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Published August 12, 2021 | Version v1.9.0
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SysBioChalmers/Human-GEM: Human 1.9.0

Creators

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

Description

  • Style (PR #294):
    • add and reformat citations in README
  • Fixes (PR #292):
    • replace deprecated Ensembl gene ids with updated ones, as reported in #278
    • update genes.tsv annotation file using script fetch_ensembl_gene_annotations
  • Features (PR #291):
    • adjust sanityCheck script to enable the detection of reusing deprecated MA ids, as discussed in #265
  • Fixes (PR #290):
    • fix the ATP hydrolysis stoichiometry in biomass equation MAR13082, as reported in #289.
  • Fixes (PR #287):
    • refactor fetch_ensembl_gene_annotations.py script to allow retrieving annotations with empty gene symbols or ENSP ID, and to show the replacement Ensembl IDs for deprecated ones, as proposed in #278
  • Features (PR #286):
    • introduces a GH Action for testing the yaml conversion with testYamlConversion.
  • Fixes (PR #285):
    • fix: merge duplicated long-chain fatty acyl-CoA mets, as reported in #268, #269
  • Style (PR #284):
    • rename default branch (master --> main) as discussed in #226
    • change default branch names in repo documents and code
  • Fixes (PR #283):
    • remove cytosolic protons from reaction in other subcellular compartments, as detailed in #282
      • revise MAR05259 by replacing proton with lysosomal version
      • remove MAR04758 that is duplicate to MAR01044
      • remove MAR01459 that is duplicate to MAR02041, whose proton is replaced with the mitochondrial version
  • Fixes (PR #281):
    • excluded gene ENSG00000197375 from MAR02590 (carnitine shuttle), due to lack of evidence (#279)
  • Style (PR #275):
    • add .gitattributes file to ensure consistent LF line endings as discussed in #264
  • Features (PR #274):
    • add rxnNotes field to Human-GEM, as planned in #272
    • adjust importYaml/exportYaml functions to enable handling of rxnNotes field

Files

SysBioChalmers/Human-GEM-v1.9.0.zip

Files (9.3 MB)

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Additional details

Related works

Is supplement to
https://github.com/SysBioChalmers/Human-GEM/tree/v1.9.0 (URL)