rhto-GEM 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-GEM v1.2.2

• Features
  • Data and analysis complementary to Lopes et al., 2020, Appl Microbiol Biotechnol. (PR #38).
• Documentation
  • Update citation of rhto-GEM paper, now available from Biotechnology & Bioengineering (PR #39).

rhto-GEM v1.2.1

• Features:
  • Curate grRules and existence of several reactions based on doi:10.1186/s12934-015-0217-5 (PR #34).
  • Curate grRules of xylose and glucose transporters based on differential expression in proteomics study doi:10.1186/s13068-019-1478-8 (PR #34).
• 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-GEM 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-GEM 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-GEM 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-GEM v1.0.0

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

rhto-GEM v0.0.2

Initial release of rhto-GEM. Details about reconstruction of model is available in ComplementaryScripts\reconstruction.