Onerxnperactivegene

createDummyModel(model, activeEntrezGeneID, TolMaxBoundary, modelExtractionAlgorithm, coreRxnAbbr, fluxEpsilon)

Add one dummy metabolite per active gene and for each reaction that has that active gene in the GPR, create a dummy metabolite, which is destroyed in the corresponding dummy reaction. This enables one to require that at least one reaction corresponding to a gene is active, rather than all genes

INPUT: model: COBRA model with various fields, including: model.S: m x n stoichiometric matrix

activeEntrezGeneID: k x 1 cell array of EntrezGeneID’s, each in the format of model.genes{i}

OPTIONAL INPUT: TolMaxBoundary: scalar number giving the default reaction upper and lower bounds magnitude modelExtractionAlgorithm: {(‘thermoKernel’),’fastCore’} if ‘fastCore’ it runs a flux consistency check first fluxEpsilon: Minimum non-zero flux value accepted for tolerance (Default: Primal feasibility tolerance X 10).

OUTPUT: dummyModel: COBRA model with dummy metabolites or reactions dummyModel.dummyMetBool: m x 1 boolean vector indicating dummy metabolites i.e. contains(model.mets,’dummy_Met_’); dummyModel.dummyRxnBool: n x 1 boolean vector indicating dummy reactions i.e. contains(model.rxns,’dummy_Rxn_’);

destroyDummyModel(model, dummyMetBool, dummyRxnBool, metsOrig, rxnsOrig)

Remove all traces of dummy metabolites and reactions

INPUT model COBRA model

OPTIONAL INPUT dummyMetBool m x 1 boolean vector indicating dummy metabolites dummyRxnBool n x 1 boolean vector indicating dummy reactions metsOrig Array indicating the metabolites before creating a dummyModel rxnsOrig Array indicating the reactions before creating dummyModel

OUTPUT model COBRA model without dummy metabolites or reactions