The COBRA Toolbox v3.6

COBRA Toolbox v3.6 – Release Summary

Highlights

• Documentation

  • Switched to relative links and fixed broken image and index links.
  • Added software lifecycle documentation and COBRA version citation notice.
  • Updated README files with version badges and stable links.

• Bug Fixes

  • Fixed major issue in verifyRuleSyntax affecting large models.
  • Corrected file handling errors in mgPipe and minor bugs in vmhFoodFinder and related functions.
  • Resolved multiple small issues across Persephone and nutrition toolboxes.

• Toolbox Updates

  • Enhanced Persephone performance and personalisation workflow.
  • Added microbiome model support in diet functions.
  • Improved nutrition toolbox functions per reviewer feedback.
  • Introduced new MicroMap function.

• Maintenance

  • Removed obsolete binary files and updated submodules.
  • Updated CI environment checks and resource tracking permissions.

New Contributors

• @emilpaulitz
• @PaulaWalsh1

Full Changelog: v3.5 → v3.6

The COBRA Toolbox v3.5

COBRA Toolbox v3.5 – Release Summary

🚀 Highlights

🚀 New Features & Functionality

• Microbiome Modelling Toolbox: manual biomass input, bug fixes, updates to DEMETER and mgPipe
• Persephone Pipeline: major additions including CI/CD support, mixed effects models, solver integration
• Nutrition Toolbox: full overhaul with enhancements and critical fixes
• New modules/tools:
  • Fast-SL algorithm
  • CHRR barrier rounding
  • MetanetX mapper, Entropic FBA
  • venn4, rFASTCORMICS, COBRArrow MATLAB API
  • Extended support for JSON and plotting options

⚙️ Core Toolbox Enhancements

• Major improvements to optimizeCardinality, writeCbModel, generateMetaboScore, and initCobraToolbox
• Solver updates for Gurobi, CPLEX, MOSEK
• Refined XomicsToModel, ModelExtraction, printRxnFormula, loadPSCMfile
• Enhanced support for growth-coupled production and gene deletion strategies

🛡️ Bug Fixes

• Resolved bugs in:
  • Resolved all the failing tests
  • curationOverOmics, xomicsToModel, testChangeCobraSolver
  • File handling (generateMexFastFva, createDummyModel)
  • Visualisation (plotOverlapResults, printRxnFormula)
  • Solver execution (optimizeCbModel, solveWBMmethod)

📚 Tutorials & Documentation

• Updated and expanded tutorials
• Enhanced HTML report generation and JSON export
• CI/CD support for automatic contributor and citation page updates

🤟 CI/CD and Testing Infrastructure

• Refinements to testAll, testCycleFreeFlux, testMinimumRequirements, etc.
• GitHub Actions workflows fully revamped: coverage, doc updates, PR validation

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22 New Contributors

• @SomyaVerma27 made their first contribution in #2107
• @yunbum-kook made their first contribution in #2111
• @AaronBrennan1 made their first contribution in #2113
• @BigDataInSilicoBiologyGroup made their first contribution in #1991
• @CodeGeasrb made their first contribution in #2182
• @rxpavan made their first contribution in #2181
• @Sami990 made their first contribution in #2180
• @bramnap made their first contribution in #2179
• @silvtal made their first contribution in #2175
• @trjhensen made their first contribution in #2188
• @annasheehy made their first contribution in #2185
• @hadjar11 made their first contribution in #2194
• @mariapirespacheco made their first contribution in #2184
• @Moremo1996 made their first contribution in #2260
• @ThummaratPaklao made their first contribution in #2271
• @fernweh-3 made their first contribution in #2276
• @FilippoMart made their first contribution in #2307
• @dana-luong made their first contribution in #2312
• @Kretaks made their first contribution in #2330
• @CCThinnes made their first contribution in #2379
• @MetNetComp made their first contribution in #2427
• @TheWileyB made their first contribution in #2477

Full Changelog: v3.4...v3.5

COBRA 3.4 = thermodynamically consistent constraint-based modelling

Addition of XomicsToModel & thermoKernel code
XomicsToModel: Omics data integration and generation of thermodynamically consistent metabolic models
by
German Preciat, Agnieszka B. Wegrzyn, Ines Thiele, Thomas Hankemeierand Ronan M.T. Fleming

in support of the paper:

Mechanistic model-driven exometabolomic characterisation of human dopaminergic neuronal metabolism
by
German Preciat1, Agnieszka B. Wegrzyn1, Edinson Lucumi Moreno1, Cornelius C.W. Willacey1, Jennifer
Modamio2, Fatima L. Monteiro2, Diana El Assal2, Alissa Schurink1, Miguel A.P. Oliveira2, Zhi Zhang2, Ben
Cousins3,4, Hulda S. Haraldsdóttir2, Siham Hachi2, Susanne Zach5, German Leparc5, Yin Tat Lee6, Bastian
Hengerer5, Santosh Vempala4, Michael A. Saunders7, Amy Harms1, Enrico Glaab2, Jens C. Schwamborn2, Ines
Thiele8, Thomas Hankemeier1† and Ronan M.T. Fleming1,2,8

1 Metabolomics and Analytics Center, Leiden Academic Centre for Drug Research, Leiden University, Netherlands,
2 Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 6 avenue du Swing, L-4367
Belvaux, Luxembourg,
3 Department of Industrial Engineering and Operations Research, Data Science Institute, Columbia
University, New York, NY,
4 School of Computer Science, Algorithms and Randomness Center, Georgia Institute of Technology, Atlanta,
GA, USA,
5 Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany,
6 Department of Computer Science and Engineering, University of Washington, USA,
7 Department of Management Science and Engineering, Stanford University, Stanford, 94305, CA, USA,
8 School of Medicine, University of Galway, University Rd, Galway, Ireland.

v3.33

Please note that each release is not a git repository and therefore the updateCobraToolbox function will not work. If you want to use that function, so that you can get cobra toolbox updates then use a terminal command like:
git clone git@github.com:opencobra/cobratoolbox.git cobratoolbox

v3.32: Merge pull request #1811 from opencobra/develop

Develop

v3.31: Merge pull request #1809 from opencobra/develop

Develop

v3.3

Merge pull request #1804 from opencobra/develop

Develop

Additional features for host microbial community co-metabolism modelling

Merge pull request #1761 from opencobra/develop

Develop

Compatibility with whole body modelling

Compatibility with whole body modelling, as described in:
Ines Thiele, Swagatika Sahoo, Almut Heinken, Johannes Hertel, Laurent Heirendt, Maike K Aurich & Ronan MT Fleming, Personalized whole-body models integrate metabolism, physiology, and the gut microbiome, Molecular Systems Biology (in press).

The COBRA Toolbox v3.0.6

Merge pull request #1477 from opencobra/develop

Regular merge of develop