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Published June 21, 2022 | Version v1.12.0
Software Open

SysBioChalmers/Human-GEM: Human 1.12.0

Authors/Creators

  • 1. BioInnovation Institute
  • 2. Chalmers University of Technology
  • 3. VU Amsterdam
  • 4. ETH Zurich

Description

Main improvements in this PR:
  • Features (PR #393):
    • speed up importYaml in loading model fields
  • Features (PR #392):
    • turn importYaml into a more generic function
  • Features (PR #388):
    • add help functions that are used together with ftINIT in RAVEN
  • Fixes (PR #382):
    • change metabolic task file format from xlsx to txt
    • inactivate human biomass reaction (MAR13082), as suggested in Mouse-GEM PR #11
    • add proper LB and UB values to annotation field, as reported in Mouse-GEM PR #12
    • turn annotateGEM into a more generic function, as discussed in Convert annotateGEM into a more generic function #380
  • Fixes (PR #379):
    • flag reactions MAR05127, MAR08749, MAR08750 as spontaneous, as identified in #349
  • Style (PR #374):
    • doc: tINIT rename 'exchange metabolites' to 'boundary metabolites in getINITModel2
  • Features (PR #367):
    • add reaction names from KEGG, to address #181
  • Fixes (PR #365):
    • merge MAR08973 into MAR04474, as suggested in #346
  • Fixes (PR #362):
    • resolves #342 by applying the suggestion to remove the gene (and thus the GPR) and mark MAR04840 as spontaneous
  • Fixes (PR #358): - correct CHEBI associations to avoid conflict during MNXref conversion

Files

SysBioChalmers/Human-GEM-v1.12.0.zip

Files (9.2 MB)

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Additional details

Related works

Is supplement to
https://github.com/SysBioChalmers/Human-GEM/tree/v1.12.0 (URL)