Code

Human 1.17#700

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haowang-bioinfo merged 211 commits intomainSysBioChalmers/Human-GEM:mainfrom developSysBioChalmers/Human-GEM:developCopy head branch name to clipboardSep 30, 2023

Commits

Commits on Sep 15, 2022

• fix: adapt simplifyGrRules to updates in Matlab children function

  JonathanRob

  committed
  8e05f05

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Commits on Jun 7, 2023

• fix: remove ubiquinone-dependent versions of all duplicated reactions but remove the FAD-dependent version of the SDH reaction

  Devlin-Moyer

  committed
  383970a

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• fix: update reactions data files

  Devlin-Moyer

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  924dd73

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• fix: deleted extra omap line that I missed when removing reactions earlier

  Devlin-Moyer

  committed
  676eaf2

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Commits on Jun 8, 2023

• fix: correct spelling errors in names of MAM00185c and MAM00185m

  Devlin-Moyer

  committed
  20076fc

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• fix: remove mitochondrial ACACB from GPRs of cytosolic MAR07672 and MAR07673

  Devlin-Moyer

  committed
  75b0170

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• fix: change subsystems for MAR07672 and MAR07673 to Fatty acid biosynthesis (even-chain)

  Devlin-Moyer

  committed
  1dfe54c

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• fix: remove MAR04156 for being redundant with MAR07672+MAR07673

  Devlin-Moyer

  committed
  d4caa65

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• fix: add new metabolite MAM01422m

  Devlin-Moyer

  committed
  a5c4d76

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• fix: edited MAR04295 to become mitochondrial version of MAR07673

  Devlin-Moyer

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  7965567

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• fix: made new reaction MAR20112 to represent mitochondrial version of MAR07672

  Devlin-Moyer

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  c799c7d

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• fix: made new reaction MAR20113 to transport MAM00185 between [c] and [m]

  Devlin-Moyer

  committed
  a52e66c

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• fix: resolved merge conflict in deprecatedReactions.tsv

  Devlin-Moyer

  committed
  ad198f7

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• fix: fixed typo in MAR20111 that was causing automated YAML validation to fail

  Devlin-Moyer

  committed
  6f266d4

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• fix: typo in model/reactions.tsv

  Devlin-Moyer

  committed
  dacbfca

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• fix: merge reactions

  Devlin-Moyer

  committed
  65bd88a

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• fix: add IVD to GPR of MAR03770

  Devlin-Moyer

  committed
  76edfde

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• fix: remove MAR11652, which I apparently forgot to do earlier

  Devlin-Moyer

  committed
  1b670e4

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• fix: moved MAR11651 from reactions.tsv to deprecatedReactions.tsv, which I apparently forgot to do earlier

  Devlin-Moyer

  committed
  37a92e5

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Commits on Jun 9, 2023

• fix: add references and EC codes from deleted reactions to duplicate kept reactions

  Devlin-Moyer

  committed
  f04966d

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• fix: merge annotations from deleted reactions into annotations for kept reactions in model/reactions.tsv

  Devlin-Moyer

  committed
  9269485

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• fix: remove MAR02369 for being redundant with MAR03149

  Devlin-Moyer

  committed
  f46d539

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• fix: merged references, EC codes, and GPRs of deleted reactions into kept ones

  Devlin-Moyer

  committed
  24a00d2

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• fix: merged annotations of removed reactions with kept ones in reactions.tsv

  Devlin-Moyer

  committed
  30a0613

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• feat: improve test output for unused entities

  mihai-sysbio

  committed
  f7f31f5

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Commits on Jun 13, 2023

• test: introduce a bug to see if it is picked up by the workflow

  mihai-sysbio

  authored
  db8ca8c

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• fix: typos introduced in #606

  Show description for e118e1d
  haowang-bioinfo

  committed
  e118e1d

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• test: revert back testYamlConversion to the original

  haowang-bioinfo

  committed
  3be0333

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Commits on Jun 14, 2023

• refactor: test yaml conversion

  mihai-sysbio

  committed
  5410ebf

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• fix: make reversible NTP <-> PPi reactions irreversible in PPi-production direction

  Devlin-Moyer

  committed
  7f4f02b

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• fix: swap products and reactants of PPi <-> -PP reactions then make them irreversible

  Devlin-Moyer

  committed
  fb0b757

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Commits on Jun 18, 2023

• fix-remove mets and rxns

  JHL-452b

  committed
  dbccdd2

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• fix-change BiGG ID annotations

  JHL-452b

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  e77f3e8

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• fix-replace mets

  JHL-452b

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  d3c6730

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• fix-remove mets and rxns

  JHL-452b

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  1ce3cb6

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• fix-change EHMN ID annotations

  JHL-452b

  committed
  b80232f

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• fix-change HMDB ID annotations

  JHL-452b

  committed
  b286a8c

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• fix-change LipidMaps ID annotations

  JHL-452b

  committed
  ba54838

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• fix-replace mets

  JHL-452b

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  72387a4

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Commits on Jun 19, 2023

• fix-replace mets

  JHL-452b

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  11a309f

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• fix-remove mets and rxns

  JHL-452b

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  6b5b0c8

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• fix-replace mets

  JHL-452b

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  880f906

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• Merge branch 'develop' into fix/merge_irrev_trans_pairs

  haowang-bioinfo

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  f4ba2e6

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• feat: fail action based on matlab exit code

  mihai-sysbio

  committed
  29113a1

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• revert: remove purposeful error

  mihai-sysbio

  authored
  927fb07

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• feat:add duplicated rxn and mets to the annotation list for further usage

  feiranl

  committed
  ce75e5a

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• fix: metabolic tasks fail visibly

  mihai-sysbio

  committed
  ba6a1c7

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• revert: purposeful error in metabolic tasks test

  mihai-sysbio

  authored
  741db2c

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• Merge pull request #625 from Devlin-Moyer/fix/merge_irrev_trans_pairs

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  haowang-bioinfo

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Commits on Jun 20, 2023

• fix: merge in latest develop branch

  Devlin-Moyer

  committed
  3b2dc0b

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• fix: resolve merge conflicts with latest develop branch

  Devlin-Moyer

  committed
  71a84e4

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• fix: removes MAR05310 for being duplicate of MAR06380 with wrong stoich & merges annotations for MAR05310 into annotations for MAR06380

  Devlin-Moyer

  committed
  b05a1a2

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• fix: replaces inaccurate GPRs of MAR06380 and MAR09887 with accurate ones

  Devlin-Moyer

  committed
  ccdb77f

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• fix: remove MAR02358 for being duplicate of MAR08482, merged annotations in reactions.tsv, and made MAR08482 reversible

  Devlin-Moyer

  committed
  84ff8a4

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• fix: remove MAR20066 for being duplicate of MAR03984 and merged their annotations

  Devlin-Moyer

  committed
  9fa2b5d

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• fix: remove MAR20020 for being duplicate of MAR04521 and merged their annotations

  Devlin-Moyer

  committed
  016eb86

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• fix: remove MAR20002 for being duplicate of MAR06631 and merged their annotations

  Devlin-Moyer

  committed
  910f5a5

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• fix: remove MAR00030 for being duplicate of MAR00025 and merged their annotations

  Devlin-Moyer

  committed
  b6fe43c

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• fix: remove MAR00032

  Devlin-Moyer

  committed
  bf2d32d

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• fix: removed MAR03767 and merged all annotations into MAR06421 and MAR06422

  Devlin-Moyer

  committed
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Commits on Jun 21, 2023

• feat-add MAM00853c to replace MAM00902c

  JHL-452b

  committed
  3b26f2f

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• fix-remove mets and rxns ID to 'Retired'

  JHL-452b

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  8c01de3

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• fix-remove mets ID to 'Retired'

  JHL-452b

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  f1b8974

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• fix-remove mets and rxns

  JHL-452b

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  873cd6a

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• fix-change KEGG ID annotations

  JHL-452b

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  b838738

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• fix-remove mets and rxns ID to 'Retired'

  JHL-452b

  committed
  e9275ad

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• fix-remove rxn

  JHL-452b

  committed
  cd671d5

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• feat-add MAM01729e to replace MAM03540e

  JHL-452b

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  359ce14

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• fix-replace mets

  JHL-452b

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  50dd63b

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• fix-change PubChem ID annotations

  JHL-452b

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  487965e

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• fix-remove mets and rxns ID to 'Retired'

  JHL-452b

  committed
  24ef6e6

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• feat-add MAM01435m to replace MAM03318m

  JHL-452b

  committed
  eb8082a

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• fix-remove mets and rxns ID to 'Retired'

  JHL-452b

  committed
  c5ec7fc

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• Merge pull request #613 from Devlin-Moyer/fix/FAD_ubiquinone_duplicates

  Show description for c3c99f8
  haowang-bioinfo

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  c3c99f8

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• fix: replace inaccurate GPR of MAR01527 and add new gene entries for several sodium channels

  Devlin-Moyer

  committed
  aa84229

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• fix: added new rows to genes.tsv for new genes

  Devlin-Moyer

  committed
  d6ea247

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• fix: added info for new genes to genes.tsv

  Devlin-Moyer

  committed
  eb4d76d

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Commits on Jun 22, 2023

• Merge pull request #494 from SysBioChalmers/fix/simplifyGrRules

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  mihai-sysbio

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  edfaf28

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Commits on Jun 23, 2023

• feat: log duplicated ids to the column of rxnRetired

  haowang-bioinfo

  committed
  29734c6

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• fix: correct misplaced retired reaction ID

  haowang-bioinfo

  committed
  9ce2c5c

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• fix: add MAR03783 as a duplicate for MAR03784

  haowang-bioinfo

  committed
  add54ab

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Commits on Jun 25, 2023

• fix-change ChEBI ID annotations

  JHL-452b

  committed
  e3d758e

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• Merge pull request #663 from JHL-452b/fix-HMDB

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  feiranl

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  cece33f

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• fix-replace mets

  JHL-452b

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  7436a50

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• Merge branch 'develop' into pr/661

  feiranl

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  063150f

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• fix-bug with the space

  feiranl

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  51e727b

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• fix-bug: removing the empty line

  feiranl

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  d4db948

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• fix-bug: introduced in the merge develop branch

  feiranl

  committed
  2fafe26

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• Merge branch 'develop' into feat/logDeprecatedIDsIn#613

  haowang-bioinfo

  committed
  63c5e7d

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• Merge pull request #661 from JHL-452b/fix-KEGG(2)

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  feiranl

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  cecf059

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• Merge branch 'develop' into feat/logDeprecatedIDsIn#613

  haowang-bioinfo

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• Merge branch 'develop' into pr/667

  feiranl

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  954fe1a

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• Merge pull request #667 from JHL-452b/fix-ChEBI(2)

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  feiranl

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  c958319

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• Merge pull request #666 from SysBioChalmers/feat/logDeprecatedIDsIn#613

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  haowang-bioinfo

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• Merge branch 'develop' into fix/remove_MAR03767

  haowang-bioinfo

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  99eb40d

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• fix: re-remove MAR03767

  haowang-bioinfo

  committed
  bcb30ee

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• log: update duplication info to rxnRetired column

  haowang-bioinfo

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Commits on Jun 26, 2023

• Merge branch 'develop' into pr/662

  feiranl

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• Merge pull request #662 from JHL-452b/fix-PubChem(2)

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  feiranl

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• Merge branch 'develop' into pr/646

  feiranl

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  bf8894f

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• Merge branch 'develop' into fix-BiGG

  feiranl

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  952203f

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• Merge pull request #646 from JHL-452b/fix-BiGG

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  feiranl

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• Merge branch 'develop' into fix-EHMN

  JHL-452b

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• fix-metabolites for model load

  JHL-452b

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  44410f4

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• fix-metabolites for model load(2)

  JHL-452b

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  4300b6b

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• Merge branch 'develop' into fix-LipidMaps

  JHL-452b

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  afdcec2

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• fix-update annotation of ‘MAM00131r’

  JHL-452b

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  4f98cd4

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• Merge pull request #649 from JHL-452b/fix-EHMN

  Show description for 4443e39
  haowang-bioinfo

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  4443e39

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• Merge branch 'develop' into fix/remove_MAR03767

  haowang-bioinfo

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• Merge pull request #660 from SysBioChalmers/fix/remove_MAR03767

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  haowang-bioinfo

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Commits on Jun 27, 2023

• Merge branch 'develop' into fix-LipidMaps

  JHL-452b

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  209e86f

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• fix: merge in latest develop branch

  Devlin-Moyer

  committed
  36ccd03

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• fix: added MAR04156 to retiredRxn column for MAR07672 and MAR07673 in model/reactions.tsv

  Devlin-Moyer

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  ae122fd

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• fix: merge in latest develop branch

  Devlin-Moyer

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  461e7c8

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• fix: remove genes that were only associated with MAR00032 and no other reactions

  Devlin-Moyer

  committed
  0567fa7

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• fix: remove MAR01630 and merge annotations with MAR01629

  Devlin-Moyer

  committed
  c041233

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• fix: remove MAR01635 and merge annotations with MAR01632

  Devlin-Moyer

  committed
  44e02a9

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• fix: remove MAR01637 and merge annotations with MAR01639 and MAR01638

  Devlin-Moyer

  committed
  8ffccca

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• fix: remove MAR01644 and merge annotations with MAR01642

  Devlin-Moyer

  committed
  0e7c587

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• fix: add BiGG id to MAM01422m

  haowang-bioinfo

  authored
  a6f4142

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• fix: remove MAR01651 and merge annotations into MAR01646

  Devlin-Moyer

  committed
  7007f8d

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• fix: remove MAR01653 and merge annotations into MAR01652

  Devlin-Moyer

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  cedbdfb

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• fix: remove MAR03754 and merge annotations into MAR03756

  Devlin-Moyer

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  08b5d74

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• fix: remove MAR03760 and merge annotations into MAR03764

  Devlin-Moyer

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  a27dd4a

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• Merge pull request #624 from Devlin-Moyer/fix/acCoA_carboxylase_rxns

  Show description for 4670c79
  haowang-bioinfo

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• test: re-introduce bug to Yaml file

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  haowang-bioinfo

  committed
  97d030b

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• fix: remove MAR07785

  Devlin-Moyer

  committed
  26752ff

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• fix: remove MAR01662 and merge annotations into MAR01663

  Devlin-Moyer

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  7a863f6

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• fix: remove MAR01666 and merge annotations into MAR01665

  Devlin-Moyer

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  90c1c9c

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• fix: remove MAR01458 and merge annotations (except wrong EC number) into MAR01642 and MAR01646

  Devlin-Moyer

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  7ee5d45

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• fix: remove now-isolated metabolites

  Devlin-Moyer

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  26f78d3

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• merge in latest develop branch

  Devlin-Moyer

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  61a511e

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• fix: removed more isolated metabolites I missed the first time

  Devlin-Moyer

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  bf407b5

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• merge in latest develop branch

  Devlin-Moyer

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  4774704

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• fix: removed genes that were only associated with MAR00030

  Devlin-Moyer

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  3b21f6f

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• merge in latest develop branch

  Devlin-Moyer

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  30b93f6

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• fix: add MAR05310 to rxnRetired column for MAR06380 in model/reactions.tsv

  Devlin-Moyer

  committed
  100ce85

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• fix: removed MAR01639 and merged annotations into MAR01638

  Devlin-Moyer

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  c818b08

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• fix: removed MAR03301 and merged annotations into MAR02804

  Devlin-Moyer

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  fb0ea6c

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• fix: removed MAR03306 and merged annotations into MAR02808

  Devlin-Moyer

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  fdaa58c

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• fix: removed MAR03311 and merged annotations into MAR02810

  Devlin-Moyer

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  5c594ab

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• fix: removed MAR04966 and merged annotations into MAR02818

  Devlin-Moyer

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  c459bce

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• fix: removed MAR03364 and merged annotations into MAR03276

  Devlin-Moyer

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  af6e183

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• fix: removed MAR03369 and merged annotations into MAR03289

  Devlin-Moyer

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  e20af6d

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• fix: reversed MAR00059 and removed the 0.5 O2 that shouldn't've been there

  Devlin-Moyer

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• feat: added MAR20114 to represent reduction of O2 by FADH2 in peroxisomes

  Devlin-Moyer

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• fix: replaced O2 with FAD and H2O2 with FADH2 in all peroxisomal reactions that contained O2 and H2O2

  Devlin-Moyer

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Commits on Jun 28, 2023

• Merge pull request #650 from JHL-452b/fix-LipidMaps

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  feiranl

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• Merge pull request #641 from Devlin-Moyer/fix/ppi_rxns_round_2

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  feiranl

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• fix: catch all potential errors in yaml conversion workflow

  mihai-sysbio

  committed
  6e5d66c

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Commits on Jul 2, 2023

• Merge pull request #658 from SysBioChalmers/fix/remove_lipid_droplet_loop

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  haowang-bioinfo

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Commits on Jul 3, 2023

• test: replicate Yaml bug reported in #6286

  haowang-bioinfo

  committed
  5f39c61

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Commits on Jul 4, 2023

• feat: add basic memote test

  mihai-sysbio

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Commits on Jul 5, 2023

• Merge pull request #672 from SysBioChalmers/fix/yaml-test-bug

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  mihai-sysbio

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• make MAR06380 reversible

  Devlin-Moyer

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  d604989

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• fix: remove MAR09887 and merge annotations into MAR06896

  Devlin-Moyer

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  2d59575

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• fix: merge in latest develop branch

  Devlin-Moyer

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• fix: typos & mistakes pointed out by reviewers

  Devlin-Moyer

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  2fd4b94

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• chore: merge in latest develop branch

  Devlin-Moyer

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• fix: only keep most accurate EC numbers for MAR04521 and MAR03984

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• chore: merge in latest develop branch

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Commits on Jul 6, 2023

• Merge pull request #655 from SysBioChalmers/fix/sodium_cotransport_gprs

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• refactor: use warning instead of disp in matlab tests

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• fix: retain MAR08482 in its original form

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• Merge branch 'develop' into fix/same_stoich_diff_gpr_dupes

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• log: update retired duplicate reaction ids

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• Merge pull request #657 from SysBioChalmers/fix/same_stoich_diff_gpr_dupes

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Commits on Jul 7, 2023

• test: revert typo purposely introduced to the "metabolites" key

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• test: revert typo purposely introduced to id MAM01261m

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• Merge pull request #635 from SysBioChalmers/fix/importExportCycle

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• Merge branch 'develop' into fix/sodium_channel_genes

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Commits on Jul 10, 2023

• refactor: improve test output in test workflow

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Commits on Jul 16, 2023

• fix: made MAR04145 irreversible and added textbook reference to rxnNotes

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• fix: merged MAR01515 into MAR08529

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• fix: merged MAR00039 into MAR07992

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• fix: merged MAR00096 into MAR04819

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• fix: merged MAR02027 into MAR0302

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• fix: merged MAR02006 into MAR03873

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• fix: remove all reactions involving MAM01268 or MAR02757 in all compartments

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• fix: remove now-isolated MAM01816n

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• fix: remove all genes that were only associated with PPARA reactions

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Commits on Jul 19, 2023

• Merge pull request #676 from SysBioChalmers/fix/citrate_synthase

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• chore: merge in latest develop branch

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• chore: merge in latest develop branch

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Commits on Jul 21, 2023

• Merge pull request #677 from SysBioChalmers/fix/ammonium-ammonia_duplicates

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Commits on Jul 28, 2023

• chore: merge in latest develop branch

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• chore: merge in latest develop branch

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Commits on Aug 1, 2023

• Merge pull request #678 from SysBioChalmers/fix/remove_ppara_rxns

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• Merge branch 'develop' into fix/sodium_channel_genes

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• fix: added in some genes I missed the first time

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• fix: add new gene entries for new genes

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• fix: update model/genes.tsv

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Commits on Aug 2, 2023

• fix: AND together SCNN1A, SCNN1B, and SCNN1G since they form a trimer

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• feat: added refs for SCNN1A/B/G/D complex/isozyme situation

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Commits on Aug 3, 2023

• Merge pull request #664 from SysBioChalmers/fix/sodium_channel_genes

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Commits on Aug 16, 2023

• fix: sync geneShortNames field with genes field

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• feat: enable the option to reset biomass equation or not

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Commits on Aug 17, 2023

• Update code/updateAnimalGEM.m

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Commits on Aug 18, 2023

• fix: ensure b field in single column

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Commits on Aug 21, 2023

• Merge pull request #692 from SysBioChalmers/fix/refineAnimalGemPipeline

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• doc: do not treat mito-version rxns as duplicates to peroxisome ones

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• Merge pull request #669 from SysBioChalmers/fix/remove_mito_bile_acid_synth

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Commits on Aug 29, 2023

• fix: update name for GAP

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• Merge pull request #696 from exaexa/mk-fix-gap

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Commits on Sep 20, 2023

• Merge branch 'develop' into fix/FAD_O2_dupes

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• fix: re-remove duplicated reaction MAR01639

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• fix: re-remove deprecated reactions from "reactions.tsv"

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Commits on Sep 21, 2023

• fix: removed MAR00059 for being less accurate version of MAR01706

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• Fixed GPR of MAR01706 and added reference

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• chore: resolve merge conflicts

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Commits on Sep 24, 2023

• Merge pull request #670 from SysBioChalmers/fix/FAD_O2_dupes

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