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Human 1.11.0

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@haowang-bioinfo haowang-bioinfo released this 07 Feb 07:25
· 1004 commits to main since this release
  • Fixes (PR #351):
    • remove duplicated reactions, as reported in #344
  • Fixes (PR #343):
    • sync met ids with new comp abbreviations in metabolites.tsv to resolve branch conflict while merging #341
  • Features (PR #341):
    • modify compartment abbreviations (Extracellular: s->e, Boundary: x->b, Peroxisome: p->x), as discussed in #314
  • Style (PR #340):
    • refine README
  • Features (PR #339):
    • continue on improving metabolite annotation with CHEBI ids
  • Features (PR #338):
    • refactor exportTsvFile function with options of .txt output format and double-quote free mode
  • Features (PR #337):
    • remove generic (de)phosphorylation reactions and 558 associated genes, as suggested by #336
  • Fixes (PR #334):
    • clean reaction name field, according to discussions in #181, #333
  • Features (PR #332):
    • refactor GitHub actions with more robust and reproducible setup, by replacing the direct usage of Python and installation of packages with the opencobra/memote container from DockerHub
  • Features/Fixes (PR #331):
    • reformat metabolic task files
      • change all metabolic task .xlsx files in /data/metabolicTasks to .txt format
      • correct the compartment of NEFA blood pool in from Boundary to Extracellular ([x] to [s]) for addressing #311
  • Features (PR #329):
    • add CHEBI:53019 'glycan G00008' to MAM00154r, as clarified in #328
  • Fixes (PR #327):
    • empty Should Fail column to Cellfie metabolic tasks, this was mentioned in #280
  • Fixes (PR #325):
    • correct metabolite annotations according to discussions in #297, #299, and #308
  • Fixes (PR #296):
    • standardize references field by systematically implementing PMID and separating entries by semicolon, as proposed in #259