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Published May 2, 2024 | Version v2.9.0
Software Open

SysBioChalmers/RAVEN: v2.9.0

Authors/Creators

  • 1. Chalmers University of Technology
  • 2. AIxBIO
  • 3. BioInnovation Institute
  • 4. Chr. Hansen
  • 5. ELIXIR Europe
  • 6. @SysBioChalmers
  • 7. Aalto University
  • 8. Gitter
  • 9. KTH Royal Institute of Technology / Science For Life Laboratory

Description

  • chore:
    • update libSBML to version 5.20.2, now including support for Apple Silicon .mexmaca64. The macOS Intel .mexmaci64 is kept at version 5.19.0, as the required compiled mex file is not included in the 5.20.2 release.
    • add .mexmaca64 glpk binary for Apple Silicon.
  • fix:
    • simplifyModel with irreversible backwards-only reactions (solves #529)
    • writeYAMLmodel do not write lines with empty entries (e.g. reactions without subsystems)
    • getModelFromKEGG includes model.annotation.defaultLB and model.annotation.defaultUB fields
    • getGenesFromGrRules can handle genes with '|'
    • getModelFromHomology remove geneFrom field (solves #533)
    • getMinNrFluxes reduce default verbosity
    • writeYAMLmodel allow empty id and name fields, in line with https://github.com/SysBioChalmers/RAVEN/wiki/RAVEN-Model-Structure
    • ravenCobraWrapper prefers to use grRules in COBRA models if present (solves GECKO issue #367)
    • optimizeProb will throw error when trying to solve MILP with glpk (also if glpk is set via cobra)
    • writeYAMLmodel will throw an informative error if it cannot write the file to the intended directory
    • mapCompartments correct horizontal concatenation of cell array
    • checkInstallation during first installation on unix machines, makeBinaryExecutables threw an error.
    • importModel correctly parses SBML file that has some missing SBO terms
  • feat:
    • randomSampling can run in parallel with MATLAB Parallel Computing Toolbox installed
    • setParam has an additional option, 'unc' if a reaction's lower and upper bound should be set as unconstrained. If available, this will use the default bounds in model.annotation (otherwise [-1000, 1000]), and considers reversibility (in which case lower bound = 0)
    • auxiliary parallelPoolRAVEN function to check if function should be running in parallel
    • use alternative ProgressBar, particularly in functions containing parfor calls
    • give execution rights in Terminal for new RAVEN functions
  • refactor:
    • remove mentions to soplex (which has been replaced by scip).
    • avoid cmd windows output by parallelPoolRaven.
    • allow randomSampling with nsamples set to 0, to only get goodRxns.

Files

SysBioChalmers/RAVEN-v2.9.0.zip

Files (267.2 MB)

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Additional details

Related works

Is supplement to
Software: https://github.com/SysBioChalmers/RAVEN/tree/v2.9.0 (URL)