Code

Human 1.18#735

Code

Merged

haowang-bioinfo merged 140 commits intomainSysBioChalmers/Human-GEM:mainfrom developSysBioChalmers/Human-GEM:developCopy head branch name to clipboardDec 8, 2023

+1,494-964

Commits

Commits on Mar 23, 2023

• chore: bump workflow dependency version

  mihai-sysbio

  committed
  88ca1a6

Commits on May 10, 2023

• Merge branch 'develop' into chore/update-workflow

  mihai-sysbio

  committed
  37c22cc

Commits on May 25, 2023

• feat-add the duplicate rxn check

  feiranl

  committed
  655053e

• refactor: separate assert statement from error message output

  haowang-bioinfo

  committed
  b12fece

Commits on May 26, 2023

• fix-give better output

  feiranl

  committed
  38c0b8b

Commits on Jul 4, 2023

• Merge branch 'develop' into chore/update-workflow

  mihai-sysbio

  committed
  6607e00

Commits on Jul 28, 2023

• fix: remove MAR06400 for being a less accurate duplicate of MAR06403

  Devlin-Moyer

  committed
  ce1c33c

• fix: remove MAR06401 for being a duplicate of MAR06402

  Devlin-Moyer

  committed
  83aab80

• fix: remove MAM02397c

  Devlin-Moyer

  committed
  a9e732a

• fix: update metabolite annotation files

  Devlin-Moyer

  committed
  a171e17

Commits on Aug 22, 2023

• chore: merge in latest develop branch

  Devlin-Moyer

  committed
  4e4cfe7

Commits on Aug 30, 2023

• fix NA[c] in metabolic tasks

  exaexa

  committed
  58da84b

Commits on Sep 27, 2023

• remove MAR07785 for being a duplicate of MAR04908

  Devlin-Moyer

  committed
  d8a9b18

• remove MAR07775 and MAR07788

  Devlin-Moyer

  committed
  27f64cb

• remove MAR04915, MAR07782, MAR07783, and MAR07790

  Devlin-Moyer

  committed
  e0ff4dd

• edit MAR03473 to exchange AMP for ADP instead of ATP & update references

  Devlin-Moyer

  committed
  5748afd

• add reactions for solo transport of AMP and ADP by SLC25A17

  Devlin-Moyer

  committed
  77dfff2

• add peroxisomal FMN metabolite

  Devlin-Moyer

  committed
  1f54fc0

• add peroxisomal hydrolysis of FAD to FMN + AMP by NUDT12

  Devlin-Moyer

  committed
  40dac08

• add other SLC25A17-mediated antiport reactions

  Devlin-Moyer

  committed
  e1c4003

• remove MAR03940 for being redundant with MAR08539+MAR08538

  Devlin-Moyer

  committed
  1697383

Commits on Sep 29, 2023

• fix: added missing eccodes entries to new reactions

  Devlin-Moyer

  committed
  4030753

Commits on Oct 2, 2023

• Merge pull request #702 from SysBioChalmers/fix/remove_MAR03940

  Show description for 4af2c44
  haowang-bioinfo

  authored
  4af2c44

Commits on Oct 5, 2023

• style: merge "Heme biosynthesis" subsystem into "Porphyrin metabolism"

  haowang-bioinfo

  committed
  72d3237

Commits on Oct 6, 2023

• Merge branch 'develop' into chore/update-workflow

  mihai-sysbio

  committed
  a8e5852

• chore: use action fork

  mihai-sysbio

  committed
  379d03d

Commits on Oct 7, 2023

• Merge pull request #703 from SysBioChalmers/mergeMultiSubsystems

  Show description for 0c8bdd1
  feiranl

  authored
  0c8bdd1

• Merge branch 'develop' into fix/perox_cofactor_trans

  feiranl

  authored
  739cbd2

Commits on Oct 8, 2023

• fix: comment-out tasks 37, 38, and 181 by adding hash tag

  haowang-bioinfo

  authored
  6f436d9

• fix: rebalance MAR20117

  haowang-bioinfo

  committed
  3eb0817

• doc: add explanation why comment-off the 3 tasks

  haowang-bioinfo

  authored
  7ec4322

Commits on Oct 9, 2023

• Merge pull request #701 from SysBioChalmers/fix/perox_cofactor_trans

  Show description for dc5ce9c
  feiranl

  authored
  dc5ce9c

Commits on Oct 14, 2023

• fix: remove ENSG00000159423 from MAR00051

  Show description for dcc2690
  haowang-bioinfo

  committed
  dcc2690

• fix: remove MAR08564 and MAR08565

  Show description for 1eb71c6
  haowang-bioinfo

  committed
  1eb71c6

• fix: remove ENSG00000109576 from MAR04222

  Show description for f739d41
  haowang-bioinfo

  committed
  f739d41

• doc: sync deletion of MAR08564+MAR08565 to data files

  haowang-bioinfo

  committed
  34c2da9

• fix/doc: make MAR04222 and MAR02765 irreversible based on Uniprot

  Show description for e503177
  haowang-bioinfo

  committed
  e503177

• doc: sync deletion of MAM00926c

  Show description for ca672c9
  haowang-bioinfo

  committed
  ca672c9

• fix: removed MAR01483 and MAR06406 for being duplicates of MAR09608 and merged annotations accordingly

  Devlin-Moyer

  committed
  94d6b14

• feat: updated references and added RHEA IDs for MAR09608

  Devlin-Moyer

  committed
  6e1c87a

• chore: merge in latest develop branch

  Devlin-Moyer

  committed
  d00cb22

• fix: accidentally swapped master and direction-specific RHEA IDs in annotations for MAR09608

  Devlin-Moyer

  committed
  d33211d

• feat: added direction-specific RHEA IDs for MAR06402 and MAR06403

  Devlin-Moyer

  committed
  4dcfc78

Commits on Oct 16, 2023

• Merge pull request #708 from SysBioChalmers/fix/refineTrpRxnGPRs

  Show description for 4d59404
  feiranl

  authored
  4d59404

• Merge branch 'develop' into fix/dupe_lipoate_biosynth

  feiranl

  authored
  4e7dad2

• Merge branch 'develop' into fix/lipoate_transport

  feiranl

  authored
  de7fece

• fix: added removed reactions to rxnRetired column for MAR09608 in reactions.tsv

  Devlin-Moyer

  committed
  bc6d7b6

• Merge pull request #706 from SysBioChalmers/fix/lipoate_transport

  Show description for 04837d1
  haowang-bioinfo

  authored
  04837d1

• Merge branch 'develop' into fix/dupe_lipoate_biosynth

  haowang-bioinfo

  committed
  7ca9471

• doc: update Rhea ids for MAR01706

  Show description for 01a5d1e
  haowang-bioinfo

  committed
  01a5d1e

• feat: add new reactions representing transport activities of SLC25A33 and SLC25A36

  Devlin-Moyer

  committed
  df1afb8

• feat: add new gene entries for SLC25A33 and SLC25A36

  Devlin-Moyer

  committed
  d5d76ec

• fix: made MAR08301 reversible, associated it with SLC25A36, and updated its references

  Devlin-Moyer

  committed
  8e11d3a

• fix: removed MAR04843, MAR07823, MAR07926, and MAR09019 for being unsupported by evidence

  Devlin-Moyer

  committed
  a7a9252

Commits on Oct 17, 2023

• fix: YAML formatting issue

  Devlin-Moyer

  committed
  37eaf10

• chore: merge in latest develop branch

  Devlin-Moyer

  committed
  57e949a

• fix: typo in metabolite ID for dTDP in MAR20162

  Devlin-Moyer

  committed
  312813e

• fix: two of the new reactions had the same ID

  Devlin-Moyer

  committed
  b86c4b3

• fix: forgot to add new rows to model/genes.tsv for SLC25A33 and SLC25A36

  Devlin-Moyer

  committed
  5b3d379

• fix: removed MAR00478 and MAR00482 for being less-accurate versions of MAR00479 and MAR01169, respectively

  Devlin-Moyer

  committed
  5de6e05

• fix: add ref from MAR00478 to refs for MAR00479

  Devlin-Moyer

  committed
  43e354d

• Merge pull request #707 from SysBioChalmers/fix/dupe_lipoate_biosynth

  Show description for 1138c5c
  haowang-bioinfo

  authored
  1138c5c

• Merge pull request #697 from exaexa/mk-fix-na

  Show description for 9f79bdd
  haowang-bioinfo

  authored
  9f79bdd

Commits on Oct 18, 2023

• fix: two of the new reactions were accidentally identical

  Devlin-Moyer

  committed
  402ecb6

• Merge pull request #710 from SysBioChalmers/fix/duplicate_glyc3P_DH_rxns

  Show description for baa778e
  haowang-bioinfo

  authored
  baa778e

Commits on Oct 19, 2023

• Merge branch 'develop' into feat-duplicateRxnCheck

  haowang-bioinfo

  committed
  bf822e6

• fix: remove duplicate rxns MAR20012 and MAR20089

  Show description for 8efc016
  haowang-bioinfo

  committed
  8efc016

• doc: merge annotations into reactions.tsv

  haowang-bioinfo

  committed
  1a0c3a7

• fix: merge GPRs of MAR06646 and MAR20012

  haowang-bioinfo

  committed
  9258fd5

• Merge pull request #582 from SysBioChalmers/feat-duplicateRxnCheck

  Show description for 4f9ec7a
  haowang-bioinfo

  authored
  4f9ec7a

• Merge branch 'develop' into fix/mito_nuc_trans

  haowang-bioinfo

  committed
  0526913

• fix: removed MAR20166 and renamed MAR20167 to MAR20166 cuz MAR20166 duplicated MAR08301

  Devlin-Moyer

  committed
  d5a281c

Commits on Oct 20, 2023

• Merge pull request #709 from SysBioChalmers/fix/mito_nuc_trans

  Show description for d6c9fe8
  haowang-bioinfo

  authored
  d6c9fe8

• Merge branch 'develop' into chore/update-workflow

  haowang-bioinfo

  committed
  ef939b7

• Merge pull request #512 from SysBioChalmers/chore/update-workflow

  Show description for 5ed02a0
  mihai-sysbio

  authored
  5ed02a0

• fix: set all FMN metabolite base IDs to MAM01828 and formulas to C17H19N4O9P

  Devlin-Moyer

  committed
  c6dd304

• fix: changed ID of MAM20022i to MAM20019i to match MAM20019r

  Devlin-Moyer

  committed
  faf04e8

• feat: added KEGG IDs to FMN and FMNH2 metabolites that were missing one

  Devlin-Moyer

  committed
  4b41a2d

• fix: added rows to deprecatedMetabolites.tsv for re-IDed FMN(H2) metabolites and added old IDs to metRetired column of metabolites.tsv

  Devlin-Moyer

  committed
  2e9c729

Commits on Oct 23, 2023

• Merge pull request #712 from SysBioChalmers/fix/fmn_fmnh2_ids

  Show description for 84198f7
  haowang-bioinfo

  authored
  84198f7

• feat: added MAM20019c to represent cytosolic FMNH2

  Devlin-Moyer

  committed
  ef44666

• fix: replaced ubiquinone metabolites with FMN metabolites in MAR04575 and added new FMN/ubiquinone redox reaction MAR20167

  Devlin-Moyer

  committed
  5491db3

Commits on Oct 25, 2023

• fix: removed LIPT1 from MAR01088 and MAR01091

  Devlin-Moyer

  committed
  80ca5e3

• fix: remove MAR06398, MAR06399, and MAM02398c

  Devlin-Moyer

  committed
  d1f8b66

• fix: added new reaction to accurately represent activity of LIPT1

  Devlin-Moyer

  committed
  63c32a2

• fix: change new reaction ID to not conflict with new DHODH reaction

  Devlin-Moyer

  committed
  6c342de

• fix: replace MAM02393m with MAM00209c in MAR08433 and MAM01701m with MAM00208c in MAR08434

  Devlin-Moyer

  committed
  d9e4046

• fix: removed protons from lipoamide transport reactions

  Devlin-Moyer

  committed
  4bf45c3

• fix: remove MAR06408 and MAM01701c

  Devlin-Moyer

  committed
  66a2fff

Commits on Oct 26, 2023

• fix: make MAR11361 reversible

  Devlin-Moyer

  committed
  7e3fd18

Commits on Oct 27, 2023

• Added THEM4 and THEM5 genes

  pranasag

  committed
  c55bfd6

• added rxn ids

  pranasag

  committed
  0edc9f8

• increments +1 from the highest, not MAR20201

  pranasag

  committed
  9d988d9

• one placeholder too many

  pranasag

  committed
  8848c14

• added new reactions MAR20167 to 70, updated the GPR of MAR11544

  pranasag

  committed
  d7aaaf4

• Changed GPRs of acyl-CoA hydrolases and added names

  pranasag

  committed
  4ec702f

• Fixed typo MAR20179 -> MAR20169

  pranasag

  committed
  917ce10

• Assigned mitochondrial ACOTs ENSG00000123130 and ENSG00000196407 to at least one reactions

  pranasag

  committed
  a0ef2cc

• Removed hexanoate, MAM03684c

  pranasag

  committed
  7635dd6

• Added missing [x] and [m] species

  pranasag

  committed
  c490f1d

• Added species MAM02120x and MAM02120m to Human-GEM.yml

  pranasag

  committed
  4139c46

• Removed deprecated species from the model

  pranasag

  committed
  ca73f3e

• Removed duplicate rxn MAR09949

  pranasag

  committed
  85203ec

Commits on Oct 29, 2023

• Added BiGG ID for MAM02120

  pranasag

  committed
  f924ff6

• Merge pull request #714 from SysBioChalmers/fix/LIPT1

  Show description for 48eda9c
  haowang-bioinfo

  authored
  48eda9c

• Merge branch 'develop' into fix/hexanoate

  haowang-bioinfo

  committed
  373fc6a

Commits on Oct 30, 2023

• Added GPRs to MAR10377 and MAR10374

  pranasag

  committed
  d4d0c50

• Merge pull request #717 from SysBioChalmers/fix/hexanoate

  Show description for 589821a
  haowang-bioinfo

  authored
  589821a

• Merge branch 'develop' into fix/dhodh_rxns

  haowang-bioinfo

  committed
  1c0a637

Commits on Oct 31, 2023

• Changed rxn ids 20167-70 -> 20169-72

  pranasag

  committed
  d5ea251

• Merge pull request #713 from SysBioChalmers/fix/dhodh_rxns

  Show description for b5ce9c9
  haowang-bioinfo

  authored
  b5ce9c9

• Merge branch 'develop' into fix/ACOT_curation

  haowang-bioinfo

  committed
  0c1e900

Commits on Nov 2, 2023

• doc: update Rhea ids to newly added reactions

  haowang-bioinfo

  committed
  32375a4

Commits on Nov 3, 2023

• Fixed GPRs for MAR00358 and 00362

  pranasag

  committed
  55a5f9d

• Small fix: changed subsystem of MAR10389 from Exchange -> Transport reactions

  pranasag

  committed
  7f376c7

• Merge pull request #715 from SysBioChalmers/fix/ACOT_curation

  Show description for 00663a4
  haowang-bioinfo

  authored
  00663a4

Commits on Nov 8, 2023

• fix: removed MAR04940

  Devlin-Moyer

  committed
  bf88f4e

• fix: removed MAR06391

  Devlin-Moyer

  committed
  5dbfb45

• fix: made MAR08771 ATP-independent & added references

  Devlin-Moyer

  committed
  698976c

• fix: updated RHEA ID for MAR08771 and merged annotations from MAR04940 & MAR06391 in reactions.tsv

  Devlin-Moyer

  committed
  71e7b2d

• fix: added new gene entries for SLC25A39 and SLC25A40 to model/Human-GEM.yml and model/genes.tsv

  Devlin-Moyer

  committed
  5cfb14b

• feat: added Ensembl transcript and protein IDs for SLC25A40

  Devlin-Moyer

  committed
  083c97b

• fix: genes, references, E.C. code, and RHEA ID for MAR04665

  Devlin-Moyer

  committed
  e7a234d

• fix: removed MAR04239 and merged annotations in reactions.tsv into those for MAR04599 and MAR06415

  Devlin-Moyer

  committed
  8706a41

• fix: corrected GPR and references for MAR04599 and MAR06415

  Devlin-Moyer

  committed
  9dc9b00

Commits on Nov 9, 2023

• doc: update Rhea id to MAR08771

  haowang-bioinfo

  authored
  39005dc

• doc: update Rhea id for MAR04665

  haowang-bioinfo

  authored
  02c376c

Commits on Nov 10, 2023

• fix: format/style of new GPR for MAR04599

  Devlin-Moyer

  committed
  6bd4f2f

• Merge pull request #724 from SysBioChalmers/fix/MAR04665

  Show description for ee82b6e
  feiranl

  authored
  ee82b6e

Commits on Nov 13, 2023

• Merge pull request #723 from SysBioChalmers/fix/glutathione_transport

  Show description for af0862d
  haowang-bioinfo

  authored
  af0862d

Commits on Nov 15, 2023

• chore: merge in latest develop branch

  Devlin-Moyer

  committed
  bc0666a

• fix: remove OGDHL from all associated reactions, delete its gene entry, and remove it from genes.tsv

  Devlin-Moyer

  committed
  14f5062

• feat: added ref to OGDH and 2-OADH reactions

  Devlin-Moyer

  committed
  58d89cf

Commits on Nov 18, 2023

• doc: update Rhea ids for MAR04599 and MAR06414

  haowang-bioinfo

  committed
  2c314cd

• Merge pull request #725 from SysBioChalmers/fix/oxoadipate_dehydrogenase

  Show description for 7451de8
  haowang-bioinfo

  authored
  7451de8

Commits on Dec 5, 2023

• fix: remove ACAD10 from YAML file

  Devlin-Moyer

  committed
  8dc0d19

• fix: remove ACAD10 from model/genes.tsv

  Devlin-Moyer

  committed
  f190474

Commits on Dec 8, 2023

• Merge pull request #740 from SysBioChalmers/fix/remove_ACAD10

  Show description for e0d8fd3
  haowang-bioinfo

  authored
  e0d8fd3

• update .all-contributorsrc [skip ci]

  

  allcontributors[bot]

  authored and

  haowang-bioinfo

  committed
  92fc74b

• update README.md [skip ci]

  haowang-bioinfo

  committed
  852a366