Issues

• Release and QC checks miss SBML, task-file and version errors

  wip
  SysBioChalmers/Human-GEM#1176 · Filter by author edkerk opened on Oct 20, 2026

• Gene-essentiality CI skips genes outside context models and runs without the growth task

  wip
  SysBioChalmers/Human-GEM#1175 · Filter by author edkerk opened on Oct 20, 2026

• Reactions sit in compartments where their enzymes do not act

  wip
  SysBioChalmers/Human-GEM#1174 · Filter by author edkerk opened on Oct 20, 2026

• Reaction equations have wrong cofactors or directions, and some duplicates form loops

  wip
  SysBioChalmers/Human-GEM#1173 · Filter by author edkerk opened on Oct 20, 2026

• Metabolite structures, charges and cross-references point to other compounds

  wip
  SysBioChalmers/Human-GEM#1172 · Filter by author edkerk opened on Oct 20, 2026

• EC numbers describe other reactions, including 221 on pure transports

  wip
  SysBioChalmers/Human-GEM#1171 · Filter by author edkerk opened on Oct 20, 2026

• Reaction names give transports the wrong direction or describe another reaction

  wip
  SysBioChalmers/Human-GEM#1170 · Filter by author edkerk opened on Oct 20, 2026

• GPRs carry genes without the activity and miss genes that have it

  wip
  SysBioChalmers/Human-GEM#1169 · Filter by author edkerk opened on Oct 20, 2026

• Errors the animal GEMs inherit from Human-GEM

  wip
  SysBioChalmers/Human-GEM#1167 · Filter by author edkerk opened on Oct 20, 2026

• MAR00036 drains 146 eicosanoids in one reaction, so one unreachable metabolite blocks all of them

  SysBioChalmers/Human-GEM#1166 · Filter by author edkerk opened on Oct 18, 2026

• 12-lipoxygenase reactions outside the cytosol, and hepoxilin and peroxidase steps assigned to glutathione peroxidases (14 reactions)

  SysBioChalmers/Human-GEM#1164 · Filter by author edkerk opened on Oct 18, 2026

• Curate the Full and Essential task files

  wip
  SysBioChalmers/Human-GEM#1163 · Filter by author edkerk opened on Oct 17, 2026
  2

• Reaction literature references are not checked against the reactions they are cited for

  SysBioChalmers/Human-GEM#1161 · Filter by author edkerk opened on Oct 16, 2026

• Peroxisomal β-oxidation GPRs join alternative enzymes with "and" and list mitochondrial enzymes (98 reactions)

  wip
  SysBioChalmers/Human-GEM#1159 · Filter by author edkerk opened on Oct 8, 2026
  1

• Free trimethyllysine release (MAR06978, MAR08029) is assigned to the signal peptidase complex

  fixed in develop
  SysBioChalmers/Human-GEM#1157 · Filter by author edkerk opened on Oct 8, 2026

• MMAA is the GPR of cobalamin transport and adenosyltransferase reactions (MAR08614-MAR08616), but it is the chaperone of MMUT

  wip
  SysBioChalmers/Human-GEM#1156 · Filter by author edkerk opened on Oct 8, 2026
  1

• DNA methyltransferase GPR (MAR04072, MAR08640, MAR08641) lists TRDMT1 and DNMT3L, and makes DNMT1 need DNMT3B

  wip
  SysBioChalmers/Human-GEM#1155 · Filter by author edkerk opened on Oct 8, 2026

• Mass and charge imbalances, and structures that disagree with formula or charge

  bug
  SysBioChalmers/Human-GEM#1153 · Filter by author edkerk opened on Oct 8, 2026
  2

• Essential tasks allow no proton exchange, so 28 of them pass only through charge-unbalanced reactions

  wip
  SysBioChalmers/Human-GEM#1152 · Filter by author edkerk opened on Oct 8, 2026
  1

• Twelve reactions convert fatty acids between the n-3 and n-6 series, so the model makes arachidonate without linoleate and DHA without linolenate

  wip
  SysBioChalmers/Human-GEM#1151 · Filter by author edkerk opened on Oct 8, 2026
  1

• The CoQ head group is made through a plant 4-coumarate route instead of HPDL

  wip
  SysBioChalmers/Human-GEM#1150 · Filter by author edkerk opened on Oct 7, 2026
  1

• Six gene-free reactions that growth needs have known human enzymes (PEDS1, COQ4, PRUNE1, FADS2, MTRR, LRAT)

  wip
  SysBioChalmers/Human-GEM#1149 · Filter by author edkerk opened on Oct 7, 2026
  1

• Urate oxidase (MAR06611) has no GPR, so every human cell can oxidise urate to allantoin

  wip
  SysBioChalmers/Human-GEM#1147 · Filter by author edkerk opened on Oct 7, 2026
  1

• SLC7/SLC3 transporter GPRs: unpaired light chains, SLC7A6 in the b0,+ rule, and light chains that do not match the exchanged substrates

  bugfixed in develop
  SysBioChalmers/Human-GEM#1142 · Filter by author chechung opened on Oct 6, 2026
  3

• Steroid hormone synthesis: CYP17A1 lyase copies, the HSD3B isomerase, cortisol side-chain cleavage and 11-oxygenated androgens

  SysBioChalmers/Human-GEM#1134 · Filter by author edkerk opened on Oct 2, 2026