/athros/BCM/jbrowse/data/; 
-cp ../../working/stage/Bactrocera_cucurbitae/* /app/data/other_species/baccuc/jbrowse/data/; 
-cp ../../css/custom.css /app/data/other_species/baccuc/jbrowse/data/; 
-cp ../../working/stage/Bactrocera_dorsalis/* /app/data/other_species/bacdor/jbrowse/data/; 
-cp ../../css/custom.css /app/data/other_species/bacdor/jbrowse/data/; 
-cp ../../working/stage/Bactrocera_oleae/* /app/data/other_species/bacole/jbrowse/data/; 
-cp ../../css/custom.css /app/data/other_species/bacole/jbrowse/data/; 
-cp ../../working/stage/Bemisia_tabaci/* /app/data/other_species/bemtab/jbrowse/data/; 
-cp ../../css/custom.css /app/data/other_species/bemtab/jbrowse/data/; 
-cp ../../working/stage/Blattella_germanica/* /app/data/BCM_i5k_pilot/blager/BCM/jbrowse/data/; 
-cp ../../css/custom.css /app/data/BCM_i5k_pilot/blager/BCM/jbrowse/data/; 
-cp ../../working/stage/Bombus_impatiens/* /app/data/other_species/bomimp/BIMP_2.1/jbrowse/data/; 
-cp ../../css/custom.css /app/data/other_species/bomimp/BIMP_2.1/jbrowse/data/; 
-cp ../../working/stage/Bombus_terrestris/* /app/data/other_species/bomter/Bter_1.0/jbrowse/data/; 
-cp ../../css/custom.css /app/data/other_species/bomter/Bter_1.0/jbrowse/data/; 
-cp ../../working/stage/Bradysia_coprophila/* /app/data/other_species/bracop/BU_Bcop_v1/jbrowse/data/; 
-cp ../../css/custom.css /app/data/other_species/bracop/BU_Bcop_v1/jbrowse/data/; 
-cp ../../working/stage/Catajapyx_aquilonaris/* /app/data/BCM_i5k_pilot/cataqu/jbrowse/data/; 
-cp ../../css/custom.css /app/data/BCM_i5k_pilot/cataqu/jbrowse/data/; 
-cp ../../working/stage/Centruroides_sculpturatus/* /app/data/BCM_i5k_pilot/censcu/jbrowse/data/; 
-cp ../../css/custom.css /app/data/BCM_i5k_pilot/censcu/jbrowse/data/; 
-cp ../../working/stage/Cephus_cinctus/* /app/data/other_species/cepcin/Ccin1/jbrowse/data//; 
-cp ../../css/custom.css /app/data/other_species/cepcin/Ccin1/jbrowse/data//; 
-cp ../../working/stage/Ceratitis_capitata/* /app/data/BCM_i5k_pilot/cercap/jbrowse/data/; 
-cp ../../css/custom.css /app/data/BCM_i5k_pilot/cercap/jbrowse/data/; 
-cp ../../working/stage/Chelonus_insularis/* /app/data/other_species/cheins/ASM1335770v1/jbrowse/data/; 
-cp ../../css/custom.css /app/data/other_species/cheins/ASM1335770v1/jbrowse/data/; 
-cp ../../working/stage/Cimex_lectularius/* /app/data/BCM_i5k_pilot/cimlec/BCM/jbrowse/data/; 
-cp ../../css/custom.css /app/data/BCM_i5k_pilot/cimlec/BCM/jbrowse/data/; 
-cp ../../working/stage/Clitarchus_hookeri/* /app/data/other_species/clihoo/jbrowse/data/; 
-cp ../../css/custom.css /app/data/other_species/clihoo/jbrowse/data/; 
-cp ../../working/stage/Contarinia_nasturtii/* /app/data/other_species/connas/AAFC_CNas_1.1/jbrowse/data/; 
-cp ../../css/custom.css /app/data/other_species/connas/AAFC_CNas_1.1/jbrowse/data/; 
-cp ../../working/stage/Copidosoma_floridanum/* /app/data/BCM_i5k_pilot/copflo/jbrowse/data/; 
-cp ../../css/custom.css /app/data/BCM_i5k_pilot/copflo/jbrowse/data/; 
-cp ../../working/stage/Diabrotica_virgifera_training/* /app/data/other_species/diavir/Dvir_v2.0_RefSeq/jbrowse/data/; 
-cp ../../css/custom.css /app/data/other_species/diavir/Dvir_v2.0_RefSeq/jbrowse/data/; 
-cp ../../working/stage/Diachasma_alloeum/* /app/data/other_species/diaall/Dall2.0/jbrowse/data/; 
-cp ../../css/custom.css /app/data/other_species/diaall/Dall2.0/jbrowse/data/; 
-cp ../../working/stage/Diaphorina_citri/* /app/data/other_species/diacit/jbrowse/data/; 
-cp ../../css/custom.css /app/data/other_species/diacit/jbrowse/data/; 
-cp ../../working/stage/Diaphorina_citri_legacy/* /app/data/other_species/diacit_legacy/jbrowse/data/; 
-cp ../../css/custom.css /app/data/other_species/diacit_legacy/jbrowse/data/; 
-cp ../../working/stage/Drosophila_biarmipes/* /app/data/modencode/drobia/Dbia_2.0/jbrowse/data/; 
-cp ../../css/custom.css /app/data/modencode/drobia/Dbia_2.0/jbrowse/data/; 
-cp ../../working/stage/Drosophila_bipectinata/* /app/data/modencode/drobip/Dbip_2.0/jbrowse/data/; 
-cp ../../css/custom.css /app/data/modencode/drobip/Dbip_2.0/jbrowse/data/; 
-cp ../../working/stage/Drosophila_elegans/* /app/data/modencode/droele/Dele_2.0/jbrowse/data/; 
-cp ../../css/custom.css /app/data/modencode/droele/Dele_2.0/jbrowse/data/; 
-cp ../../working/stage/Drosophila_eugracilis/* /app/data/modencode/droeug/Deug_2.0/jbrowse/data/; 
-cp ../../css/custom.css /app/data/modencode/droeug/Deug_2.0/jbrowse/data/; 
-cp ../../working/stage/Drosophila_ficusphila/* /app/data/modencode/drofic/Dfic_2.0/jbrowse/data/; 
-cp ../../css/custom.css /app/data/modencode/drofic/Dfic_2.0/jbrowse/data/; 
-cp ../../working/stage/Drosophila_kikkawai/* /app/data/modencode/drokik/Dkik_2.0/jbrowse/data/; 
-cp ../../css/custom.css /app/data/modencode/drokik/Dkik_2.0/jbrowse/data/; 
-cp ../../working/stage/Drosophila_rhopaloa/* /app/data/modencode/drorho/Drho_2.0/jbrowse/data/; 
-cp ../../css/custom.css /app/data/modencode/drorho/Drho_2.0/jbrowse/data/; 
-cp ../../working/stage/Drosophila_takahashii/* /app/data/modencode/drotak/Dtak_2.0/jbrowse/data/; 
-cp ../../css/custom.css /app/data/modencode/drotak/Dtak_2.0/jbrowse/data/; 
-cp ../../working/stage/Dufourea_novaeangliae/* /app/data/other_species/dufnov/jbrowse/data/; 
-cp ../../css/custom.css /app/data/other_species/dufnov/jbrowse/data/; 
-cp ../../working/stage/Ephemera_danica/* /app/data/BCM_i5k_pilot/ephdan/Edan_2.0/jbrowse/data//; 
-cp ../../css/custom.css /app/data/BCM_i5k_pilot/ephdan/Edan_2.0/jbrowse/data//; 
-cp ../../working/stage/Eufriesea_mexicana/* /app/data/other_species/eufmex/ASM148370v1/jbrowse/data/; 
-cp ../../css/custom.css /app/data/other_species/eufmex/ASM148370v1/jbrowse/data/; 
-cp ../../working/stage/Euglossa_dilemma/* /app/data/other_species/eugdil/jbrowse/data/; 
-cp ../../css/custom.css /app/data/other_species/eugdil/jbrowse/data/; 
-cp ../../working/stage/Eurytemora_affinis/* /app/data/BCM_i5k_pilot/euraff/jbrowse/data/; 
-cp ../../css/custom.css /app/data/BCM_i5k_pilot/euraff/jbrowse/data/; 
-cp ../../working/stage/Eurytemora_affinis_-_training/* /app/data/BCM_i5k_pilot/euraff/jbrowse/data/; 
-cp ../../css/custom.css /app/data/BCM_i5k_pilot/euraff/jbrowse/data/; 
-cp ../../working/stage/Fopius_arisanus/* /app/data/other_species/fopari/jbrowse/data/; 
-cp ../../css/custom.css /app/data/other_species/fopari/jbrowse/data/; 
-cp ../../working/stage/Frankliniella_occidentalis/* /app/data/BCM_i5k_pilot/fraocc/Focc_3.0/jbrowse/data/; 
-cp ../../css/custom.css /app/data/BCM_i5k_pilot/fraocc/Focc_3.0/jbrowse/data/; 
-cp ../../working/stage/Galleria_mellonella/* /app/data/other_species/galmel/ASM364042v2/jbrowse/data/; 
-cp ../../css/custom.css /app/data/other_species/galmel/ASM364042v2/jbrowse/data/; 
-cp ../../working/stage/Gerris_buenoi/* /app/data/BCM_i5k_pilot/gerbue/jbrowse/data//; 
-cp ../../css/custom.css /app/data/BCM_i5k_pilot/gerbue/jbrowse/data//; 
-cp ../../working/stage/Habropoda_laboriosa/* /app/data/other_species/hablab/jbrowse/data/; 
-cp ../../css/custom.css /app/data/other_species/hablab/jbrowse/data/; 
-cp ../../working/stage/Halyomorpha_halys/* /app/data/BCM_i5k_pilot/halhal/Hhal_1.1/jbrowse/data/; 
-cp ../../css/custom.css /app/data/BCM_i5k_pilot/halhal/Hhal_1.1/jbrowse/data/; 
-cp ../../working/stage/Heliothis_virescens/* /app/data/other_species/helvir/jbrowse/data//; 
-cp ../../css/custom.css /app/data/other_species/helvir/jbrowse/data//; 
-cp ../../working/stage/Holacanthella_duospinosa/* /app/data/other_species/holduo/ASM273828v1/jbrowse/data/; 
-cp ../../css/custom.css /app/data/other_species/holduo/ASM273828v1/jbrowse/data/; 
-cp ../../working/stage/Homalodisca_vitripennis/* /app/data/BCM_i5k_pilot/homvit/jbrowse/data/; 
-cp ../../css/custom.css /app/data/BCM_i5k_pilot/homvit/jbrowse/data/; 
-cp ../../working/stage/Hyalella_azteca/* /app/data/BCM_i5k_pilot/hyaazt/Hazt_2.0.1/jbrowse/data/; 
-cp ../../css/custom.css /app/data/BCM_i5k_pilot/hyaazt/Hazt_2.0.1/jbrowse/data/; 
-cp ../../working/stage/Laodelphax_striatellus/* /app/data/other_species/laostr/ASM333518v2/jbrowse/data/; 
-cp ../../css/custom.css /app/data/other_species/laostr/ASM333518v2/jbrowse/data/; 
-cp ../../working/stage/Lasioglossum_albipes/* /app/data/other_species/lasalb/jbrowse/data/; 
-cp ../../css/custom.css /app/data/other_species/lasalb/jbrowse/data/; 
-cp ../../working/stage/Latrodectus_hesperus/* /app/data/BCM_i5k_pilot/lathes/GCA_000697925.1/jbrowse/data/; 
-cp ../../css/custom.css /app/data/BCM_i5k_pilot/lathes/GCA_000697925.1/jbrowse/data/; 
-cp ../../working/stage/Leptinotarsa_decemlineata/* /app/data/BCM_i5k_pilot/lepdec/Ldec_2.0/jbrowse/data/; 
-cp ../../css/custom.css /app/data/BCM_i5k_pilot/lepdec/Ldec_2.0/jbrowse/data/; 
-cp ../../working/stage/Leptinotarsa_decemlineata_training/* /app/data/BCM_i5k_pilot/lepdec/jbrowse/data/; 
-cp ../../css/custom.css /app/data/BCM_i5k_pilot/lepdec/jbrowse/data/; 
-cp ../../working/stage/Limnephilus_lunatus/* /app/data/BCM_i5k_pilot/limlun/jbrowse/data/; 
-cp ../../css/custom.css /app/data/BCM_i5k_pilot/limlun/jbrowse/data/; 
-cp ../../working/stage/Locusta_migratoria/* /app/data/other_species/locmig/jbrowse/data//; 
-cp ../../css/custom.css /app/data/other_species/locmig/jbrowse/data//; 
-cp ../../working/stage/Loxosceles_reclusa/* /app/data/BCM_i5k_pilot/loxrec/GCA_001188405.1/jbrowse/data/; 
-cp ../../css/custom.css /app/data/BCM_i5k_pilot/loxrec/GCA_001188405.1/jbrowse/data/; 
-cp ../../working/stage/Mamestra_configurata/* /app/data/other_species/mamcon/GCA_002192655.1/jbrowse/data/; 
-cp ../../css/custom.css /app/data/other_species/mamcon/GCA_002192655.1/jbrowse/data/; 
-cp ../../working/stage/Manduca_sexta/* /app/data/other_species/mansex/JHU_Msex_v1.0/jbrowse/data/; 
-cp ../../css/custom.css /app/data/other_species/mansex/JHU_Msex_v1.0/jbrowse/data/; 
-cp ../../working/stage/Mayetiola_destructor/* /app/data/other_species/maydes/jbrowse/data/; 
-cp ../../css/custom.css /app/data/other_species/maydes/jbrowse/data/; 
-cp ../../working/stage/Medauroidea_extradentata/* /app/data/other_species/medext/GCA_003012365.1/jbrowse/data/; 
-cp ../../css/custom.css /app/data/other_species/medext/GCA_003012365.1/jbrowse/data/; 
-cp ../../working/stage/Megachile_rotundata/* /app/data/other_species/megrot/jbrowse/data/; 
-cp ../../css/custom.css /app/data/other_species/megrot/jbrowse/data/; 
-cp ../../working/stage/Melipona_quadrifasciata/* /app/data/other_species/melqua/jbrowse/data/; 
-cp ../../css/custom.css /app/data/other_species/melqua/jbrowse/data/; 
-cp ../../working/stage/Microplitis_demolitor/* /app/data/other_species/micdem/jbrowse/data/; 
-cp ../../css/custom.css /app/data/other_species/micdem/jbrowse/data/; 
-cp ../../working/stage/Neodiprion_lecontei/* /app/data/other_species/neolec/Nlec1.1/jbrowse/data/; 
-cp ../../css/custom.css /app/data/other_species/neolec/Nlec1.1/jbrowse/data/; 
-cp ../../working/stage/Neodiprion_lecontei_training/* /app/data/other_species/neolec/jbrowse/data/; 
-cp ../../css/custom.css /app/data/other_species/neolec/jbrowse/data/; 
-cp ../../working/stage/Nicrophorus_vespilloides/* /app/data/other_species/nicves/jbrowse/data/; 
-cp ../../css/custom.css /app/data/other_species/nicves/jbrowse/data/; 
-cp ../../working/stage/Nylanderia_fulva/* /app/data/other_species/nylful/TAMU_Nfulva_1.0/jbrowse/data/; 
-cp ../../css/custom.css /app/data/other_species/nylful/TAMU_Nfulva_1.0/jbrowse/data/; 
-cp ../../working/stage/Odontomachus_brunneus/* /app/data/other_species/odobru/Obru_v1/jbrowse/data/; 
-cp ../../css/custom.css /app/data/other_species/odobru/Obru_v1/jbrowse/data/; 
-cp ../../working/stage/Oncopeltus_fasciatus/* /app/data/BCM_i5k_pilot/oncfas/jbrowse/data/; 
-cp ../../css/custom.css /app/data/BCM_i5k_pilot/oncfas/jbrowse/data/; 
-cp ../../working/stage/Oncopeltus_fasciatus_training/* /app/data/BCM_i5k_pilot/oncfas/jbrowse/data/; 
-cp ../../css/custom.css /app/data/BCM_i5k_pilot/oncfas/jbrowse/data/; 
-cp ../../working/stage/Onthophagus_taurus/* /app/data/BCM_i5k_pilot/onttau/jbrowse/data/; 
-cp ../../css/custom.css /app/data/BCM_i5k_pilot/onttau/jbrowse/data/; 
-cp ../../working/stage/Orussus_abietinus/* /app/data/BCM_i5k_pilot/oruabi/BCM/jbrowse/data/; 
-cp ../../css/custom.css /app/data/BCM_i5k_pilot/oruabi/BCM/jbrowse/data/; 
-cp ../../working/stage/Osmia_lignaria/* /app/data/other_species/osmlig/USDA_OLig_1.0/jbrowse/data/; 
-cp ../../css/custom.css /app/data/other_species/osmlig/USDA_OLig_1.0/jbrowse/data/; 
-cp ../../working/stage/Pachypsylla_venusta/* /app/data/BCM_i5k_pilot/pacven/jbrowse/data/; 
-cp ../../css/custom.css /app/data/BCM_i5k_pilot/pacven/jbrowse/data/; 
-cp ../../working/stage/Parasteatoda_tepidariorum/* /app/data/BCM_i5k_pilot/partep/jbrowse/data/; 
-cp ../../css/custom.css /app/data/BCM_i5k_pilot/partep/jbrowse/data/; 
-cp ../../working/stage/Photinus_pyralis/* /app/data/other_species/phopyr/Ppyr1.3/jbrowse/data/; 
-cp ../../css/custom.css /app/data/other_species/phopyr/Ppyr1.3/jbrowse/data/; 
-cp ../../working/stage/Rhagoletis_zephyria/* /app/data/other_species/rhazep/jbrowse/data/; 
-cp ../../css/custom.css /app/data/other_species/rhazep/jbrowse/data/; 
-cp ../../working/stage/Rhipicephalus_microplus/* /app/data/other_species/rhimic/jbrowse/data/; 
-cp ../../css/custom.css /app/data/other_species/rhimic/jbrowse/data/; 
-cp ../../working/stage/Rhyzopertha_dominica/* /app/data/other_species/rhydom/RdoDt3_tmp/jbrowse/data/; 
-cp ../../css/custom.css /app/data/other_species/rhydom/RdoDt3_tmp/jbrowse/data/; 
-cp ../../working/stage/Saccharomyceseubayanus/* /app/data/other_species/saceub/SEUB3.0/jbrowse/data/; 
-cp ../../css/custom.css /app/data/other_species/saceub/SEUB3.0/jbrowse/data/; 
-cp ../../working/stage/Tigriopus_californicus/* /app/data/other_species/tigcal/jbrowse/data/; 
-cp ../../css/custom.css /app/data/other_species/tigcal/jbrowse/data/; 
-cp ../../working/stage/Tribolium_castaneum/* /app/data/other_species/tricas/jbrowse/data/; 
-cp ../../css/custom.css /app/data/other_species/tricas/jbrowse/data/; 
-cp ../../working/stage/Trichogramma_pretiosum/* /app/data/BCM_i5k_pilot/tripre/jbrowse/data/; 
-cp ../../css/custom.css /app/data/BCM_i5k_pilot/tripre/jbrowse/data/; 
-cp ../../working/stage/Varroa_destructor/* /app/data/other_species/vardes/Vdes_3.0/jbrowse/data/; 
-cp ../../css/custom.css /app/data/other_species/vardes/Vdes_3.0/jbrowse/data/; 
-cp ../../working/stage/Varroa_jacobsoni/* /app/data/other_species/varjac/vjacob_1.0/jbrowse/data/; 
-cp ../../css/custom.css /app/data/other_species/varjac/vjacob_1.0/jbrowse/data/; 
diff --git a/scripts/stage/organism_list.txt b/scripts/stage/organism_list.txt
index 09ae054..388e08c 100644
--- a/scripts/stage/organism_list.txt
+++ b/scripts/stage/organism_list.txt
@@ -1,5 +1,5 @@
-            common_name             |                          directory                           
-------------------------------------+--------------------------------------------------------------
+            common_name             |                                directory                                
+------------------------------------+-------------------------------------------------------------------------
  10_-_Onthophagus_taurus_training   | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
  11_-_Onthophagus_taurus_training   | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
  12_-_Onthophagus_taurus_training   | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data
@@ -63,18 +63,20 @@
  Clitarchus_hookeri                 | /app/data/other_species/clihoo/jbrowse/data
  Contarinia_nasturtii               | /app/data/other_species/connas/AAFC_CNas_1.1/jbrowse/data
  Copidosoma_floridanum              | /app/data/BCM_i5k_pilot/copflo/jbrowse/data
+ Culex_quinquefasciatus             | /app/data/other_species/culqui/VPISU_Cqui_1.0_pri_paternal/jbrowse/data
  Diabrotica_virgifera_training      | /app/data/other_species/diavir/Dvir_v2.0_RefSeq/jbrowse/data
  Diachasma_alloeum                  | /app/data/other_species/diaall/Dall2.0/jbrowse/data
  Diaphorina_citri                   | /app/data/other_species/diacit/jbrowse/data
  Diaphorina_citri_legacy            | /app/data/other_species/diacit_legacy/jbrowse/data
+ Diprion_similis                    | /app/data//other_species/dipsim/iyDipSimi1.1/jbrowse/data
  Drosophila_biarmipes               | /app/data/modencode/drobia/Dbia_2.0/jbrowse/data
- Drosophila_bipectinata             | /app/data/modencode/drobip/Dbip_2.0/jbrowse/data
- Drosophila_elegans                 | /app/data/modencode/droele/Dele_2.0/jbrowse/data
- Drosophila_eugracilis              | /app/data/modencode/droeug/Deug_2.0/jbrowse/data
- Drosophila_ficusphila              | /app/data/modencode/drofic/Dfic_2.0/jbrowse/data
- Drosophila_kikkawai                | /app/data/modencode/drokik/Dkik_2.0/jbrowse/data
- Drosophila_rhopaloa                | /app/data/modencode/drorho/Drho_2.0/jbrowse/data
- Drosophila_takahashii              | /app/data/modencode/drotak/Dtak_2.0/jbrowse/data
+ Drosophila_bipectinata             | /app/data/other_species/drobip/ASM1815384v1/jbrowse/data
+ Drosophila_elegans                 | /app/data/other_species/droele/ASM1815250v1/jbrowse/data
+ Drosophila_eugracilis              | /app/data/other_species/droeug/ASM1815383v1/jbrowse/data
+ Drosophila_ficusphila              | /app/data/other_species/drofic/ASM1815226v1/jbrowse/data
+ Drosophila_kikkawai                | /app/data/other_species/drokik/ASM1815253v1/jbrowse/data
+ Drosophila_rhopaloa                | /app/data/other_species/drorho/ASM1815211v1/jbrowse/data
+ Drosophila_takahashii              | /app/data/other_species/drotak/ASM1815269v1/jbrowse/data
  Dufourea_novaeangliae              | /app/data/other_species/dufnov/jbrowse/data
  Ephemera_danica                    | /app/data/BCM_i5k_pilot/ephdan/Edan_2.0/jbrowse/data/
  Eufriesea_mexicana                 | /app/data/other_species/eufmex/ASM148370v1/jbrowse/data
@@ -87,10 +89,12 @@
  Gerris_buenoi                      | /app/data/BCM_i5k_pilot/gerbue/jbrowse/data/
  Habropoda_laboriosa                | /app/data/other_species/hablab/jbrowse/data
  Halyomorpha_halys                  | /app/data/BCM_i5k_pilot/halhal/Hhal_1.1/jbrowse/data
+ Helicoverpa_zea                    | /app/data/other_species/helzea/ilHelZeax1.1/jbrowse/data
  Heliothis_virescens                | /app/data/other_species/helvir/jbrowse/data/
  Holacanthella_duospinosa           | /app/data/other_species/holduo/ASM273828v1/jbrowse/data
  Homalodisca_vitripennis            | /app/data/BCM_i5k_pilot/homvit/jbrowse/data
  Hyalella_azteca                    | /app/data/BCM_i5k_pilot/hyaazt/Hazt_2.0.1/jbrowse/data
+ Ladona_fulva                       | /app/data/other_species/ladful/Lful_2.0/jbrowse/data
  Laodelphax_striatellus             | /app/data/other_species/laostr/ASM333518v2/jbrowse/data
  Lasioglossum_albipes               | /app/data/other_species/lasalb/jbrowse/data
  Latrodectus_hesperus               | /app/data/BCM_i5k_pilot/lathes/GCA_000697925.1/jbrowse/data
@@ -99,6 +103,7 @@
  Limnephilus_lunatus                | /app/data/BCM_i5k_pilot/limlun/jbrowse/data
  Locusta_migratoria                 | /app/data/other_species/locmig/jbrowse/data/
  Loxosceles_reclusa                 | /app/data/BCM_i5k_pilot/loxrec/GCA_001188405.1/jbrowse/data
+ Lucilia_sericata                   | /app/data/other_species/lucser/ASM1558622v1/jbrowse/data
  Mamestra_configurata               | /app/data/other_species/mamcon/GCA_002192655.1/jbrowse/data
  Manduca_sexta                      | /app/data/other_species/mansex/JHU_Msex_v1.0/jbrowse/data
  Mayetiola_destructor               | /app/data/other_species/maydes/jbrowse/data
@@ -106,8 +111,11 @@
  Megachile_rotundata                | /app/data/other_species/megrot/jbrowse/data
  Melipona_quadrifasciata            | /app/data/other_species/melqua/jbrowse/data
  Microplitis_demolitor              | /app/data/other_species/micdem/jbrowse/data
- Neodiprion_lecontei                | /app/data/other_species/neolec/Nlec1.1/jbrowse/data
+ Neodiprion_fabricii                | /app/data/other_species/neofab/iyNeoFabr1.1/jbrowse/data
+ Neodiprion_lecontei                | /app/data/other_species/neolec/iyNeoLeco1.1/jbrowse/data
  Neodiprion_lecontei_training       | /app/data/other_species/neolec/jbrowse/data
+ Neodiprion_pinetum                 | /app/data/other_species/neopin/iyNeoPine1.1/jbrowse/data
+ Neodiprion_virginiana              | /app/data/other_species/neovir/iyNeoVirg1.1/jbrowse/data
  Nicrophorus_vespilloides           | /app/data/other_species/nicves/jbrowse/data
  Nylanderia_fulva                   | /app/data/other_species/nylful/TAMU_Nfulva_1.0/jbrowse/data
  Odontomachus_brunneus              | /app/data/other_species/odobru/Obru_v1/jbrowse/data
@@ -120,13 +128,17 @@
  Parasteatoda_tepidariorum          | /app/data/BCM_i5k_pilot/partep/jbrowse/data
  Photinus_pyralis                   | /app/data/other_species/phopyr/Ppyr1.3/jbrowse/data
  Rhagoletis_zephyria                | /app/data/other_species/rhazep/jbrowse/data
- Rhipicephalus_microplus            | /app/data/other_species/rhimic/jbrowse/data
+ Rhipicephalus_microplus            | /app/data/other_species/rhimic/ASM1333972v1/jbrowse/data
  Rhyzopertha_dominica               | /app/data/other_species/rhydom/RdoDt3_tmp/jbrowse/data
  Saccharomyces eubayanus            | /app/data/other_species/saceub/SEUB3.0/jbrowse/data
+ Schistocerca_americana             | /app/data/other_species/schame/iqSchAmer2.1/jbrowse/data
+ Schistocerca piceifrons            | /app/data/other_species/schpic/iqSchPice1.1/jbrowse/data/
  Tigriopus_californicus             | /app/data/other_species/tigcal/jbrowse/data
  Tribolium_castaneum                | /app/data/other_species/tricas/jbrowse/data
+ Tribolium_madens                   | /app/data/other_species/trimad/Tmad_KSU_1.1/jbrowse/data
  Trichogramma_pretiosum             | /app/data/BCM_i5k_pilot/tripre/jbrowse/data
  Varroa_destructor                  | /app/data/other_species/vardes/Vdes_3.0/jbrowse/data
  Varroa_jacobsoni                   | /app/data/other_species/varjac/vjacob_1.0/jbrowse/data
-(128 rows)
+ Venturia_canescens                 | /app/data/other_species/vencan/ASM1945775v1/jbrowse/data
+(140 rows)
 
diff --git a/scripts/stage/organism_list.txt2 b/scripts/stage/organism_list.txt2
index 54691ba..c83a107 100644
--- a/scripts/stage/organism_list.txt2
+++ b/scripts/stage/organism_list.txt2
@@ -61,18 +61,20 @@ Cimex_lectularius|/app/data/BCM_i5k_pilot/cimlec/BCM/jbrowse/data
 Clitarchus_hookeri|/app/data/other_species/clihoo/jbrowse/data
 Contarinia_nasturtii|/app/data/other_species/connas/AAFC_CNas_1.1/jbrowse/data
 Copidosoma_floridanum|/app/data/BCM_i5k_pilot/copflo/jbrowse/data
+Culex_quinquefasciatus|/app/data/other_species/culqui/VPISU_Cqui_1.0_pri_paternal/jbrowse/data
 Diabrotica_virgifera_training|/app/data/other_species/diavir/Dvir_v2.0_RefSeq/jbrowse/data
 Diachasma_alloeum|/app/data/other_species/diaall/Dall2.0/jbrowse/data
 Diaphorina_citri|/app/data/other_species/diacit/jbrowse/data
 Diaphorina_citri_legacy|/app/data/other_species/diacit_legacy/jbrowse/data
+Diprion_similis|/app/data//other_species/dipsim/iyDipSimi1.1/jbrowse/data
 Drosophila_biarmipes|/app/data/modencode/drobia/Dbia_2.0/jbrowse/data
-Drosophila_bipectinata|/app/data/modencode/drobip/Dbip_2.0/jbrowse/data
-Drosophila_elegans|/app/data/modencode/droele/Dele_2.0/jbrowse/data
-Drosophila_eugracilis|/app/data/modencode/droeug/Deug_2.0/jbrowse/data
-Drosophila_ficusphila|/app/data/modencode/drofic/Dfic_2.0/jbrowse/data
-Drosophila_kikkawai|/app/data/modencode/drokik/Dkik_2.0/jbrowse/data
-Drosophila_rhopaloa|/app/data/modencode/drorho/Drho_2.0/jbrowse/data
-Drosophila_takahashii|/app/data/modencode/drotak/Dtak_2.0/jbrowse/data
+Drosophila_bipectinata|/app/data/other_species/drobip/ASM1815384v1/jbrowse/data
+Drosophila_elegans|/app/data/other_species/droele/ASM1815250v1/jbrowse/data
+Drosophila_eugracilis|/app/data/other_species/droeug/ASM1815383v1/jbrowse/data
+Drosophila_ficusphila|/app/data/other_species/drofic/ASM1815226v1/jbrowse/data
+Drosophila_kikkawai|/app/data/other_species/drokik/ASM1815253v1/jbrowse/data
+Drosophila_rhopaloa|/app/data/other_species/drorho/ASM1815211v1/jbrowse/data
+Drosophila_takahashii|/app/data/other_species/drotak/ASM1815269v1/jbrowse/data
 Dufourea_novaeangliae|/app/data/other_species/dufnov/jbrowse/data
 Ephemera_danica|/app/data/BCM_i5k_pilot/ephdan/Edan_2.0/jbrowse/data/
 Eufriesea_mexicana|/app/data/other_species/eufmex/ASM148370v1/jbrowse/data
@@ -85,10 +87,12 @@ Galleria_mellonella|/app/data/other_species/galmel/ASM364042v2/jbrowse/data
 Gerris_buenoi|/app/data/BCM_i5k_pilot/gerbue/jbrowse/data/
 Habropoda_laboriosa|/app/data/other_species/hablab/jbrowse/data
 Halyomorpha_halys|/app/data/BCM_i5k_pilot/halhal/Hhal_1.1/jbrowse/data
+Helicoverpa_zea|/app/data/other_species/helzea/ilHelZeax1.1/jbrowse/data
 Heliothis_virescens|/app/data/other_species/helvir/jbrowse/data/
 Holacanthella_duospinosa|/app/data/other_species/holduo/ASM273828v1/jbrowse/data
 Homalodisca_vitripennis|/app/data/BCM_i5k_pilot/homvit/jbrowse/data
 Hyalella_azteca|/app/data/BCM_i5k_pilot/hyaazt/Hazt_2.0.1/jbrowse/data
+Ladona_fulva|/app/data/other_species/ladful/Lful_2.0/jbrowse/data
 Laodelphax_striatellus|/app/data/other_species/laostr/ASM333518v2/jbrowse/data
 Lasioglossum_albipes|/app/data/other_species/lasalb/jbrowse/data
 Latrodectus_hesperus|/app/data/BCM_i5k_pilot/lathes/GCA_000697925.1/jbrowse/data
@@ -97,6 +101,7 @@ Leptinotarsa_decemlineata_training|/app/data/BCM_i5k_pilot/lepdec/jbrowse/data
 Limnephilus_lunatus|/app/data/BCM_i5k_pilot/limlun/jbrowse/data
 Locusta_migratoria|/app/data/other_species/locmig/jbrowse/data/
 Loxosceles_reclusa|/app/data/BCM_i5k_pilot/loxrec/GCA_001188405.1/jbrowse/data
+Lucilia_sericata|/app/data/other_species/lucser/ASM1558622v1/jbrowse/data
 Mamestra_configurata|/app/data/other_species/mamcon/GCA_002192655.1/jbrowse/data
 Manduca_sexta|/app/data/other_species/mansex/JHU_Msex_v1.0/jbrowse/data
 Mayetiola_destructor|/app/data/other_species/maydes/jbrowse/data
@@ -104,8 +109,11 @@ Medauroidea_extradentata|/app/data/other_species/medext/GCA_003012365.1/jbrowse/
 Megachile_rotundata|/app/data/other_species/megrot/jbrowse/data
 Melipona_quadrifasciata|/app/data/other_species/melqua/jbrowse/data
 Microplitis_demolitor|/app/data/other_species/micdem/jbrowse/data
-Neodiprion_lecontei|/app/data/other_species/neolec/Nlec1.1/jbrowse/data
+Neodiprion_fabricii|/app/data/other_species/neofab/iyNeoFabr1.1/jbrowse/data
+Neodiprion_lecontei|/app/data/other_species/neolec/iyNeoLeco1.1/jbrowse/data
 Neodiprion_lecontei_training|/app/data/other_species/neolec/jbrowse/data
+Neodiprion_pinetum|/app/data/other_species/neopin/iyNeoPine1.1/jbrowse/data
+Neodiprion_virginiana|/app/data/other_species/neovir/iyNeoVirg1.1/jbrowse/data
 Nicrophorus_vespilloides|/app/data/other_species/nicves/jbrowse/data
 Nylanderia_fulva|/app/data/other_species/nylful/TAMU_Nfulva_1.0/jbrowse/data
 Odontomachus_brunneus|/app/data/other_species/odobru/Obru_v1/jbrowse/data
@@ -118,11 +126,17 @@ Pachypsylla_venusta|/app/data/BCM_i5k_pilot/pacven/jbrowse/data
 Parasteatoda_tepidariorum|/app/data/BCM_i5k_pilot/partep/jbrowse/data
 Photinus_pyralis|/app/data/other_species/phopyr/Ppyr1.3/jbrowse/data
 Rhagoletis_zephyria|/app/data/other_species/rhazep/jbrowse/data
-Rhipicephalus_microplus|/app/data/other_species/rhimic/jbrowse/data
+Rhipicephalus_microplus|/app/data/other_species/rhimic/ASM1333972v1/jbrowse/data
 Rhyzopertha_dominica|/app/data/other_species/rhydom/RdoDt3_tmp/jbrowse/data
 Saccharomyceseubayanus|/app/data/other_species/saceub/SEUB3.0/jbrowse/data
+Schistocerca_americana|/app/data/other_species/schame/iqSchAmer2.1/jbrowse/data
+Schistocercapiceifrons|/app/data/other_species/schpic/iqSchPice1.1/jbrowse/data/
 Tigriopus_californicus|/app/data/other_species/tigcal/jbrowse/data
 Tribolium_castaneum|/app/data/other_species/tricas/jbrowse/data
+Tribolium_madens|/app/data/other_species/trimad/Tmad_KSU_1.1/jbrowse/data
 Trichogramma_pretiosum|/app/data/BCM_i5k_pilot/tripre/jbrowse/data
 Varroa_destructor|/app/data/other_species/vardes/Vdes_3.0/jbrowse/data
 Varroa_jacobsoni|/app/data/other_species/varjac/vjacob_1.0/jbrowse/data
+Venturia_canescens|/app/data/other_species/vencan/ASM1945775v1/jbrowse/data
+(140rows)
+