├── .all-contributorsrc ├── .deprecated ├── README.md ├── code │ ├── GPRs │ │ └── getComplexesFromGeneRules.m │ └── modelCuration │ │ ├── GPRs │ │ ├── EnzymeComplexes │ │ │ ├── addCuratedComplexRulesToModel.m │ │ │ ├── createComplexStructure.m │ │ │ ├── curated_CORUM_grRules_20180924.txt │ │ │ └── updateGrRulesAndGenes_20181018.m │ │ ├── combineModelGPRs.m │ │ ├── combineModelGPRsScript.m │ │ ├── compare_HMR_iHsa_Recon3D_GPRs.m │ │ ├── integrateGeneRules.m │ │ └── removeNonPrimaryGeneIDs.m │ │ ├── MetAssociation │ │ ├── HMR_master_met_curation.m │ │ ├── HMR_update_met_attributes.m │ │ ├── Recon3MetAssoc2MNXByBiGG.m │ │ ├── addAltsToModelField.m │ │ ├── addManuallyCuratedMetAssoc.m │ │ ├── alphabetizeMetFormulas.m │ │ ├── buildMNXmodel.m │ │ ├── compareMNXmetFormulas.m │ │ ├── compareRxnMNXIDsWithMets.m │ │ ├── compressModelField.m │ │ ├── curateHMR2Mets.m │ │ ├── evalMetMNXIDs.m │ │ ├── filterMetMNXIDsViaRxns.m │ │ ├── fixFormulasWithFULLR.m │ │ ├── getHuman1MetAssoc.m │ │ ├── mapMetsToAltModel.m │ │ ├── mapModelMets.m │ │ ├── metConsistencyCheckViaMNX.m │ │ └── updateBiGGIDs_issue124.m │ │ ├── RxnAssociation │ │ ├── Recon3RxnAssoc2MNXByBiGG.m │ │ ├── Recon3Rxns2HMR.JSON │ │ ├── Recon3Rxns2HMR.m │ │ ├── addManuallyCuratedRxnAssoc.m │ │ ├── addtionalManualCuration.m │ │ ├── applyJSON2RxnAssoc.m │ │ ├── checkDuplicateRxn_mod.m │ │ ├── getHuman1RxnAssoc.m │ │ ├── ihumanRxns2MNX.JSON │ │ ├── integrateRxnAssocViaIDsAndMets.m │ │ ├── mapRxnsViaMets.m │ │ ├── rxnAssocByBiGG.m │ │ ├── rxnAssocByMNX.m │ │ └── verifyRxnAssoc2MNX.m │ │ ├── balanceProtonsInRxns.m │ │ ├── constrainReactions.m │ │ ├── createNewHumanBiomassRxn.m │ │ ├── curateATPmetabolism.m │ │ ├── curateBiomassReactions.m │ │ ├── curateExchangeRxns.m │ │ ├── curateExchangeRxns_issue117.m │ │ ├── curateLipidPools.m │ │ ├── curateMetFormula4PAPS.m │ │ ├── curateMitochMembraneComp.m │ │ ├── curateModelECcodes.m │ │ ├── curateModelSubsystems.m │ │ ├── deleteInactivatedReactions.m │ │ ├── enableYamlBasedWorkflow.m │ │ ├── iHsaAdditionalIntegration.m │ │ ├── implementeMAID.m │ │ ├── loadHumanGEM.m │ │ ├── mergeGlutamateSubsystem.m │ │ ├── miscModelCurationScript_20180921.m │ │ ├── miscModelCurationScript_20181005.m │ │ ├── miscModelCurationScript_20181012.m │ │ ├── miscModelCurationScript_20190323.m │ │ ├── modelIntegration │ │ ├── convertRecon3DToRaven.m │ │ ├── curateDuplicatedRxns.m │ │ ├── curateRxnAssoc.m │ │ ├── integrateRecon3DToHMR.m │ │ ├── removeDuplicateMetsInRecon3D.m │ │ └── updateMetAssoc.m │ │ ├── protonBalance4Rxns.m │ │ ├── rebalanceHumanGEM.m │ │ ├── removeBoundaryCompartment.m │ │ ├── removeConflictingInchiStrings.m │ │ ├── removeSinkDMRxns.m │ │ ├── repairModelLeaks.m │ │ ├── updateHMR2Genes.m │ │ └── updateMetChargesFormulas.m └── data │ ├── BiGG │ ├── getMetsFromBiGG.m │ └── getRxnsFromBiGG.m │ ├── HMR2 │ ├── HMR2Curation.m │ └── rxnAssocInitCheck.m │ ├── Maps │ └── currencyMets.tsv │ ├── MetaNetX │ ├── getMetsFromMNX.m │ ├── getRxnsFromMNX.m │ └── mapIDsViaMNXref.m │ ├── Reactome │ └── reactome_stable_ids.txt │ ├── iHsa │ ├── addHMRrxnIDsToiHsa.m │ ├── iHsaAdditionalIntegration_modelChanges_mets.tsv │ ├── iHsaAdditionalIntegration_modelChanges_rxns.tsv │ ├── iHsaMetsToAdd.tsv │ ├── iHsaRxnAssocToAdd.tsv │ └── iHsaRxnsToAdd.tsv │ └── modelCuration │ ├── associateMitoImporter_20190520.tsv │ ├── curateATPmetabolism_rxnChanges.tsv │ ├── curateExchangeReactions_issue117_mets.tsv │ ├── curateExchangeReactions_issue117_rxns.tsv │ ├── curateExchangeRxns_rxnChanges.tsv │ ├── curateFormulas4PAPS_rxnChanges.tsv │ ├── curateMitochMembraneComp_rxnChanges.tsv │ ├── fixFormulasWithFULLR.tsv │ ├── fullRebalance │ ├── rebalance_mets_duplicated.tsv │ ├── rebalance_mets_new.tsv │ ├── rebalance_mets_newCompVersions.tsv │ ├── rebalance_mets_updatedAnnotation.tsv │ ├── rebalance_mets_updatedFormula.tsv │ ├── rebalance_modelChanges_mets.tsv │ ├── rebalance_modelChanges_rxns.tsv │ ├── rebalance_rxns_duplicated.tsv │ ├── rebalance_rxns_inactivate.tsv │ ├── rebalance_rxns_new.tsv │ ├── rebalance_rxns_reactivate.tsv │ ├── rebalance_rxns_updatedAnnotation.tsv │ ├── rebalance_rxns_updatedEqn.tsv │ └── rebalance_rxns_updatedGrRules.tsv │ ├── grRulesCuration_20190206.tsv │ ├── inactivationRxns.tsv │ ├── lipidPools │ ├── lipidPoolMetReplacements.tsv │ ├── lipidPool_modelChanges_mets.tsv │ ├── lipidPool_modelChanges_rxns.tsv │ ├── newLipidPoolMets.tsv │ ├── newLipidPoolRxns.tsv │ └── oldLipidPoolRxns.tsv │ ├── newExchangeRxns_issue117.tsv │ ├── newHumanBiomassRxn_modelChanges_mets.tsv │ ├── newHumanBiomassRxn_modelChanges_rxns.tsv │ ├── newHumanBiomassRxns.tsv │ ├── pseudogeneCheck.tsv │ ├── redundantRxns.JSON │ ├── removedSinkDMrxns.tsv │ ├── repairModelLeaks_rxnChanges.tsv │ ├── rxns4biomass_20181129.tsv │ ├── subsystem_name_curated.tsv │ └── variable_mass_rxns_to_constrain.tsv ├── .gitattributes ├── .github ├── CONTRIBUTING.md ├── ISSUE_TEMPLATE │ └── BUG_REPORT.md ├── pull_request_template.md └── workflows │ ├── check-metabolictasks.yml │ ├── yaml-conversion.yml │ └── yaml-validation.yml ├── .gitignore ├── .standard-GEM.md ├── LICENSE.md ├── README.md ├── code ├── DepMapGeneEss │ ├── ConvertGeneEssInputData.R │ ├── PlotGeneEss.R │ ├── PrepDepMapData.m │ ├── data │ │ └── DepMap data files go here.txt │ ├── enrichment_test.m │ ├── evaluateDepMapEssentialityPredictions.m │ ├── generate_DepMap_models_ftINIT.m │ ├── generate_DepMap_models_ftINIT_Cluster.m │ ├── getTaskEssentialGenes.m │ ├── getTaskEssentialGenesCluster.m │ ├── run_evaless_depmap.sh │ └── run_gen_depmap_models.sh ├── GPRs │ ├── addComplexesToGeneRules.m │ ├── cleanGrRules.m │ ├── extractAllianceGenomeOrthologs.m │ ├── fetch_ensembl_gene_annotations.py │ ├── getGenesFromGrRules.m │ ├── replaceGrRules.m │ ├── simplifyGrRules.m │ ├── translateGrRules.m │ └── updateGrRules.m ├── HumanGEMInstaller.m ├── README.md ├── addBoundaryMets.m ├── addMetCompsField.m ├── addMetabolicNetwork.m ├── annotateGEM.m ├── curateReactionNames.py ├── estimateEssentialGenes.m ├── evalGeneEssentialityPred.m ├── evaluateHart2015Essentiality.m ├── gapfill4EssentialTasks.m ├── getCompNetwork.m ├── getModelFromOrthology.m ├── getSubNetworksInComp.m ├── getTaskEssentialGenes.m ├── io │ ├── docModelChanges.m │ ├── exportHumanGEM.m │ ├── exportTsvFile.m │ ├── exportYaml.m │ ├── importTsvFile.m │ ├── importYaml.m │ ├── increaseHumanGEMVersion.m │ └── writeModelChanges.m ├── misc │ ├── adjust_pvalues.m │ ├── countEmpty.m │ ├── countFrequency.m │ ├── flattenCell.m │ ├── getNonEmptyList.m │ ├── nestCell.m │ ├── prettyJson.m │ ├── reformatElements.m │ └── writecell2file.m ├── modelCuration │ ├── GlycolysisCuration.m │ ├── README.md │ ├── addAAnewRxn20230518.m │ ├── addMAMetIDs.m │ ├── addRxnACOD1_20221102.m │ ├── changeCompAbbrevs.m │ ├── completeMARxnids.m │ ├── getCompFromDeepLoc2.m │ ├── getCompFromUniprotCellAtlas.py │ ├── getSmiles.py │ ├── removeDuplicateRxns_issue345.m │ └── reportPeroxGenesFromBetaoxidationGPRsInMito.py ├── qc │ ├── crossCompChargeDiff.m │ ├── detectDuplicateRxns.m │ ├── identifyMassVariableRxns.m │ └── overlapRxnDetection.m ├── removeReactionsFull.m ├── standardizeMetFormulas.m ├── tINIT │ ├── checkTasksGenes.m │ ├── getAATripletReactions.m │ ├── getEssentialGenes.m │ ├── getHumanGEMINITSteps.m │ ├── getINITModel2.m │ ├── prepHumanModelForftINIT.m │ ├── removeDrugReactions.m │ └── restoreModelGrRules.m ├── test │ ├── memoteTest.py │ ├── sanityCheck.py │ ├── testMetabolicTasks.m │ └── testYamlConversion.m ├── updateAnimalAnnotations.m └── updateAnimalGEM.m ├── data ├── README.md ├── datasets │ ├── Hart2015_RNAseq.txt │ └── Hart2015_TableS2.xlsx ├── deprecatedIdentifiers │ ├── deprecatedMetabolites.tsv │ └── deprecatedReactions.tsv ├── metabolicTasks │ ├── metabolicTasks_CellfieConsensus.txt │ ├── metabolicTasks_Essential.txt │ ├── metabolicTasks_Full.txt │ └── metabolicTasks_VerifyModel.txt └── modelCuration │ ├── CellAtlasCompartments_science_2017.tsv │ ├── DeepLoc2_compartment.csv │ ├── README.md │ ├── 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