v2.5.3

• fix:
  • getModelFromHomology did not remove non-matching reactions after changes introduced in v2.5.2 (PR #362)

v2.5.2

• fix:
  • setParam when multiple 'obj' values are changed at the same time (solves #350) (PR #352)
  • getModelFromHomology keeps reactions with complex grRules if homology was found for at least one of the original genes. (PR #355)
• feat:
  • deleteUnusedGenes has flag for verbosity (PR #355)

v2.5.1

Main improvements in this release:

• fix:
  • ravenCobraWrapper parsing of PubMed IDs and other reaction references (PR #347)
  • writeYaml avoid empty entries (PR #347)

v2.5.0

Main improvements in this release:

• fix:
  • exportModel prevent duplicated InChI prefix (PR #335)
  • contractModel keep complexes (AND relationship) together, resulting in some redundancy but correct grRules (PR #337)
  • getModelFromHomology correct brackets if multiple orthologs are included (PR #337)
  • constructEquation by default uses rev field to indicate reversibility (PR #338)
  • importModel correctly parse taxonomy URL if https:\\ is defined (PR #338)
  • importModel prevent duplicating SBO terms (PR #338)
  • exportModel extracts chemical formulae from model.inchis if available (PR #341)
• feat:
  • expandModel can give list of reactions to check (PR #337)
  • setParam can take 1 reaction ID as char, and if multiple reactions can changed it can take different paramTypes (e.g. {'lb','ub','ub','lb'}) (PR #337)
  • addGenesRaven throw detailed warning instead of error if gene already exist (PR #337)
  • new model fields model.annotation.authors, model.annotation.sourceUrl, model.version and model.date (solves #311)
  • writeYaml writes meta data in yml file (solves #311)
• refactor:
  • rename model.description to model.name (solves #311)
• doc:
  • README.md link to 'master' Zenodo URL, not version-specific (PR #337)

v2.4.3

Main improvements in this release:

• Fix:
  • importModel and exportModel, export SBML with https for identifiers.org, keep backwards compatibility to load http links (PR #328)
• Documentation:
  • README.md links to "overall" Zenodo DOI, instead of version-specific DOI (PR #327)
  • getKEGGModelForOrganism more detailed error message if download of HMM fails (PR #329)

v2.4.2

Main improvements in this release:

• Fix:
  • simplifyModel: remove the boundary compartment when removing boundary mets. (PR #319)
  • removeGenes: fix bug where canRxnCarryFlux failed to evaluate if rxns with non-standardized grRules can carry any flux. (PR #320)
• Refactor:
  • removeGenes: drastic speed improvement (>19-fold in ecHumanGEM). (PR #323)

v2.4.1

Main improvements in this release:

• Updating database files:
  • corrected capitalization of metBiGGID field for RAVEN <-> COBRA model conversion. This included modifications for functions ravenCobraWrapper, standardizeModelFieldOrder and file COBRA_structure_fields.csv. (PR #299)
  • updated function ravenCobraWrapper and COBRA_structure_fields.csv, cobraNamespaces.csv files according to the latest COBRA model structure (PR #313)
• Features:
  • getModelFromHomology: added a feature to retain homologous genes from template and target species (PR #301)
  • exportForGit: implemented more flexible folder selection with subDirs flag to write all files in one folder or model-specific subfolders (PR #303)
  • updateDocumentation: a newly added function for automatic HTML documents generation for RAVEN functions (PR #304)
  • getMetaCycModelForOrganism: added a check for the existence of query FASTA file under current path (PR #307)
  • randomSampling: added an option to set minFlux to 1 during each solveLP run. This allows removing loops in each sample. (PR #308)
  • addMets: implemented more flexible input when only one metabolite is added or metNames is not specified (PR #308)
  • writeYaml: added a preserveQuotes flag that defaults to true to ensure an export for a YAML compatible file. All mets/rxns are now stored within quotes and COBRApy's function load_yaml_model can properly load the model with no errors. (PR #309)
  • setColorToMapRxns; setOmicDataToRxns: newly added functions complementing for yeastGemMap manuscript (under review) (PR #314)
• Fixes:
  • ravenCobraWrapper: added a compatibility for COBRA models which come with non-unique metabolite ids after removing the compartment info, as it is common with BiGG models (PR #302)
  • importModel: COBRA's function writeCbModel adds M_ prefix to modelID. Unlikely that such prefix is meant to be included in model.id, M_ prefix is now removed when importing SBML file. (PR #303)
  • parseHPA; parseHPArna: added a compatibility with Human Protein Atlas (HPA), version 19 (PR #312)
• Code refactoring:
  • getIndexes: more informative error message (PR #308)
  • parseHPArna: reduced the amount of repeated code and separated the pieces that actually differ between Human Protein Atlas (HPA) versions (PR #312)
• Format changes:
  • removed authorship and timestamps from all RAVEN functions, as git blame and similar functionalities are better ways to keep track of code authorship. Also, exportToTabDelimited no longer writes a fake author in the output file if no author is provided in the model structure. (PR #300)

v2.4.0

Main improvements in this release:

• Features:
  • removed MOSEK compatibility (PR #258)
  • added Zenodo badge, re-arranged badges and updated citation information in README.md (PR #275)
  • compareMultipleModels: allowed execution permission for Unix systems (PR #276)
  • parseTaskList can now also read tab-separated ".txt" files (PR #284)
  • constructPathwayFromCelldesigner is now classified as the legacy function due to its malfunction in MATLAB 2014b and later. An error is thrown if this function is used in any incompatible MATLAB version. (PR #287)
  • checkInstallation: RAVEN is now added to MATLAB path automatically, since this is imperative for RAVEN functionality (PR #289)
  • added .gitattributes file, which allows to prevent issues with different end-of-line (EOL) characters that are used by Windows and Unix/macOS (PR #291)
• Fixes:
  • optimizeProb: fixed LP and MILP inconsistencies (PR #258)
  • checkTasks/fitTasks: fixed "IN" and "OUT" metabolites parsing (PR #277)
  • getMetaCycModelOrganism: fixed a bug resulting in the output with mismatched genes and grRules fields. This was done by updating genes according to the newly generated rxnGeneMat. (PR #278)
  • exportModel: fixed an issue for the models without subSystems field. Previously, models without subSystems resulted in invalid SBML files, as they specified that the 'groups' package was used but no groups were specified. Now if a model has no subSystems field, the SBML package 'groups' is not considered when exporting to SBML. (PR #279)
  • checkInstallation: renamed empty to emptyModel thereby preventing the issues with the MATLAB built-in function empty() (PR #289)
  • ravenCobraWrapper: add exceptions for metabolite KEGG and PubChem IDs (PR #290)
  • ravenCobraWrapper: grRules are no longer saved during RAVEN -> COBRA conversion to prevent potential discrepancies between grRules and rules fields (PR #295)
• External software, database updates:
  • Updated MetaCyc to version 23.5 (PR #224)
  • Updated KEGG to Release 94.0 (PR #293)
  • Updated HMMER to 3.3 and MAFFT to 7.467 (PR #293). Updated BLAST+ to 2.10.0 and DIAMOND to 0.9.32. (PR #294)
• Code refactoring:
  • refactored LP and MILP parsing (PR #258)
  • refactored ravenCobraWrapper (PR #286)

v2.3.1

This is the first RAVEN version archived in Zenodo. Use the following link to cite this version.

Main improvements in this release:

• Documentation:
  • standardized the definition part and comments for compartalization module functions: predictLocalization, parseScores and getWoLFScores (PR #268)
• External software fixes:
  • re-added HMMER (Unix) 3.2.1 binaries due to the problems with existing ones (PR #267)
• Features:
  • in parseScores and getWoLFScores renamed geneScoreStruct(ure) to GSS, like it is named in predictLocalization (PR #268)
  • addition of a new compareMultipleModels function (PR #270)
• Fixes:
  • fixed an issue in predictLocalization when the added transport reactions had their subSystems in incorrect format (PR #268)

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)