├── .standard-GEM.md ├── LICENSE.md ├── README.md ├── code ├── .deprecated │ ├── README.md │ ├── missingFields │ │ ├── addBiGGidentifiers.m │ │ ├── addGeneNames.m │ │ ├── changeRules.m │ │ ├── deleteRepeated.m │ │ ├── findInDB.m │ │ ├── findSubSystem.m │ │ ├── getAllPath.m │ │ └── getMissingFields.m │ ├── modelCuration │ │ ├── MissingTransDeadEnd.m │ │ ├── SubstrateUsage.m │ │ ├── UpdateDBnewRxn.m │ │ ├── addBiologRxnToGEM.m │ │ ├── addBiomassUpdate.m │ │ ├── addDBnewRxn.m │ │ ├── addFAEnewRxn.m │ │ ├── addGapfillingRxnToGEM.m │ │ ├── addMetabolomicsRxnToGEM.m │ │ ├── addRxnSubsystem.m │ │ ├── addSULnewRxn.m │ │ ├── addiSce926changes.m │ │ ├── changerxn.m │ │ ├── changerxnDirection.m │ │ ├── checkRxnBalance.m │ │ ├── checkSmatrixMNX.m │ │ ├── checkrxnDirection.m │ │ ├── curationsOnV8_4_2.m │ │ ├── display_rxnMetInfo.m │ │ ├── downloadMNXdb.m │ │ ├── fixBiomassComp.m │ │ ├── get_lnRevIdx.m │ │ ├── makeFormulasCompliant.m │ │ ├── mapKEGGID.m │ │ ├── mapMNXMID.m │ │ ├── modMetsandSmatrix.m │ │ ├── modelCorrections.m │ │ ├── modifyID.m │ │ ├── takeOutFromFormula.m │ │ ├── updateMetaboliteAnnotation.m │ │ └── updateMetaboliteFormula.m │ └── otherChanges │ │ ├── addSLIMErxns.m │ │ ├── clusterBiomass.m │ │ ├── convertYmn2FBC2.m │ │ ├── getNewIndex.m │ │ └── migrateKEGGpathways.m ├── __init__.py ├── getEarlierModelVersion.m ├── increaseVersion.m ├── io.py ├── loadYeastModel.m ├── missingFields │ ├── BiGGidsCompliance.ipynb │ ├── GetMNXID.m │ ├── README.md │ ├── addConfidenceScores.m │ ├── addSBOterms.m │ ├── addYMDBconcentrations.m │ ├── loadDeltaG.m │ ├── mapIDsViaMNXref.m │ └── saveDeltaG.m ├── modelCuration │ ├── CheckBalanceforSce.m │ ├── CheckEnergyProduction.m │ ├── README.md │ ├── TEMPLATEcuration.m │ ├── checkMetBalance.m │ ├── curateMetsRxnsGenes.m │ ├── minimal_Y6.m │ ├── v8_6_1.m │ ├── v8_6_2.m │ ├── v8_6_3.m │ ├── v8_7_0.m │ ├── v8_7_1.m │ ├── v9_0_0.m │ └── v9_0_2.m ├── modelTests │ ├── README.md │ ├── cobrapy-compliance.ipynb │ ├── essentialGenes.m │ ├── findDuplicatedRxns.m │ └── growth.m ├── otherChanges │ ├── README.md │ ├── anaerobicModel.m │ ├── changeGAM.m │ ├── fitGAM.m │ ├── rescalePseudoReaction.m │ ├── scaleBioMass.m │ └── sumBioMass.m ├── requirements │ ├── ci-requirements.in │ ├── ci-requirements.txt │ ├── dev-requirements.in │ ├── dev-requirements.txt │ ├── requirements.in │ └── requirements.txt └── saveYeastModel.m ├── data ├── .deprecated │ ├── databases │ │ ├── DBnewGeneAnnotation.tsv │ │ ├── FAEgeneNames.tsv │ │ ├── TransRxnGeneAnnotation.tsv │ │ ├── Yeast7.6MNXMetMappingList.tsv │ │ └── Yeast7.6MNXRxnMappingList.tsv │ └── modelCuration │ │ ├── Biolog_newRxnMatrix.tsv │ │ ├── Biolog_newRxnMetAnnotation.tsv │ │ ├── Biolog_newRxnProp.tsv │ │ ├── Biomass_newRxnMatrix.tsv │ │ ├── Biomass_newRxnMet.tsv │ │ ├── Biomass_newRxnProp.tsv │ │ ├── FAEnewRxnMatrix.tsv │ │ ├── FAEnewRxnMetAnnotation.tsv │ │ ├── FAEnewRxnProp.tsv │ │ ├── GapfillingnewRxnMatrix.tsv │ │ ├── GapfillingnewRxnProp.tsv │ │ ├── MetaCyc_deltaG.tsv │ │ ├── Metabolomics_newRxnMatrix.tsv │ │ ├── Metabolomics_newRxnMetAnnotation.tsv │ │ ├── Metabolomics_newRxnProp.tsv │ │ ├── Missingmetaboliteformulas.tsv │ │ ├── grpContribution_deltaG.tsv │ │ ├── iSce926curatedGeneRules.tsv │ │ ├── iSce926newGenes.tsv │ │ ├── memote_revIdx.tsv │ │ ├── metabolite_manual_curation.tsv │ │ ├── modMetsandSmatrix.tsv │ │ ├── modifyID.tsv │ │ ├── rxnDirectionInfo.tsv │ │ └── volatileSulfurCompounds │ │ ├── VoSulGenes.tsv │ │ ├── VoSulMets.tsv │ │ ├── VoSulRxns.tsv │ │ └── VoSulRxnsCoeffs.tsv ├── databases │ ├── BiGGmetDictionary.csv │ ├── BiGGmetDictionary_newIDs.csv │ ├── BiGGrxnDictionary.csv │ ├── BiGGrxnDictionary_newIDs.csv │ ├── README.md │ ├── SGDgeneNames.tsv │ ├── YMDBconcentrations.csv │ ├── Yeast_complex_portal_2022.tsv │ ├── kegg.tsv │ ├── lipidAbbreviations.csv │ ├── model_metDeltaG.csv │ ├── model_rxnDeltaG.csv │ ├── smilesDB.tsv │ └── swissprot.tsv ├── modelCuration │ ├── README.md │ ├── v8_6_1 │ │ ├── complexAnnotation.tsv │ │ ├── complexAnnotationGenes.tsv │ │ ├── newGPRsfromDBs.tsv │ │ ├── newGPRsfromDBsGenes.tsv │ │ ├── transRxnNewGPR.tsv │ │ ├── transRxnNewGPRGenes.tsv │ │ └── uniqueSubsystems.tsv │ ├── v8_6_3 │ │ ├── VolPolyPGenes.tsv │ │ ├── VolPolyPMets.tsv │ │ ├── VolPolyPRxns.tsv │ │ └── VolPolyPRxnsCoeffs.tsv │ ├── v8_7_0 │ │ ├── DBnewRxnsCoeffs.tsv │ │ ├── DBnewRxnsGenes.tsv │ │ ├── DBnewRxnsMets.tsv │ │ ├── DBnewRxnsRxns.tsv │ │ ├── Function annotation.tsv │ │ ├── code │ │ │ ├── get_seed_data.py │ │ │ └── run_dgpredictor.py │ │ ├── compartmental localization.tsv │ │ ├── dgpred_rxnG.csv │ │ └── modelseed_metG.csv │ └── v8_7_1 │ │ ├── SGD_with_Uniprot.csv │ │ └── get_uniprot_id.py ├── physiology │ ├── Biolog_Substrate.tsv │ ├── README.md │ ├── biomassComposition_Cofactor_Ion.tsv │ ├── biomassComposition_Forster2003.tsv │ ├── biomassComposition_Lahtvee2017.tsv │ ├── chemostatData_Tobias2013.tsv │ └── chemostatData_VanHoek1998.tsv └── testResults │ ├── essentialGenes.md │ 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