Issues

• Environments are applied by separate MATLAB and Python code, anaerobicModel changed meaning in 9.1.0, and media with carnitine have no environment

  curation
  SysBioChalmers/yeast-GEM#431 · Filter by author edkerk opened on Nov 4, 2026

• frd1 is predicted inviable anaerobically because OSM1 is only on the NADH-linked r_4264

  curation
  SysBioChalmers/yeast-GEM#430 · Filter by author edkerk opened on Nov 4, 2026

• Check reaction directions against thermodynamics in Model QC, and regenerate the ΔG tables reproducibly

  SysBioChalmers/yeast-GEM#428 · Filter by author edkerk opened on Nov 3, 2026

• feat: PubMed ids in reactions.tsv, and DOI references

  SysBioChalmers/yeast-GEM#427 · Filter by author edkerk opened on Oct 28, 2026

• r_0939 is annotated for NADP but uses NAD; r_1191 and r_1260 carry genes that are not the transporters

  SysBioChalmers/yeast-GEM#425 · Filter by author edkerk opened on Oct 23, 2026

• r_1603 makes the thiamine pyrimidine from AIR without oxygen, but the Thi5 family uses PLP and histidine and needs O2

  curation
  SysBioChalmers/yeast-GEM#424 · Filter by author edkerk opened on Oct 7, 2026

• Reconsider small and inconsistently named subsystems

  curation
  SysBioChalmers/yeast-GEM#420 · Filter by author edkerk opened on Oct 7, 2026

• Ferrocytochrome b5 in the ER (s_4209) has charge 3 and ferricytochrome cross-references

  curation
  SysBioChalmers/yeast-GEM#419 · Filter by author edkerk opened on Oct 5, 2026

• Proton leak (r_2129) is unbounded and can absorb oxygen without ATP

  SysBioChalmers/yeast-GEM#418 · Filter by author edkerk opened on Sep 25, 2026

• ecYeastGEM: enzyme-constrained model available via ecModels; automated reconstruction planned

  SysBioChalmers/yeast-GEM#416 · Filter by author edkerk opened on Sep 24, 2026

• Curation backlog: non-blocking findings from model-qc.yml

  SysBioChalmers/yeast-GEM#408 · Filter by author edkerk opened on Sep 1, 2026

• Implement YAML-based curation

  SysBioChalmers/yeast-GEM#379 · Filter by author edkerk opened on Dec 22, 2024
  2

  

• Yeast-GEM visualization?

  SysBioChalmers/yeast-GEM#367 · Filter by author forxhunter opened on Jul 29, 2024
  4

• feat: function to report if flux vector is ΔG-compatible

  enhancement
  SysBioChalmers/yeast-GEM#353 · Filter by author edkerk opened on Sep 28, 2023

• duplicate metabolites identified

  SysBioChalmers/yeast-GEM#338 · Filter by author feiranl opened on Jun 6, 2023
  1

• reaction references

  SysBioChalmers/yeast-GEM#334 · Filter by author mihai-sysbio opened on Apr 11, 2023

• feat: single ec-code annotation per reaction

  SysBioChalmers/yeast-GEM#319 · Filter by author edkerk opened on Jun 5, 2022
  5

  

• feat: KEGG pathway annotation

  SysBioChalmers/yeast-GEM#317 · Filter by author edkerk opened on Jun 5, 2022

• Feat-stoichiometry coefficients for subunits in the enzyme complex

  SysBioChalmers/yeast-GEM#297 · Filter by author feiranl opened on Jan 31, 2022
  10

• Fix-amino acid pathways localization

  bugwip
  SysBioChalmers/yeast-GEM#294 · Filter by author feiranl opened on Jan 31, 2022
  1

  

• feat: have SLIMEr as option

  SysBioChalmers/yeast-GEM#289 · Filter by author edkerk opened on Dec 11, 2021

• feat: curate grRules with GPRuler output

  SysBioChalmers/yeast-GEM#288 · Filter by author edkerk opened on Dec 11, 2021
  

• doc: tutorial for yeast-GEM

  SysBioChalmers/yeast-GEM#286 · Filter by author edkerk opened on Dec 10, 2021

• feat:Missing annotations for Rhea and ModelSEED database

  help wanted
  SysBioChalmers/yeast-GEM#231 · Filter by author feiranl opened on Jun 19, 2020
  3

• fix: remove generic reactions

  question
  SysBioChalmers/yeast-GEM#219 · Filter by author BenjaSanchez opened on May 5, 2020
  5