Releases: SysBioChalmers/yeast-GEM
yeast 8.4.2
- Features:
- Fixes:
NOTE: This release is made with the main version of COBRA; however, as they have dropped tagged releases for the time being, /ModelFiles/dependencies.txt
points to a specific commit from their master branch.
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).
- Switched to
- 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
andmapMNXMID.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
andwrite_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).
- New functions
- 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:
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:
- Tests:
- Documentation/Others:
yeast 8.3.4
- Features:
- Fixes:
- Corrected typo in gene ID (PR #186).
yeast 8.3.3
- Features:
- Fixes:
- Documentation:
yeast 8.3.2
- Features:
- Fixes:
yeast 8.3.1
- Features:
- Fixes/Others:
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:
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.