Published June 15, 2020
| Version v8.4.0
Software
Open
SysBioChalmers/yeast-GEM: yeast 8.4.0
Description
- 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:
- 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).
- Configured repo to ensure that files always use
NOTE: This release was made with the development version of COBRA toolbox, as the latest release is not able to preserve BiGG ids.
Files
SysBioChalmers/yeast-GEM-v8.4.0.zip
Files
(6.0 MB)
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Additional details
Related works
- Is supplement to
- https://github.com/SysBioChalmers/yeast-GEM/tree/v8.4.0 (URL)