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Human 1.19#823

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edkerk merged 150 commits intomainSysBioChalmers/Human-GEM:mainfrom developSysBioChalmers/Human-GEM:developCopy head branch name to clipboardJun 24, 2024

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Commits on May 21, 2023

• fix: Fixed a bug in importYaml.m for when you have an old MATLAB version. I don't think that code had ever been run, it was just not right.

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• feat: Added gene essentiality prediction from DepMap data. The code currently only processes the model available in the repo, and does not compare with any older model version. The code is however …

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Commits on May 22, 2023

• Update code/DepMapGeneEss/Instructions.txt

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• Update code/DepMapGeneEss/PrepDepMapData.m

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• Update code/DepMapGeneEss/enrichment_test.m

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Commits on May 24, 2023

• Update code/DepMapGeneEss/ConvertGeneEssInputData.R

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• Update code/DepMapGeneEss/PlotGeneEss.R

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Commits on Jul 6, 2023

• refactor: move the gene essentiality instrucitons to Human-GEM-guide

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Commits on Nov 23, 2023

• Feat: create metabolites_SMILES_inchi.tsv

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Commits on Dec 6, 2023

• fix: remove MAR03748 and MAR03780 and merge annotations in reactions.tsv into MAR06416/7 and MAR06419/20

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Commits on Dec 8, 2023

• fix: update GPRs of MAR06416, MAR06419, MAR06421, and MAR06523 and remove TMEM91 from the model

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• fix: remove MAR02532 and MAR02534

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• feat: add references for MAR06523

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• fix: remove MAR06329 for being redundant with MAR03149 + MAR03150 + MAR03151 + MAR03153

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• fix: remove MAR06283 for being redundant with MAR03156 + MAR03157 + MAR03158 + MAR03160

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• fix: remove MAR06279 for being redundant with MAR03157 + MAR03158 + MAR03160

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• fix: remove MAR05449 for being redundant with MAR03163 + MAR03164 + MAR03166 + MAR03885

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• fix: remove MAR01009 for being redundant with MAR03885 and MAR03149,50,51,53,56,57,58,60,63,64,66

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• fix: removed MAR03422

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Commits on Dec 9, 2023

• feat: added missing thiamine and lipoyl intermediates in BCKDH and 2-OADH reactions

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Commits on Dec 10, 2023

• feat: added thiamine-dependent decarboxylation reactions for BCKDH and 2-OADH reactions and thiamine-to-lipoyl transfer for 2-OADH

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• fix: adjusted existing BCKDH and 2-OADH reactions to connect to new thiamine-dependent steps

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• fix: removed extra space that made YAML validation fail

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• Merge pull request #743 from SysBioChalmers/fix/BCKDH_duplicates

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• Merge branch 'develop' into fix/remove_MAR03422

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• Merge branch 'develop' into fix/BCKDH_genes

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• fix: removed MAM02158m, MAM02158n, and MAM02986n

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• Merge pull request #752 from SysBioChalmers/fix/remove_MAR03422

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• fix: GPRs for MAR03269 and MAR03380

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Commits on Dec 13, 2023

• fix: remove MAR00789

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• fix: remove MAR03426 and merge annotations in reactions.tsv with reactions it duplicated

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• feat: add code to report Perox genes from beta-oxidation GPRs in mito

  haowang-bioinfo

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• Merge pull request #760 from SysBioChalmers/fix/MAR03269_MAR03380

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• fix-GPR: remove ENSG00000115425 from MAR02028

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• fix-GPR: remove ENSG00000115425 from MAR02148

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• fix-GPR: remove ENSG00000115425 from MAR02149

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• fix-GPR: remove ENSG00000115425 from MAR02187

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• fix-GPR: remove ENSG00000115425 from MAR02207

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Commits on Dec 14, 2023

• chore: merge in latest develop branch

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• fix: merged in latest develop branch and corrected weird annotation inconsistencies in reactions.tsv

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• chore: merge in latest develop branch

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• fix-GPR: remove ENSG00000113790 from GPRs of b-oxidation rxns in mito

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Commits on Dec 16, 2023

• fix-GPR: remove ENSG00000060971 from MAR02381

  haowang-bioinfo

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• fix: remove accidentally introduced typo

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Commits on Dec 18, 2023

• fix: removed MAR00965

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• fix: corrected GPR of MAR00970

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• Merge pull request #750 from SysBioChalmers/fix/BCKDH_genes

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• Merge pull request #768 from SysBioChalmers/fix/linolenoyl_beta_oxidation

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• Merge pull request #770 from SysBioChalmers/removePeroGenesFromBetaoxidationGPRsInMito

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• chore: resolved merge conflicts with latest develop branch

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Commits on Dec 22, 2023

• doc: update rxnRetired column for MAR03160

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Commits on Dec 23, 2023

• Merge pull request #751 from SysBioChalmers/fix/octanoyl_beta_ox_dupes

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Commits on Dec 26, 2023

• fix: remove MAR03322 and MAR03296

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• fix-gpr: remove DECR2 from mitochondria beta-oxidation reactions

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• fix-gpr: remove DECR1 from peroxisome beta-oxidation reactions

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• doc: update rxnRetired column to genes.tsv

  haowang-bioinfo

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• fix: remove MAR04005 due to wrong compartment assignment

  haowang-bioinfo

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• doc: sync MAR04005 removal to TSV files

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• fix: remove MAR05019 for being a duplicate of MAR03142+MAR03143

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• fix: remove MAR04967 for being a duplicate of MAR03143+MAR03144+MAR03146

  Devlin-Moyer

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• fix: remove MAR05024 for being a duplicate of MAR03142+MAR03143+MAR03144+MAR03146

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• fix-met: remove MAM00678c and MAM03035c

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• fix: removed EHHADH from the GPR of MAR03288

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Commits on Dec 27, 2023

• Merge pull request #788 from SysBioChalmers/fix/DECR1DECR2_rxnsGPRs

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• Merge branch 'develop' into fix/decanoyl_beta_ox_dupes

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• Merge pull request #789 from SysBioChalmers/fix/decanoyl_beta_ox_dupes

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Commits on Dec 28, 2023

• fix: remove MAR05187 for duplicating MAR03486+MAR03386

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• fix: remove MAR05186 for misrepresenting catalytic activity of ALDH2A2

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• fix-gpr: MAR03386 and MAR03486

  Devlin-Moyer

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• fix: remove KRTAP11-1 for not being an enzyme

  Devlin-Moyer

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• fix: remove MAR05358 for duplicating MAR03452+MAR03453+MAR03454+MAR03455

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• fix: remove MAR05195 for duplicating MAR03456

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• fix: remove MAR05302 for duplicating MAR03457

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• fix: remove MAR05229 for duplicating MAR03458

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• fix: remove MAR05208 for duplicating MAR03281+MAR03282+MAR03283

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• fix: remove MAR05356 for duplicating MAR03275+MAR03277+MAR03278+MAR03279

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• fix: remove MAR05191 for duplicating MAR03280+MAR03281+MAR03282+MAR03283

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• fix: remove MAR05123 for duplicating MAR03284+MAR03285+MAR03286+MAR03287

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• fix: remove MAR05075 for duplicating MAR03288

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• fix: remove MAR05072 for duplicating MAR03290+MAR03292+MAR03293

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• fix: replaced MAM03274m with MAM00091m in MAR05360

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• fix: removed MAM03274m for duplicating MAM00091m

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• fix: removed MAM03653m for duplicating MAM00072m

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• fix: removed MAM03221m for duplicating MAM00089m

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• fix: removed MAM03182m for duplicating MAM03009m

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• fix: removed MAM03978m for duplicating MAM01576m

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• fix: removed MAM03203m for duplicating MAM01575m

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• fix: removed MAM02698m for duplicating MAM03021m

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• fix: removed MAM03650m for duplicating MAM01577m

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• chore: merge in latest develop branch

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Commits on Dec 31, 2023

• fix a small type in rxn ID

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• fix: standardized format of new GPR for MAR00970

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Commits on Jan 2, 2024

• Merge pull request #790 from SysBioChalmers/fix/MAR03288_GPR

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• fix: consistent formatting of names of thiamine conjugates

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• fix: added MAM20081m to MAR03800 as a product

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• fix: typo in KEGG ID for MAM20077m

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• fix: formula for MAR20177 (accidentally used the new formula for MAR03800)

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Commits on Jan 4, 2024

• feat-code for getting smiles and inchi of metabolites

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Commits on Jan 8, 2024

• Merge pull request #753 from SysBioChalmers/fix/thiamine_in_oxoacid_dehydrogenase_rxns

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• doc: add removed rxn id to "rxnRetired" column

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• Merge pull request #794 from SysBioChalmers/fix/remove_MAR00965

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• Merge branch 'develop' into fix/phytanoyl_alpha_ox

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• fix: typos in refences field

  mihai-sysbio

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• chore: merge in latest develop branch

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Commits on Jan 10, 2024

• Merge pull request #731 from JHL-452b/feat_smiles_inchi

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Commits on Jan 11, 2024

• Merge pull request #803 from SysBioChalmers/chore/pmid-typos

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Commits on Jan 28, 2024

• fix: renamed MAM02746 metabolites to (3R)-phytanic acid

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• fix: brought back previously-deprecated MAM03884 metabolites and renamed to (3S)-phytanic acid

  Devlin-Moyer

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• fix: brought back previously-deprecated MAR00659 and MAR01617

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• fix: renamed MAM02747 metabolites to (3R)-phytanoyl-CoA

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• fix: replaced MAM02746c with MAM03884c in MAR03388

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• fix: made MAR03481 and MAR06779 both ATP-dependent and CoA-hydrolyzing

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• fix: replaced MAM02746x with MAM03884x in MAR03389

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• fix: renamed MAM00655x to (3R)-2-hydroxyphytanoyl-CoA

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• created MAM20083x to represent peroxisomal (2R)-pristanal

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• fix: replaced MAM00564x with MAM20083x in MAR03486

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• fix: renamed MAM02766 metabolites to (3S)-pristanic acid

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• fix: brought back previously-deprecated MAM00077x and MAR03488 and replaced MAM00564x with MAM20083x in MAR03488

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• fix: renamed MAM02766 metabolites to (2S)-pristanic acid (wrongly renamed them to (3S)-pristanic acid in earlier commit)

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• fix: replaced MAM02766x with MAM00077x in MAR03493

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• feat: created MAM00077c and MAM00077e

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• fix: removed deprecated MetaNetX ID from annotations for MAM02766 metabolites

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• fix: replace MAM02766c with MAM00077c in MAR03390

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• feat: created MAR20179 and MAR20180 to represent export and exchange of (2R)-pristanic acid

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Commits on Feb 23, 2024

• fix: removed MAR04774, MAR04775, and MAM02955c from YAML file

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• chore: moved row for MAM02955c from model/metabolites.tsv to data/deprecatedIdentifiers/deprecatedMetabolties.tsv

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• chore: moved rows for MAR04774 and MAR04775 from model/reactions.tsv to data/deprecatedIdentifiers/deprecatedReactions.tsv

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• feat: added references for tagatose metabolism reactions

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• fix: GPRs for mitochondrial 2-enoyl-CoA hydratase reactions

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Commits on Mar 13, 2024

• fix: fill in exchange reaction names

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Commits on Mar 19, 2024

• Merge pull request #811 from SysBioChalmers/fix/exchangeRxnNames

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Commits on Apr 4, 2024

• fix: undid changes to GPR of MAR03181 that should not have been made

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Commits on Apr 23, 2024

• Merge pull request #574 from SysBioChalmers/feat/AddGeneEssDepMap

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• Merge pull request #792 from SysBioChalmers/fix/phytanoyl_alpha_ox

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• Merge branch 'develop' into fix/dupe_linoleoyl_gamma_linolenoyl_beta_ox_paths

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• Merge pull request #793 from SysBioChalmers/fix/dupe_linoleoyl_gamma_linolenoyl_beta_ox_paths

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• fix: changed GPR of MAR03281 to ENSG00000084754 (which I missed earlier)

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• chore: resolve merge conflict with latest develop branch

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• chore: resolve merge conflicts with latest version of develop branch

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Commits on Apr 24, 2024

• Merge pull request #808 from SysBioChalmers/fix/remove_EHHADH_from_mito_gprs

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  feiranl

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• Merge pull request #807 from SysBioChalmers/fix/tagatose

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  feiranl

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• Merge pull request #805 from SysBioChalmers/fix/phytanic_stereo

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  feiranl

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• feat: added MAR20181-3 to represent transport functions of SLC25A19

  Devlin-Moyer

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  34f6271

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• fix: removed MAR01788, MAR01789, MAR04205, MAR08745, and MAR08747

  Devlin-Moyer

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Commits on Apr 25, 2024

• fix: modified unbalance reactions

  JHL-452b

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Commits on Apr 26, 2024

• Merge pull request #816 from JHL-452b/fix-Correction_of_unbalanced_reactions

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  feiranl

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Commits on May 6, 2024

• Merge pull request #815 from SysBioChalmers/fix/thiamine_transport

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  feiranl

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Commits on May 7, 2024

• chore: update checkout action from v3 to v4

  mihai-sysbio

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• Merge pull request #818 from SysBioChalmers/chore/update-actions

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  feiranl

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Commits on Jun 24, 2024

• chore: input-output round

  edkerk

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