CovertLab · cyrus-bio · Sep 20, 2024 · Sep 19, 2024 · Sep 20, 2024
diff --git a/.gitignore b/.gitignore
@@ -61,3 +61,7 @@ cache/
 ##################
 .nextflow*
 nextflow_temp
+
+# Other files #
+##################
+/notebooks/fbagd/ck/
diff --git a/ecoli/experiments/metabolism_redux_sim.py b/ecoli/experiments/metabolism_redux_sim.py
@@ -63,8 +63,8 @@ def run_ecoli_with_metabolism_redux_classic(
     raw_output=False,
     save=True,
     save_times=[1, 10, 200, 400, 1300],
-    condition="with_aa",  # basal, with_aa
-    fixed_media="minimal_plus_amino_acids",  # minimal, minimal_plus_amino_acids
+    condition="acetate",  # basal, with_aa
+    fixed_media="minimal_acetate",  # minimal, minimal_plus_amino_acids
 ):
     # filename = 'default'
     sim = EcoliSim.from_file(CONFIG_DIR_PATH + filename + ".json")

diff --git a/notebooks/cofactors/final_paper_validation.ipynb b/notebooks/cofactors/final_paper_validation.ipynb
diff --git a/notebooks/cofactors/growth_rates.ipynb b/notebooks/cofactors/growth_rates.ipynb
diff --git a/notebooks/cofactors/julia_plots_final.ipynb b/notebooks/cofactors/julia_plots_final.ipynb
diff --git a/notebooks/cofactors/precise.ipynb b/notebooks/cofactors/precise.ipynb
diff --git a/notebooks/cofactors/sankey.ipynb b/notebooks/cofactors/sankey.ipynb