SysBioChalmers/yeast-GEM

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• Curate r_1603: the thiamine pyrimidine (HMP-P) synthase uses PLP and histidine and needs O2

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  curation

  Difficulty 4/5 3-5 days Newbie friendliness 55/100

  SysBioChalmers/yeast-GEM#424 · Opened Oct 7, 2026

• Reconsider small and inconsistently named subsystems

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  curation

  Difficulty 5/5 Over a week Newbie friendliness 35/100

  SysBioChalmers/yeast-GEM#420 · Opened Oct 7, 2026

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

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  curation

  Difficulty 2/5 1-3 hours Newbie friendliness 77/100

  SysBioChalmers/yeast-GEM#419 · Opened Oct 5, 2026

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

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  Difficulty 4/5 3-5 days Newbie friendliness 45/100

  SysBioChalmers/yeast-GEM#418 · Opened Sep 25, 2026

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

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  Difficulty 5/5 Over a week Newbie friendliness 25/100

  SysBioChalmers/yeast-GEM#416 · Opened Sep 24, 2026

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

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  Difficulty 5/5 Over a week Newbie friendliness 25/100

  SysBioChalmers/yeast-GEM#408 · Opened Sep 1, 2026

• Implement YAML-based curation

  May be free again @edkerk claimed this 655 days ago, and no pull request is open. Open

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  SysBioChalmers/yeast-GEM#379 · 2 comments · 1 reaction · 1 assignee · Opened Dec 22, 2024

• Yeast-GEM visualization?

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  SysBioChalmers/yeast-GEM#367 · 4 comments · Opened Jul 29, 2024

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

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  enhancement

  SysBioChalmers/yeast-GEM#353 · Opened Sep 28, 2023

• duplicate metabolites identified

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  SysBioChalmers/yeast-GEM#338 · 1 comment · Opened Jun 6, 2023

• reaction references

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  SysBioChalmers/yeast-GEM#334 · Opened Apr 11, 2023

• feat: single ec-code annotation per reaction

  May be free again @edkerk claimed this 1584 days ago, and no pull request is open. Open

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  SysBioChalmers/yeast-GEM#319 · 5 comments · 1 assignee · Opened Jun 5, 2022

• feat: KEGG pathway annotation

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  SysBioChalmers/yeast-GEM#317 · 1 reaction · Opened Jun 5, 2022

• Feat-stoichiometry coefficients for subunits in the enzyme complex

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  SysBioChalmers/yeast-GEM#297 · 10 comments · Opened Jan 31, 2022

• Fix-amino acid pathways localization

  May be free again @LarsBlank claimed this 1711 days ago, and no pull request is open. Open

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  bug wip

  SysBioChalmers/yeast-GEM#294 · 1 comment · 1 assignee · Opened Jan 31, 2022

• feat: have SLIMEr as option

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  SysBioChalmers/yeast-GEM#289 · Opened Dec 11, 2021

• feat: curate grRules with GPRuler output

  May be free again @cheng-yu-zhang claimed this 1734 days ago, and no pull request is open. Open

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  SysBioChalmers/yeast-GEM#288 · 2 assignees · Opened Dec 11, 2021

• doc: tutorial for yeast-GEM

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  SysBioChalmers/yeast-GEM#286 · Opened Dec 10, 2021

• feat:Missing annotations for Rhea and ModelSEED database

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  help wanted

  SysBioChalmers/yeast-GEM#231 · 3 comments · 1 reaction · Opened Jun 19, 2020

• fix: remove generic reactions

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  question

  SysBioChalmers/yeast-GEM#219 · 5 comments · Opened May 5, 2020

• feat: allow contributions from python users

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  format fix standby

  SysBioChalmers/yeast-GEM#218 · 1 comment · Opened Apr 24, 2020

• fix: mass- and charge balance reactions

  May be free again @eiden309 claimed this 2355 days ago, and no pull request is open. Open

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  bug help wanted

  SysBioChalmers/yeast-GEM#194 · 2 comments · 1 reaction · 2 assignees · Opened Jul 22, 2019

• fix: biomass tests from memote

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  memote standby

  SysBioChalmers/yeast-GEM#138 · 1 comment · Opened Jul 13, 2018

• fix: stoichiometric consistency due to SLIME rxns

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  help wanted memote question

  SysBioChalmers/yeast-GEM#135 · Opened Jul 13, 2018

• ATP/NADH issue

  May be free again @feiranl claimed this 3161 days ago, and no pull request is open. Open

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  question

  SysBioChalmers/yeast-GEM#64 · 6 comments · 2 assignees · Opened Feb 12, 2018

• feat: compartment curation

  May be free again @feiranl claimed this 3173 days ago, and no pull request is open. Open

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  SysBioChalmers/yeast-GEM#61 · 6 comments · 2 assignees · Opened Jan 31, 2018

• fix: flux prediction through PPP

  May be free again @zhengmingzhu claimed this 3173 days ago, and no pull request is open. Open

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  help wanted

  SysBioChalmers/yeast-GEM#59 · 11 comments · 2 assignees · Opened Jan 30, 2018

• feat: apply curations from mitoYeast-GEM paper

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  enhancement help wanted

  SysBioChalmers/yeast-GEM#12 · 3 comments · Opened Oct 25, 2017