Modelgeneration

• Fluxconsistency
  • Dca
  • Greedy
• Modelverification
• Massbalance
• Modelproperties
• Stoichconsistency

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

removeCompartments(model, comp, newComp)

function [modelDecomp] = RemoveCompartments(model,comp,NewComp)

Function removes list of compartments in metabolite names. It removes duplicates and empty entries.

model Model structure comp List of compartments to remove or replace (e.g., {‘c’,’n’} newComp New compartment (optional, default: ‘[c]’)

modelDecomp Decompartementalized model structure IT Nov 2009 SM Feb 2014 - line 31, updated function name “AddReaction” to “addReaction” IT April 2024 - updated script

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