v2.3.0

Main improvements in this release:

• Documentation:
  • Tutorials were entirely revised and reorganised into tutorial1-tutorial6 (tutorial2018 was renamed to tutorial6). Updated MS Word file, now called RAVEN tutorials.docx. Fixed the dependency for SupplementaryTables.xlsx in tutorial6 (PR #261 #262).
  • In tutorial5, the more accurate runtime estimates for getKEGGModelForOrganism were added for macOS, Unix and Windows systems (PR #242)
  • Updated README.md (PR #257)
• External software, database updates:
  • Updated KEGG to Release 91.0 (PR #248)
  • Updated CD-HIT to 4.8.1, HMMER to 3.2.1 and MAFFT to 7.427 (PR #248). Updated BLAST+ to 2.9.0 and DIAMOND to 0.9.26 (PR #253).
  • Added CD-HIT for Windows (PR #248), M2HTML (version 1.5) (PR #255)
• Features:
  • Functions exportModel, importModel, and ravenCobraWrapper were updated to enable writing and reading of SBO terms to and from an SBML file (PR #235)
  • Modified the directory names for external binaries. Those now no longer include the version numbers (PR #237 #239).
  • checkFunctionUniqueness now checks for multiple RAVEN versions in MATLAB path and gives a fatal error if it is the case (PR #241)
  • For the KEGG reconstruction module, added the possibility to run the protein clustering with CD-HIT in Windows. The printed messages once running getKEGGModelForOrganism were completely revised: it now reports the start and completion of the stages, including intermediate reports for HMMs search (PR #248).
  • checkInstallation: RAVEN version is no longer hard-coded. Added the binary check for DIAMOND. Enabled the external binaries check in Windows. Divided external binaries into two categories which are now reported separately (PR #254).
• Fixes:
  • Fixed a bug where mergeModels would incorrectly modify the S matrix if different metabolites share the same metabolite names (model.metNames). Based on standard that corresponding metabolites across different compartments have unique metabolite IDs (model.mets), function updated to match metabolites by IDs instead of names (PR #223).
  • Fixed a bug in getIndexes where the function would ignore the returnLogical input if the type input was set to metscomps (PR #236)
  • Moved several functions from core to the more appropriate external, plotting directories: constructPathwayFromCelldesigner, makeFakeBlastStructure, parseScores and setTitle (PR #238)
  • Fixed a bug in getElementalBalance where if the user supplied reaction indexes, the function would effectively "sort" those indexes in the output without the user knowing (PR #240). The follow-up fix fixes the problem regardless of input type (index numbers, reaction IDs, or logical vector) (PR #246).
  • Fixed importModel parsing of metabolite formula when importing old SBML file (level 2) where formula are in metabolite IDs and not in notes field (PR #243)
  • Fixed the check if query FASTA file is in current directory (PR #244)
  • Bug fix in setExchangeBounds function, where closeOthers variable was not updated (PR #249)
  • Renamed getVersion function to getToolboxVersion to prevent conflicts with MATLAB's matlabxl toolbox (Issue #233; PR #250)
  • Fixed usage of the params input in the optimizeProb function to avoid errors and ignoring of optional parameter specification (PR #256)
  • Fixed a bug in combineMetaCycKEGGmodels regarding exceeded index in array grRulesToMove (PR #260)

v2.2.2

Main improvements in this release:

• feature:

  • new function setMetExchange allows users to set the exchange flux bounds for a given list of metabolites. This should be helpful for specifying e.g., media conditions, or other nutrient uptake/export fluxes (PR #222)
  • setParam can set upper and lower bounds with a defined variance in percentage: setting this value to 5 results in the lower bound being set at 97.5% of the provided value, and the upper bound at 102.5%. This is inverted for negative bounds. (PR #225)
  • addTransport now allows adding multiple rxns and provides the list of added rxn IDs as optional output (PR #226)
  • enable illegal character removal of grRules in exportModel (PR #226)
  • allow multiple compartments either in rows or columns in addMets (PR #226)

• fix:

  • getRxnsFromKEGG: increased the number for preallocated reactions from 11k to 15k as KEGG now includes reactions (PR #229)
  • getKEGGModelForOrganism: fixed several small typos (PR #229)
  • slightly decrease tolerance when using gurobi solver, particularly when solving MILP, because fillGaps does not function well with less strict tolerance (PR #226)
  • refine error message in addRxnsGenesMets (PR #226)
  • fix getModelFromHomology bugs: keeping rxns without homologous genes while using multiple template models, and partial matches of gene ids when updating grRules: YAL001W is not YAL001W-A (PR #226)
  • fix fillGaps bug to keep all genes from template models, not only the ones annotated to gap-filling reactions (PR #226)

• chore:

  • detach HMR2 (Human Metabolic Reactions 2), which is upgraded to Human-GEM and distributed through its own repo. No functions mentioned HMR2, removal of binary is sufficient (PR #227)

v2.2.1

Main improvements in this release:

• feat:

  • option to specify prefix of reaction id in addTransport (PR #213)
  • new changeGrRule function that replaces multiple grRules at the same time (PR #213)

• fix:

  • removeGenes doesn't throw an error if gene is not in model (PR #213)
  • getModelFromHomology works with newer removeGenes functionality (PR #213)
  • execute permissions fix (PR #214)
  • minor bug where exportToTabDelimited would encounter an error if parsing a model structure with field subSystem containing empty character arrays (e.g. no subSystem assigned/known) (PR #215)
  • bug in exportModel that caused invalid SBML files due to empty rule and constraint fields (e222b0b)

v2.2.0

Main improvements in this release:

• fix:
  • getKEGGModelForOrganism various bug fixes on HMMs file extraction (PR #203), argument optimization (PR #207, #209)
  • ravenCobraWrapper now regenerates comps field if missing in a COBRA model (PR #200)
  • getBlastFromExcel bug fix reported in #180 (PR #201)
  • addTransport misc bugfixes (PR #195)
  • FSEOF differiciate missing or empty subSystems elements, standardizeGrRules output rxn ids instead of index (PR #194)
• feature:
  • randomSampling can output the reactions that are not part of loops for subsequent runs (PR #197)
  • specifying prefix, retaining order of reactions and informative transport/exchange reaction names now supported when adding new reactions (PR #189)
  • improved features and new function added for tINIT reconstructions (PR #170)

v2.1.0

Main improvements in this release:

• fix:
  • update rxnGeneMat when new genes added (PR #178)
  • getBlastFromExcel parses all required fields and is Mac compatible (PR #181)
  • getAllSubGraphs for more than 100 subgraphs (PR #186)
• feature
  • updated tracking of toolbox versions with exportForGit and getVersion (PR #176)
  • update MetaCyc to version 22.5, including various bugfixes and features (PR #182)
• doc:
  • update RAVEN 2 reference (PR #177)

v2.0.4

Main improvements in this release:

• fix:
  • exportForGit write toolbox version on PC and Mac (#169)
  • checkModelStruct doesn't warn about duplicate SBO terms (PR #167)
• feat:
  • generateNewIds can define new sequential reaction and metabolite IDs using a specified prefix (PR #167)
  • addRxns has allowNewGenes flag to automatically add genes not present in the model; uses default UB and LB if provided in model and no other bounds are specified; no need to specify eqnType if stoichCoeffs are used (PR #167)
• refactor:
  • RAVEN_structure_fields is documented as CSV instead of XLSX (ae84fd3)
  • shorter warning message in standardizeGrRules if embedded (PR #167)
  • addMets and addRxns use new generateNewIds function (PR #167)
  • addGenesRaven and `addRxns don't standardize grRules during each run (PR #167)

v2.0.3

Main improvements in this release:

• fix:
  • exportModel handeling numeric compartments (PR #153)
  • importModel extracting grRules from non-FBCv2 models (PR #154)
  • constructEquations various bugs (PR #155, #156)
  • getModelFromHomology when single template model is provided (PR #157)
  • importModel if FBCv2, but groups not used for subsystems (PR #161)
• feat:
  • KEGG functionality improved and updated to KEGG 87.1 (PR #134)
  • exportForGit writes RAVEN commit id if version unavailable (PR #160)
  • getDiamond as alternative to getBlast that uses NCBI Blast+ (PR #162)
• style:
  • Excel files have taxonomy mentioned earlier in the model tab, no default author names etc. are used for export (PR #158)

v2.0.2

Main improvements in this release:

• fix:
  • getKEGGModelFromOrganism checks that fastaFile and outDir are provided as string (#146)
  • order of MIRIAM annotations in ravenCobraWrapper, and removed duplicate metSBOterms field (PR #148)
• feat:
  • alternative input for addRxns and changeRxns, using arrays of metabolites and stoichiometric coefficients (PR #147)
• doc:
  • getModelFromKEGG include note on use of generic KEGG model for use in gap-filling (PR #149)

v2.0.1

Main improvements in this release:

Solves #108 #110 #119 #120 #121 #125 #127 #128 #132

• various bugfixes
• ravenCobraWrapper supports more annotations
• libSBML 5.17 is preferred, due to significant speed improvement
• improved documentation of various functions
• deepLoc output supported in localization prediction
• new reconstruction tutorial
• include changelog of pre-GitHub development

v2.0.0

As detailed in "Wang H et al. (2018) bioRxiv doi:10.1101/321067"

Main improvements in this release:

• fix generation of folders by exportForGit
• fix dealing with grRules in model I/O
• rename addGenes to addGenesRaven for full cobra-compatibility
• remove version.txt from devel branch, only master branch has numbered releases