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)