yeast 8.4.1

• Features:
  • Switched to pip-tools for managing python dependencies, distinguishing between user requirements /requirements/requirements.txt and developer requirements /requirements/dev-requirements.txt (PR #235).
• Fixes:
  • Closes #201: Changed generic protein name to avoid confusion (PR #237).
  • Closes #205: Finished correcting reactions' stoichiometry based on KEGG data (PR #237).
  • Closes #215: Corrected wrong gene rule in reaction (PR #237).
  • Closes #225: Moved MNX rxn ids from notes to the proper annotation field (PR #226).
• Documentation:
  • Closes #223: Clarified releasing steps, including authorship criteria for Zenodo releases, in contributing guidelines (PR #233).
  • Closes #227: Removed authorships/dates from all scripts, as it is redundant information (PR #230).
  • Added admin guidelines for managing python dependencies (PR #235).
  • Included links for model visualization in README file (PR #240).

NOTE: This release is (still) made with the development version of COBRA toolbox, as their latest release is not able to preserve BiGG ids.

yeast 8.4.0

• Features:
  • New functions mapKEGGID.m and mapMNXMID.m for adding ids in model. Used them to add missing KEGG and MetaNetX ids for both metabolites and reactions (PR #220).
  • Closes #197: Added missing MetaNetX ids using KEGG ids and ChEBI ids (PR #220).
  • Added BiGG ids for all matched metabolites/reactions using MetaNetX + manual curation, together with lists containing new BiGG ids for the unmatched ones (PR #188).
  • New functions read_yeast_model and write_yeast_model for easier usage in python (PR #224).
  • Closes #172: Model can now be loaded with BiGG ids as main ids, for better compliance with cobrapy (PR #224).
• Fixes:
  • Closes #102: Every component of the model is now preserved when the model is opened with cobrapy, including gene names (PR #216).
  • Manual curation of MetaNetX, KEGG and ChEBI ids for metabolites/reactions (PRs #188 and #220).
  • Closes #187: Removed some duplicate reactions in the model (PR #188).
  • Mass/charge balanced most unbalanced reactions in model using checkSmatrixMNX.m, bringing the number down to 17 reactions (PR #222).
• Others:
  • Configured repo to ensure that files always use LF as EOL character (PR #221).
  • Gene SBO terms are now recorded, after update in COBRA toolbox (PR #188).

NOTE: This release was made with the development version of COBRA toolbox, as the latest release is not able to preserve BiGG ids.

yeast 8.3.5

• Fixes:
  • Closes #129: Removed non-S288C genes (PR #211).
  • Closes #198: Fixes function for converting model to anaerobic (PR #199).
• Tests:
  • Added growth tests for carbon & nitrogen limitation (#199).
  • Added test for computing gene essentiality (PR #200).
• Documentation/Others:
  • Clarified with README's the purpose of each script/data folder (#209).
  • Closes #206: Updated citation guidelines (PR #210).
  • Updated contribution guidelines + issue/PR templates (PR #210).
  • Created folders with deprecated scripts (PR #209).

yeast 8.3.4

• Features:
  • Fixes #171: Added 101 GPR rules to transport rxns according to TCDB database (PR #178).
  • Added 18 met formulas from manual search (PR #155).
  • Performed gap-filling for connecting 29 dead-end mets, by adding 28 transport rxns (PR #185). Added documentation to the gap-filling functions in PR #195.
• Fixes:
  • Corrected typo in gene ID (PR #186).

yeast 8.3.3

• Features:
  • Fixes #107: Two new pseudoreactions (cofactor pseudoreaction and ion pseudoreaction) added to the model as extra requirements to the biomass pseudoreaction (PRs #174 & #183).
• Fixes:
  • addSBOterms.m adapted to identify new pseudoreactions (PR #180).
  • Removed non-compliant symbol from a reaction name to avoid parsing errors (PR #179).
• Documentation:
  • Model keywords modified to comply with the sysbio rulebook (PR #173).
  • Added citation guidelines (PR #181).

yeast 8.3.2

• Features:
  • Fixes #154: MetaNetX IDs added from the yeast7.6 MetaNetX model & from existing ChEBI and KEGG IDs in the model (PR #167).
  • Introduced contributing guidelines + code of conduct (PR #175).
• Fixes:
  • Fixes #161: Added as rxnNotes and metNotes the corresponding PR number (#112, #142, #149 or #156) in which each rxn and met was introduced (PR #170).
  • Fixes #169: Compartment error for r_4238 (PR #170).
  • Corrected confidence score of rxns from PR #142 (PR #170).

yeast 8.3.1

• Features:
  • Added 21 reactions & 14 metabolites based on metabolomics data (PR #156).
  • Added metadata to the excel version of the model (PR #163).
  • Added ComplementaryData/physiology with biological data of yeast (PR #159).
• Fixes/Others:
  • Fixed bug that underestimated the biomass content (PR #159).
  • Fitted GAM to chemostat data (PR #159).

NOTE: This version of the model was generated with the devel branch of RAVEN, as the master branch has a bug when saving dependencies.

yeast 8.3.0

• Features:
  • Added 225 new reactions and 148 new metabolites, based on growth data from a Biolog substrate usage experiment on carbon, nitrogen, sulfur and phosphorus substrates (PR #149).
• Fixes/Others:
  • Removed verbose details from README.md (PR #150).
  • Updated RAVEN, which added extra annotation to the .yml file (PR #151).
  • Minor changes to saveYeastModel.m (PR #152).
  • Model is now stored simulating minimal media conditions (PR #157).

NOTE: The .xlsx version of this model has incorrect compartment information in the equation formulas (RXNS tab), due to a bug in the associated saving function.

yeast 8.2.0

• Features:
  • Fixes #38: Added 183 new reactions, 277 new metabolites and 163 new genes based on the latest genome annotation in SGD, uniprot, KEGG, Biocyc & Reactome (PR #142).
• Fixes:
  • grRules deleted from pseudoreactions, removing with this 49 genes (PR #145).
• Chores:
  • Updated COBRA, which changed the number of decimals in some stoichiometric coefficients in .txt (PR #143)

yeast 8.1.3

• Features:
  • Added SBO terms for all metabolites and reactions, based on an automatic script now part of saveYeastModel.m (PR #132).
  • increaseVersion.m now avoids conflicts between devel and master by erroring before releasing and guiding the admin to change first devel (PR #133).
  • Website now available in gh-pages branch: http://sysbiochalmers.github.io/yeast-GEM/
• Fixes:
  • Standardize naming of pseudo-metabolites "lipid backbone" & "lipid chain" (PR #130).
• Chores:
  • Updated COBRA, which swapped around the order of the bqbiol:is and bqbiol:isDescribedBy qualifiers in the .xml file (PR #131).