Findthermoconsistentfluxsubset

findThermoConsistentFluxSubset(model, param, removeMetBool, removeRxnBool)[source]

Find the thermodynamically flux consistent subset of an input model, optionally after removing certain metabolites and reactions

INPUT model: structure with field:

  • .S - m x n stoichiometric matrix

  • .lb - n x 1 Lower bounds

  • .ub - n x 1 Upper bounds

OPTIONAL INPUT param param.epsilon: smallest flux that is considered nonzero param.printLevel: print level model.SConsistentMetBool model.SConsistentRxnBool model.fluxConsistentMetBool flux consistent metabolites model.fluxConsistentRxnBool flux consistent reactions

removeMetBool: m x 1 logical index of metabolites to

remove before computing the thermodynamically consistent subset

removeRxnBool n x 1 logical index of reactions to

remove before computing the thermodynamically consistent subset

ADVANCED OPTIONAL INPUT (Do not play with these parameters unless you know what you are doing) param.iterationMethod: method to iteratively enlarge the thermodynamically consistent subset

param.formulation: mathematical formulation of inner iteration param.relaxBounds: Relax bounds that don’t include zero. Default is false. param.nMax

OUTPUT thermoFluxConsistentMetBool m x 1 boolean vector indicating thermodynamically flux consistent mets thermoFluxConsistentRxnBool n x 1 boolean vector indicating thermodynamically flux consistent rxns

model input model with the following fields added

*.thermoFluxConsistentMetBool m x 1 boolean vector indicating thermodynamically flux consistent mets *.thermoFluxConsistentRxnBool n x 1 boolean vector indicating thermodynamically flux consistent rxns *.thermoFwdFluxConsistentRxnBool n x 1 boolean vector indicating forward thermodynamically flux consistent rxns *.thermoRevFluxConsistentRxnBool n x 1 boolean vector indicating reverse thermodynamically flux consistent rxns

thermoConsistModel subset of the input model that is thermodynamically consistent

EXAMPLES: See COBRA.papers/2022_cardOpt/driver_testFindThermoFluxConsistency.mlx

COBRA.tutorials/analysis/vonBertalanffy/findThermoConsistentFluxSubset/tutorial_findThermoConsistentFluxSubset.mlx