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yeast 8.4.0#229

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BenjaSanchez merged 79 commits intomasterSysBioChalmers/yeast-GEM:masterfrom develSysBioChalmers/yeast-GEM:develCopy head branch name to clipboardJun 15, 2020

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Commits on Mar 15, 2019

• feat-met.BiGGID: add BiGG identifiers for metabolites and reactions

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Commits on Apr 21, 2020

• test: model properly loaded by cobrapy

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• fix: replace proteins with geneNames

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Commits on Apr 24, 2020

• Merge pull request #216 from SysBioChalmers/fix/gene-names

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• Revert "feat-met.BiGGID: add BiGG identifiers for metabolites and reactions"

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Commits on Apr 27, 2020

• Merge branch 'devel' into feat/bigg_compliance

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• fix-met.annot: KEGG id

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Commits on Apr 28, 2020

• fix-rxn: remove duplicated rxns

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Commits on Apr 29, 2020

• feat: BiGG dictionaries

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Commits on May 16, 2020

• fix-rxn.annot: correct reaction IDs and add new reaction IDs (MetaNetX and KEGG)

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• fix-met.annot: correct metabolite IDs and add new metabolite IDs (MetaNetX, KEGG and ChEBI)

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• feat-rxn.annot: added new rxnKEGGIDs into model via ID mapping

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• feat-met.annot: added new metKEGGIDs into model via ID mapping

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• feat-met.annot: added new metMetaNetXID into model via ID mapping

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• fix-met.annot: remove metabolite ID with modifyID.m and correct modifyID.tsv

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• style: change notes annotation in modifyID.m to PR (#220)

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• Update README.md

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Commits on May 17, 2020

• style-rxn.prop: shorten rxnNotes added in modifyID.m

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• fix-rxn.annot: correct rxnName

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• style-met.prop: shorten metNotes added in modifyID.tsv

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Commits on May 18, 2020

• feat: add .gitattributes for unified line endings

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Commits on May 19, 2020

• fix: update .gitattributes

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• fix: normalize all line endings

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• feat: add checks for MetaCyc/modelSEED data import in mapKEGGID.m

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• fix: improve indexing in mapMNXMID.m

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• Revert line endings commits

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• feat: specify EOL behaviour in gitattributes

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• Merge pull request #221 from SysBioChalmers/fix/normalizeLineEndings

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• Merge remote-tracking branch 'origin/devel' into fix/update_IDs

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• Merge branch 'devel' into feat/bigg_compliance

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• fix-data: split BiGG files in two separate lists

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• fix-data: remove helper lists

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• fix-data: remove compartment info from met BiGG dict

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• fix-data: keep original compartment abbreviations

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• fix-data: automatic lipid id generation

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• fix-data: manual lipid id curation

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• fix-data: remove copy suffix from rxn BiGG dict

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• style: minor formatting changes in mapKEGGID.m and mapMNXMID.m

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• fix: resolve issue with shortening rxnNotes and metNotes

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Commits on May 20, 2020

• fix-data: redefine BiGG ids for SLIME rxns

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• fix-data: exchange rxn notation in BiGG dict with new ids

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• fix-data: pseudo-mets & pseudo-rxns in both BiGG dicts

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• fix: cd back to the original filefolder at the end

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• Merge pull request #220 from SysBioChalmers/fix/update_IDs

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• fix-data: ER membrane notation in rxns

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• fix: changes to .gitignore

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• fix-data: simple transport notation for rxn BiGG ids

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Commits on May 21, 2020

• Merge branch 'devel' into feat/bigg_compliance

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• fix-data: rename compartments in new rxn ids in BiGG dict

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• fix-data: misc manual fixes in new rxn BiGG dict

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• fix-data: remove redundant chain position in new rxn BiGG dict

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• chore: update cobratoolbox/RAVEN

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Commits on May 25, 2020

• feat: met+rxn BiGG ids

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Commits on May 26, 2020

• feat: automatic curation of reactions via MetaNetX reac_prop.tsv

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Commits on May 27, 2020

• fix-rxn: balance reaction via modification of metabolite formula and charges

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• fix-rxn: balance reaction via modification of model.S

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• fix: remove requirement of coenzyme A in biomass equation for anaerobic model

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• Merge pull request #188 from SysBioChalmers/feat/bigg_compliance

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• Merge branch 'devel' into fix/unbalanced_rxns

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• feat: better python io functions

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• test: check if model changes with cobrapy

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• fix: cd to the right filefolder

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• style: remove repetitive codes

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Commits on May 28, 2020

• feat: BiGG compliance flag in read_yeast_model

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• feat: load missing ids from bigg dicts

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• fix: add exception for repeated BiGG ids

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• fix: revert back to original matlab-compliant model

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Commits on May 29, 2020

• doc: add description for output

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• fix: indexing issues when updating model.S

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• fix: -R4 in TRX1

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Commits on Jun 1, 2020

• fix: resolve unbalanced rxns due to H+/H2O

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Commits on Jun 5, 2020

• fix-bug for wrong mets in the readme

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• chore-cd to the right folder

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• feat-update the model with the balance of H+/H2O

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Commits on Jun 7, 2020

• doc: rename to avoid conflict with COBRA function

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• feat: display_rxnMetInfo.m to facilitate curation of reaction balance

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Commits on Jun 10, 2020

• Merge pull request #224 from SysBioChalmers/feat/python-compatibility

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Commits on Jun 12, 2020

• Merge pull request #222 from SysBioChalmers/fix/unbalanced_rxns

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• chore: update dependencies

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