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yeast 8.4.0
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@BenjaSanchez BenjaSanchez released this 15 Jun 11:06
v8.4.0
1ed4e7c
  • 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.

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