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 keep BiGG ids.
mapKEGGID.mandmapMNXMID.mfor adding ids in model. Used them to add missing KEGG and MetaNetX ids for both metabolites and reactions (PR #220).read_yeast_modelandwrite_yeast_modelfor easier usage in python (PR #224).checkSmatrixMNX.m, bringing the number down to 17 reactions (PR #222).LFas EOL character (PR #221).NOTE: This release was made with the development version of COBRA toolbox, as the latest release is not able to keep BiGG ids.