modelGeneration

checkCobraModelUnique(model, renameFlag)

Checks uniqueness of reaction and metabolite names

USAGE:

model = checkCobraModelUnique(model, renameFlag)

INPUT:

model: COBRA model structure

OPTIONAL INPUT:
renameFlag: Renames non-unique reaction names and metabolites

(Default = false)

OUTPUT:

model: COBRA model structure isUnique: true if the model has unique reaction and metabolite names

checkDuplicateRxn(model, method, removeFlag, printLevel, boundsFlag)

Checks model for duplicate reactions and removes them. By default, it detects the columns of S that are identical upto scalar multiplication

USAGE:

[modelOut, removedRxnInd, keptRxnInd] = checkDuplicateRxn(model, method, removeFlag, printLevel, boundsFlag)

INPUTS:

model: Cobra model structure

OPTIONAL INPUTS:
method: S –> checks rxn S matrix (default),

rxnAbbr –> checks rxn abbreviations, FR –> checks F + R matrix, where \(S:=-F + R\), which ignores reaction direction

OUTPUTS:

modelOut: COBRA model structure without (with) duplicate reactions removedRxnInd: Reaction numbers in model that were (should be) removed keptRxnInd: Reaction numbers in model that were (should be) kept

checkModelPreFBA(model, param)

checks if a model is (stoichiometrically and flux) consistent, which are necessary conditions prior to FBA

INPUT model COBRA model, or a fileName containing a model

OPTIONAL INPUT param parameters

OUTPUT isConsistent {1,0} if stoichiometrically and flux consistent, or not

detectDeadEnds(model, removeExternalMets)

Returns a list of indices of metabolites which either participate in only one reaction or can only be produced or consumed (i.e. all reactions involving the metabolite either only produce or only consume it, respecting the reaction lower and upper bounds).

USAGE:

outputMets = detectDeadEnds(model, removeExternalMets)

INPUT:

model: COBRA model structure

OPTIONAL INPUT:
removeExternalMets: Dont return metabolites that participate in reactions of the following type:

“A <=>/-> ” or ” <=>/-> A” or exclusively present in inconsistent reactions as defined in Gevorgyan et al, Bioinformatics, 2008

OUTPUT:
outputMets: List of indicies of metabolites which can ether

only be produced or consumed.

fastLeakTest(model, testRxns, demandTest)

Tests if any metabolites in a model are leaking. A metabolite is leaking if the exchange reaction can carry secretion flux in the closed model (no uptake flux through any exchange reactions is permitted).

USAGE:

[LeakMets, modelClosed, FluxExV] = fastLeakTest(model, testRxns, demandTest)

INPUTS:

model: Model structure testRxns: List of exchange reactions to be testetd for leaks demandTest: Optional: if ‘true’ is entered, demand reactions

for all metabolites in the model are created

OUTPUTS:

LeakMets: List of exchange reactions for leaking metabolites modelClosed: Model strucutre that has been tested for leaks FluxExV: Flux vector for computed exchange reactions in the closed model

printObjective(model)

Prints out the Stoichiometric Coefficients for each Metabolite, with the name of the objective

USAGE:

objectiveAbbr = printObjective(model)

INPUT:

model: COBRA model structure

OUTPUT:

objectiveAbbr: Objective reaction abbreviation

removeDeadEnds(model)

Removes all dead end metabolites and reactions from the model

USAGE:

[model, removedMets, removedRxns] = removeDeadEnds(model)

INPUT:

model: COBRA model structure

OUTPUTS:
model: COBRA model structure w/o dead end metabolites and

reactions

removedMets: List of removed metabolites removedRxns: List of removed reactions

setConstraintsIrrevModel(constrOpt, model, modelIrrev, rev2irrev)

Sets constraints for a subset of rxns while converting reversible to irreversible reaction names and handling the constraint directions correctly

USAGE:

constrOptIrrev = setConstraintsIrrevModel(rxnNameList, constrValue, constrSense, model, modelIrrev)

INPUTS:

constrOpt: Constraint options

  • rxnList - Reaction selection cell array (for reversible representation)

  • values - Constraint values

  • sense - Constraint senses ordered as rxnNameList

model: Model in reversible format modelIrrev: Model in irreversible format rev2irrev: Reversible to irreversible reaction index conversion

obtained from convertToIrreversible

OUTPUTS:

constrOpt: Constraint options in irrev model

  • rxnList - Reaction selection cell array

  • rxnInd - Selection index for constraints in irreversible model (e.g. [2 4 5 9 10])

  • values - Correctly ordered constraint values

  • sense - Correctly ordered constraint senses

test4HumanFctExt(model, test, optionSinks)

test for the ~288 human functions

USAGE:

[TestSolution,TestSolutionName,TestedRxns,PercTestedRxns] = test4HumanFctExt(model,test,optionSinks)

INPUT:

model: model structure (Recon1, with desired in silico condition) test: possible statements: Recon1, IECori, IEC, all (default)

(choose IECori if you intend to test the IEC model OR a model that contains lumen (‘u’) as compartment otw choose IEC); all check for Recon1 and IEC

option: if true = set sink reactions to 0 (default, leave unchanged).

Note that all lb’s of exchanges and demands will be set to 0

OUTPUT:

TestSolution: array containing the optimal value for the different tests TestSolutionName: array containing the names for the different tests

testATPYieldFromCsources(model, modelName, extraCellCompIn, extraCellCompOut, minCard)

computes the ATP yield from various carbon sources in Recon2 or Recon3.

USAGE:

[Table_csources,TestedRxns,PercTestedRxns] = testATPYieldFromCsources(model,modelName)

INPUT:

model model structure modelName name of the model structure, by default Recon3 extraCellCompIn abbreviation for extracellular compartment

(in-going), default [e]

extraCellCompOut abbreviation for extracellular compartment

(out-going), default [e]

OUTPUT:

Table_csources: table listing ATP yield computed for the carbon sources TestedRxns: list of reactions that are contributing to ATP production from carbon sources PercTestedRxns: Fraction that tested reactions make up compared with all reactions in model