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rhto v1.3.0:

  • Fix
    • Remove incorrect isoenzymes by manual curation of grRules (PR #44)
    • Remove duplicate transport reactions (PR #45)
    • Correct EC codes of mitochondrial 3-ketoacyl-CoA thiolases (PR #45)
  • Documentation
    • Update citation and model stats in README.md

rhto v1.2.2:

rhto v1.2.1:

  • Features
  • Fix
    • Bug in sumBioMass resulted in incorrect fitted carbohydrate fraction of biomass equation, also resulting in incorrect NGAM (PR #33).
    • Remove four duplicate reactions (r_4235, y200008, r_1000, r_4262) (PR #34).
  • Refactor
    • Standardize two complex gene associations (r_0831, r_0832) (PR #34).

rhto v1.2.0:

  • Features
    • Set alternative carbon source exchange reactions as reversible (glycerol, xylose) (PR #28).
    • init_rhto-GEM.m script that prepares MATLAB environment with path to repo's folders (PR #28).
    • makeLipidRxns now takes list of acyl-chain configurations, instead of defining these by itself from a list of allowed acyl-chains. (PR #28).
    • Correct gene associations of mitochondrial beta-oxidation reaction (PR #29).
    • Curate subsystems and EC numbers (PR #29).
    • Update DNA, RNA and amino acid pseudoreactions, based on frequency of nucleotides and amino acids in genome, transcript and protein FASTA files (PR #30).
    • Scale carbohydrate fraction to ensure that biomass pseudoreaction generates 1 gDCW (PR #30).
    • Refit energetics (PR #30).
  • Fix
    • Curate acyl-chains: simplify number of possible chain combinations, based on measured chain distribution (e.g. 16:1 level is around 1% and therefore not included in the biomass), and distribution of acyl-chains on TAGs (10.1007/s00253-017-8126-7): sn-1 is 16:0 or 18:0, sn-2 is 18:1, 18:2 or 18:3; sn-3 is 16:0, 18:0 or 18:1. (PR #28).
    • Use template SLIMER reactions (PR #28).
    • Various curations of lipid metabolism (PR #28, PR #30).

rhto v1.1.1:

  • Features
    • Make Memote snapshot report via Travis with every push to master, report available at https://sysbiochalmers.github.io/rhto-GEM/ (PR #23).
    • Sort reactions and metabolites when saving model, for easier diff (PR #23).
    • Include phosphoketolase and phosphate transacetalyase reactions (PR #23).
    • Increase annotation coverage for metabolites and reactions by mapping to MetaNetX (PR #23).
    • Script for gene essentiality validation (PR #23).
  • Fix
    • Remove duplicated reactions, introduced at various steps of reconstruction (PR #23).
    • Set fatty-CoA-ligases as irreversible, as they could otherwise form ATP regenerating loops that are unlikely to appear in vivo (PR #23).
    • Refit energetics with new NGAM and GAM values (PR #23).
  • Refactor
    • Change style of graph with growth rate validation (PR #23).
    • Refactor various simulation scripts (PR #23).
    • All new (non yeast-GEM) reactions are assigned identifiers with prefix t_ (PR #23).

rhto v1.1.0:

  • Features
    • Include model of Yarrowia lipolytica iYali4.1.1 as template during reconstruction (PR #18).
    • Standardize identifiers: all new metabolites have ids m_xxxx, while new reactions are t_xxxx or tr_xxxx (for transport reactions) (PR #18).
    • Reduced the amount of hard-coded ids in scripts (PR #18).
  • Fix
    • Include missing reactions such as complex I (PR #18).
    • Re-fit energetics (NGAM and GAM) (PR #18).
  • Reorder
    • Reorganize reconstruction process: use TSV files for lists of curations (PR #18).
    • Include legend in validation graph (PR #18).

rhto v1.0.0:

  • Documentation
    • Update readme.md to include correct links to Zenodo and bioRxiv (PR #15).

rhto v0.0.2:

  • Features
    • Include script ComplementaryScripts\validation\growthPrediction.m to valide model by comparing growth predictions (PR #13).
    • Include script ComplementaryScripts\analysis\fseof_target_prediction.m for FSEOF target prediction (PR #13).
  • Fixes
    • Energetics script r7_energetics.m correctly reads file with flux data (PR #13).
    • Correct unlogical and duplicate grRules (PR #13).
    • Correct subSystems naming, removing orphan indices from template model (PR #13).
  • Documentation
    • Readme.md has detailed text on how to cite the model (PR #13).
    • Readme.md contains version badge and Zenodo doi badge (PR #13).

rhto v0.0.1:

Initial release of rhto-GEM.