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@edkerk edkerk released this 16 Nov 21:39
· 217 commits to main since this release
v2.7.7
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Learn about vigilant mode.

Main improvements in this PR:

  • fix:

    • checkInstallation ensures that binaries (blastp etc.) and MEX files (TranslateSBML etc.) are executable on Mac, as this is not the case if RAVEN is installed as MATLAB Add-On
    • checkInstallation runtests on MATLAB < 2018b
    • getModelFromHomology no longer includes "OLD_" genes from the template model(s) if this gene is only involved in "OR" gene associations (= isoenzyme), but only if involved in "AND" gene associations (= subunit).
    • constructS trim spaces around metabolites for matching

  • feat:

    • writeYAMLmodel and readYAMLmodel functionality
    • support in various functions for a model.metSmiles field, which contains SMILES for each metabolite
    • solveLP (via optimizeProb) reports shadow prices and reduced costs
    • new runRobustnessAnalysis, runDynamicFBA, runPhenotypePhasePlane, runProductionEnvelope and runSimpleOptKnock functions
    • printFluxes can print multiple flux vectors
    • convertToIrrev gives output specifying match between reversible and novel irreversible reactions

  • refactor:

    • randomSampling speed-up with hot-start LPs
    • expandModel speed improvement
Assets 2
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