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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.
| selected citations These citations are derived from selected sources. This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically). | 1 | |
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