Onerxnperactivegene

createDummyModel(model, activeEntrezGeneID, TolMaxBoundary, modelExtractionAlgorithm, coreRxnAbbr, fluxEpsilon)[source]

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

USAGE:

[dummyModel, coreRxnAbbr] = createDummyModel (model, activeEntrezGeneID, TolMaxBoundary, modelExtractionAlgorithm, coreRxnAbbr, fluxEpsilon)

INPUTS:

  • model – COBRA model with the following fields:

    • .S - m x n stoichiometric matrix

    • .b - m x 1 accumulation (right hand side of S*v = b)

    • .c - n x 1 linear objective coefficient vector

    • .lb - n x 1 lower flux bounds

    • .ub - n x 1 upper flux bounds

    • .csense - m x 1 constraint sense for each metabolite

    • .mets - m x 1 metabolite identifiers

    • .rxns - n x 1 reaction identifiers

    • .rxnNames - n x 1 reaction names

    • .genes - g x 1 gene identifiers

    • .rules - n x 1 gene-reaction association rules

    • .rxnGeneMat - n x g reaction-gene mapping matrix

    • .subSystems - n x 1 reaction subsystems

    • .C - coupling constraint matrix

    • .ctrs - coupling constraint identifiers

    • .SIntRxnBool - n x 1 boolean, true for internal reactions

    • .SConsistentRxnBool - n x 1 boolean, stoichiometrically consistent reactions

    • .SConsistentMetBool - m x 1 boolean, stoichiometrically consistent metabolites

    • .fluxConsistentRxnBool - n x 1 boolean, flux consistent reactions

    • .thermoFluxConsistentRxnBool - n x 1 boolean, thermodynamically flux consistent reactions

    • .dummyMetBool - m x 1 boolean, true for dummy metabolites

    • .dummyRxnBool - n x 1 boolean, true for dummy reactions

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

OPTIONAL INPUTS:

  • TolMaxBoundary – scalar giving the default reaction upper and lower bound magnitude

  • modelExtractionAlgorithm – {(‘thermoKernel’), ‘fastCore’} if ‘fastCore’ it runs a flux consistency check first

  • coreRxnAbbr – core reaction identifiers to retain

  • fluxEpsilon – Minimum non-zero flux value accepted for tolerance (Default: Primal feasibility tolerance x 10)

OUTPUTS:

  • dummyModel – COBRA model with dummy metabolites and reactions added, including:

    • .dummyMetBool - m x 1 boolean vector indicating dummy metabolites

    • .dummyRxnBool - n x 1 boolean vector indicating dummy reactions

  • coreRxnAbbr – updated core reaction identifiers

destroyDummyModel(model, dummyMetBool, dummyRxnBool, metsOrig, rxnsOrig)[source]

Remove all traces of dummy metabolites and reactions

USAGE:

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

INPUT:

model – COBRA model with the following fields:

  • .S - m x n stoichiometric matrix

  • .b - m x 1 accumulation (right hand side of S*v = b)

  • .c - n x 1 linear objective coefficient vector

  • .lb - n x 1 lower flux bounds

  • .ub - n x 1 upper flux bounds

  • .csense - m x 1 constraint sense for each metabolite

  • .mets - m x 1 metabolite identifiers

  • .rxns - n x 1 reaction identifiers

  • .rxnNames - n x 1 reaction names

  • .rules - n x 1 gene-reaction association rules

  • .rxnGeneMat - n x g reaction-gene mapping matrix

  • .subSystems - n x 1 reaction subsystems

  • .C - coupling constraint matrix

  • .SIntMetBool - m x 1 boolean, true for internal metabolites

  • .SIntRxnBool - n x 1 boolean, true for internal reactions

  • .SConsistentMetBool - m x 1 boolean, stoichiometrically consistent metabolites

  • .SConsistentRxnBool - n x 1 boolean, stoichiometrically consistent reactions

  • .fluxConsistentMetBool - m x 1 boolean, flux consistent metabolites

  • .fluxConsistentRxnBool - n x 1 boolean, flux consistent reactions

  • .thermoFluxConsistentMetBool - m x 1 boolean, thermodynamically flux consistent metabolites

  • .thermoFluxConsistentRxnBool - n x 1 boolean, thermodynamically flux consistent reactions

OPTIONAL INPUTS:

  • 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 a dummyModel

OUTPUT:

model – COBRA model without dummy metabolites or reactions