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Published May 18, 2022 | Version v8.6.0
Software Open

SysBioChalmers/yeast-GEM: yeast 8.6.0

Authors/Creators

  • 1. Chr. Hansen
  • 2. Chalmers University of Technology
  • 3. Aalto University
  • 4. Gitter

Description

  • Fixes:
    • Closes #265: Make r_0446 (formate-tetrahydrofolate ligase) irreversible, to prevent non-zero flux through TCA cycle (PR #290).
  • Features:
    • Add pathways responsible for the formation of hydrogen sulfide as well as other volatile sulfur compounds during fermentation (PR #300).
    • Closes #302: Simplify model curation with curateRxnsGenesMets function (PR #300).
    • Remove COBRA Toolbox and MATLAB-git dependencies for the MATLAB-based curation pipeline (PR #303).
    • Closes #308: Distribute yeast-GEM.mat in RAVEN's format, to include grRules and metComps fields (PR #301).
  • Refactor:
    • Change format of yeast-GEM.txt file to include metabolite names and compartments, instead of metabolite identifiers, to simplify diff-ing (metabolite identifiers are already trackable in the yml-file) (PR #312).

Files

SysBioChalmers/yeast-GEM-v8.6.0.zip

Files (6.2 MB)

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Additional details

Related works

Is supplement to
https://github.com/SysBioChalmers/yeast-GEM/tree/v8.6.0 (URL)