Code

yeast 8.4.0#229

Code

Merged

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

+29,657-6,737

Commits

Commits on Mar 15, 2019

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

  snmendoz

  committed
  3b83df2

Commits on Apr 21, 2020

• test: model properly loaded by cobrapy

  Show description for 52c24ab
  BenjaSanchez

  committed
  52c24ab

• fix: replace proteins with geneNames

  Show description for 434d240
  BenjaSanchez

  committed
  434d240

Commits on Apr 24, 2020

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

  Show description for 4722c45
  BenjaSanchez

  authored
  4722c45

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

  Show description for 325be62
  BenjaSanchez

  committed
  325be62

Commits on Apr 27, 2020

• Merge branch 'devel' into feat/bigg_compliance

  BenjaSanchez

  committed
  0a8150a

• fix-met.annot: KEGG id

  Show description for ff435cb
  

  BenjaSanchez

  and

  snmendoz

  committed
  ff435cb

Commits on Apr 28, 2020

• fix-rxn: remove duplicated rxns

  Show description for 4785040
  

  BenjaSanchez

  and

  snmendoz

  committed
  4785040

Commits on Apr 29, 2020

• feat: BiGG dictionaries

  Show description for 93d99ca
  

  BenjaSanchez

  and

  snmendoz

  committed
  93d99ca

Commits on May 16, 2020

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

  Show description for 6f593ef
  eiden309

  committed
  6f593ef

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

  Show description for 48df2c6
  eiden309

  committed
  48df2c6

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

  Show description for 001c5a5
  eiden309

  committed
  001c5a5

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

  Show description for 22eab97
  eiden309

  committed
  22eab97

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

  Show description for ce55eeb
  eiden309

  committed
  ce55eeb

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

  Show description for b3418ad
  eiden309

  committed
  b3418ad

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

  Show description for 76846e1
  eiden309

  committed
  76846e1

• Update README.md

  edkerk

  authored
  f0687d8

Commits on May 17, 2020

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

  Show description for b3deb51
  

  eiden309

  and

  edkerk

  authored
  b3deb51

• fix-rxn.annot: correct rxnName

  Show description for 859e2ab
  

  eiden309

  and

  edkerk

  authored
  859e2ab

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

  Show description for daa5737
  

  eiden309

  and

  edkerk

  authored
  daa5737

Commits on May 18, 2020

• feat: add .gitattributes for unified line endings

  eiden309

  committed
  029b34d

Commits on May 19, 2020

• fix: update .gitattributes

  eiden309

  committed
  77906f8

• fix: normalize all line endings

  eiden309

  committed
  682263d

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

  Show description for b8a5d32
  eiden309

  committed
  b8a5d32

• fix: improve indexing in mapMNXMID.m

  eiden309

  committed
  80ff31a

• Revert line endings commits

  Show description for f28c99f
  edkerk

  committed
  f28c99f

• feat: specify EOL behaviour in gitattributes

  Show description for 67a5b4e
  

  edkerk

  and

  eiden309

  committed
  67a5b4e

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

  Show description for 248d2be
  edkerk

  authored
  248d2be

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

  edkerk

  committed
  eadc9f8

• Merge branch 'devel' into feat/bigg_compliance

  BenjaSanchez

  committed
  24570ce

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

  Show description for d21cae3
  

  BenjaSanchez

  and

  snmendoz

  committed
  d21cae3

• fix-data: remove helper lists

  Show description for 5132b88
  BenjaSanchez

  committed
  5132b88

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

  Show description for cdbd689
  BenjaSanchez

  committed
  cdbd689

• fix-data: keep original compartment abbreviations

  Show description for e533f93
  BenjaSanchez

  committed
  e533f93

• fix-data: automatic lipid id generation

  Show description for ef49b1e
  BenjaSanchez

  committed
  ef49b1e

• fix-data: manual lipid id curation

  Show description for 71f8217
  BenjaSanchez

  committed
  71f8217

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

  Show description for 1987a59
  BenjaSanchez

  committed
  1987a59

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

  eiden309

  committed
  2d09bc9

• fix: resolve issue with shortening rxnNotes and metNotes

  eiden309

  committed
  c41e0ec

Commits on May 20, 2020

• fix-data: redefine BiGG ids for SLIME rxns

  Show description for dc4ecc2
  BenjaSanchez

  committed
  dc4ecc2

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

  Show description for 5784e29
  BenjaSanchez

  committed
  5784e29

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

  Show description for d98fa22
  BenjaSanchez

  committed
  d98fa22

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

  feiranl

  committed
  6290b49

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

  Show description for 14a3b7b
  BenjaSanchez

  authored
  14a3b7b

• fix-data: ER membrane notation in rxns

  Show description for 0f2a766
  BenjaSanchez

  committed
  0f2a766

• fix: changes to .gitignore

  Show description for 219203e
  BenjaSanchez

  committed
  219203e

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

  Show description for d35822e
  BenjaSanchez

  committed
  d35822e

Commits on May 21, 2020

• Merge branch 'devel' into feat/bigg_compliance

  BenjaSanchez

  committed
  87785e3

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

  Show description for 037c93f
  BenjaSanchez

  committed
  037c93f

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

  Show description for 59b6d88
  BenjaSanchez

  committed
  59b6d88

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

  Show description for 8a51b6f
  BenjaSanchez

  committed
  8a51b6f

• chore: update cobratoolbox/RAVEN

  Show description for 8ed678f
  BenjaSanchez

  committed
  8ed678f

Commits on May 25, 2020

• feat: met+rxn BiGG ids

  Show description for 5ffdb0d
  

  BenjaSanchez

  and

  snmendoz

  committed
  5ffdb0d

Commits on May 26, 2020

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

  eiden309

  committed
  7f72dea

Commits on May 27, 2020

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

  eiden309

  committed
  89fb8a3

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

  eiden309

  committed
  cd8a356

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

  eiden309

  committed
  35600d9

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

  Show description for 8444355
  BenjaSanchez

  authored
  8444355

• Merge branch 'devel' into fix/unbalanced_rxns

  BenjaSanchez

  committed
  1f7c113

• feat: better python io functions

  Show description for e1d1945
  BenjaSanchez

  committed
  e1d1945

• test: check if model changes with cobrapy

  Show description for 3963759
  BenjaSanchez

  committed
  3963759

• fix: cd to the right filefolder

  feiranl

  committed
  9469493

• style: remove repetitive codes

  feiranl

  committed
  a81a2cf

Commits on May 28, 2020

• feat: BiGG compliance flag in read_yeast_model

  Show description for 8ccaa3e
  BenjaSanchez

  committed
  8ccaa3e

• feat: load missing ids from bigg dicts

  Show description for 9b0ec0a
  BenjaSanchez

  committed
  9b0ec0a

• fix: add exception for repeated BiGG ids

  Show description for 32e3391
  BenjaSanchez

  committed
  32e3391

• fix: revert back to original matlab-compliant model

  Show description for eb459aa
  BenjaSanchez

  committed
  eb459aa

Commits on May 29, 2020

• doc: add description for output

  eiden309

  committed
  60342ad

• fix: indexing issues when updating model.S

  eiden309

  committed
  53c81d9

• fix: -R4 in TRX1

  edkerk

  committed
  17d84c9

Commits on Jun 1, 2020

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

  eiden309

  committed
  1979871

Commits on Jun 5, 2020

• fix-bug for wrong mets in the readme

  feiranl

  committed
  57e0cab

• chore-cd to the right folder

  feiranl

  committed
  afcb9fe

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

  feiranl

  committed
  e6205e9

Commits on Jun 7, 2020

• doc: rename to avoid conflict with COBRA function

  eiden309

  committed
  15e6ccb

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

  eiden309

  committed
  2ef9281

Commits on Jun 10, 2020

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

  Show description for 984dca1
  BenjaSanchez

  authored
  984dca1

Commits on Jun 12, 2020

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

  Show description for 39ada1b
  BenjaSanchez

  authored
  39ada1b

• chore: update dependencies

  Show description for 9e36261
  BenjaSanchez

  committed
  9e36261