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Human 1.18#735

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

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Commits

Commits on Mar 23, 2023

• chore: bump workflow dependency version

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Commits on May 10, 2023

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

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Commits on May 25, 2023

• feat-add the duplicate rxn check

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• refactor: separate assert statement from error message output

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Commits on May 26, 2023

• fix-give better output

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Commits on Jul 4, 2023

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

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Commits on Jul 28, 2023

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

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• fix: remove MAR06401 for being a duplicate of MAR06402

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• fix: remove MAM02397c

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• fix: update metabolite annotation files

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Commits on Aug 22, 2023

• chore: merge in latest develop branch

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Commits on Aug 30, 2023

• fix NA[c] in metabolic tasks

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Commits on Sep 27, 2023

• remove MAR07785 for being a duplicate of MAR04908

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• remove MAR07775 and MAR07788

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• remove MAR04915, MAR07782, MAR07783, and MAR07790

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

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

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• add peroxisomal FMN metabolite

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

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• add other SLC25A17-mediated antiport reactions

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• remove MAR03940 for being redundant with MAR08539+MAR08538

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Commits on Sep 29, 2023

• fix: added missing eccodes entries to new reactions

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Commits on Oct 2, 2023

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

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Commits on Oct 5, 2023

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

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Commits on Oct 6, 2023

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

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• chore: use action fork

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Commits on Oct 7, 2023

• Merge pull request #703 from SysBioChalmers/mergeMultiSubsystems

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• Merge branch 'develop' into fix/perox_cofactor_trans

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Commits on Oct 8, 2023

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

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• fix: rebalance MAR20117

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

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Commits on Oct 9, 2023

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

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Commits on Oct 14, 2023

• fix: remove ENSG00000159423 from MAR00051

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• fix: remove MAR08564 and MAR08565

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• fix: remove ENSG00000109576 from MAR04222

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

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

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• doc: sync deletion of MAM00926c

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

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• feat: updated references and added RHEA IDs for MAR09608

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• chore: merge in latest develop branch

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

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

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Commits on Oct 16, 2023

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

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• Merge branch 'develop' into fix/dupe_lipoate_biosynth

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• Merge branch 'develop' into fix/lipoate_transport

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

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

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• Merge branch 'develop' into fix/dupe_lipoate_biosynth

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• doc: update Rhea ids for MAR01706

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

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• feat: add new gene entries for SLC25A33 and SLC25A36

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

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

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Commits on Oct 17, 2023

• fix: YAML formatting issue

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• chore: merge in latest develop branch

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• fix: typo in metabolite ID for dTDP in MAR20162

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

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

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

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• fix: add ref from MAR00478 to refs for MAR00479

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

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

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Commits on Oct 18, 2023

• fix: two of the new reactions were accidentally identical

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

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Commits on Oct 19, 2023

• Merge branch 'develop' into feat-duplicateRxnCheck

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• fix: remove duplicate rxns MAR20012 and MAR20089

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• doc: merge annotations into reactions.tsv

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• fix: merge GPRs of MAR06646 and MAR20012

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

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• Merge branch 'develop' into fix/mito_nuc_trans

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

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Commits on Oct 20, 2023

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

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

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

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

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

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

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

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Commits on Oct 23, 2023

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

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• feat: added MAM20019c to represent cytosolic FMNH2

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

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Commits on Oct 25, 2023

• fix: removed LIPT1 from MAR01088 and MAR01091

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• fix: remove MAR06398, MAR06399, and MAM02398c

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

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

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

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• fix: removed protons from lipoamide transport reactions

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• fix: remove MAR06408 and MAM01701c

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Commits on Oct 26, 2023

• fix: make MAR11361 reversible

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Commits on Oct 27, 2023

• Added THEM4 and THEM5 genes

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• added rxn ids

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• increments +1 from the highest, not MAR20201

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• one placeholder too many

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

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• Changed GPRs of acyl-CoA hydrolases and added names

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• Fixed typo MAR20179 -> MAR20169

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

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• Removed hexanoate, MAM03684c

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• Added missing [x] and [m] species

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

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• Removed deprecated species from the model

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• Removed duplicate rxn MAR09949

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Commits on Oct 29, 2023

• Added BiGG ID for MAM02120

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

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• Merge branch 'develop' into fix/hexanoate

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Commits on Oct 30, 2023

• Added GPRs to MAR10377 and MAR10374

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

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• Merge branch 'develop' into fix/dhodh_rxns

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Commits on Oct 31, 2023

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

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

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• Merge branch 'develop' into fix/ACOT_curation

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Commits on Nov 2, 2023

• doc: update Rhea ids to newly added reactions

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Commits on Nov 3, 2023

• Fixed GPRs for MAR00358 and 00362

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

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

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Commits on Nov 8, 2023

• fix: removed MAR04940

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• fix: removed MAR06391

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• fix: made MAR08771 ATP-independent & added references

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

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

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• feat: added Ensembl transcript and protein IDs for SLC25A40

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

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

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• fix: corrected GPR and references for MAR04599 and MAR06415

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Commits on Nov 9, 2023

• doc: update Rhea id to MAR08771

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• doc: update Rhea id for MAR04665

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Commits on Nov 10, 2023

• fix: format/style of new GPR for MAR04599

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

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Commits on Nov 13, 2023

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

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Commits on Nov 15, 2023

• chore: merge in latest develop branch

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

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

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Commits on Nov 18, 2023

• doc: update Rhea ids for MAR04599 and MAR06414

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

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Commits on Dec 5, 2023

• fix: remove ACAD10 from YAML file

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• fix: remove ACAD10 from model/genes.tsv

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Commits on Dec 8, 2023

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

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• update .all-contributorsrc [skip ci]

  

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• update README.md [skip ci]

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