modelGeneration¶

checkCobraModelUnique
(model, renameFlag)[source]¶ Checks uniqueness of reaction and metabolite names
Usage
model = checkCobraModelUnique(model, renameFlag)Input
 model – COBRA model structure
Optional input
 renameFlag – Renames nonunique reaction names and metabolites (Default = false)
Outputs
 model – COBRA model structure
 isUnique – true if the model has unique reaction and metabolite names

checkDuplicateRxn
(model, method, removeFlag, printLevel, boundsFlag)[source]¶ 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)Input
 model – Cobra model structure
Optional input
 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

checkObjective
(model)[source]¶ Prints out the Stoichiometric Coefficients for each Metabolite, with the name of the objective
Usage
objectiveAbbr = checkObjective(model)Input
 model – COBRA model structure
Output
 objectiveAbbr – Objective reaction abbreviation

detectDeadEnds
(model, removeExternalMets)[source]¶ 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)[source]¶ 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

removeDeadEnds
(model)[source]¶ 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)[source]¶ 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
Output
 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
 constrOpt –
Constraint options

test4HumanFctExt
(model, test, optionSinks)[source]¶ test for the ~288 human functions
Usage
[TestSolution,TestSolutionName,TestedRxns,PercTestedRxns] = test4HumanFctExt(model,test,optionSinks)Inputs
 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
Outputs
 TestSolution – array containing the optimal value for the different tests
 TestSolutionName – array containing the names for the different tests

testATPYieldFromCsources
(model, modelName)[source]¶ computes the ATP yield from various carbon sources in Recon2 or Recon3.
Usage
[Table_csources,TestedRxns,PercTestedRxns] = testATPYieldFromCsources(model,modelName)Inputs
 model – model structure
 modelName name of the model structure, by default Recon3
Outputs
 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