experimentalData

• alberty2006

boundsToFiles(model)

Prints out the model bounds as a tab delimited text file

USAGE:

boundsToFiles(model)

INPUT:

model:

readMetRxnBoundsFiles(model, setDefaultConc, setDefaultFlux, concMinDefault, concMaxDefault, metBoundsFile, rxnBoundsFile, printLevel)

Sets default concentration and flux bounds, and/or optionally read in upper and lower bounds from files.

Upper and lower bounds on metabolite concentrations and reaction fluxes may be read in and mapped to the model. Bounds read from files overwrite reconstruction bounds, or default bounds.

USAGE:

model = readMetRxnBoundsFiles(model, setDefaultConc, setDefaultFlux, concMinDefault, concMaxDefault, metBoundsFile, rxnBoundsFile, printLevel)

INPUTS:

model: structure with fields:

• model.mets

• model.rxns

setDefaultConc: 1 = sets default bounds on conc setDefaultFlux: 1 = sets all reactions reversible [-1000, 1000] concMaxDefault: Default upper bound on metabolite

concentrations in M

concMinDefault: Default lower bound on metabolite

concentrations in M

OPTIONAL INPUTS:

metBoundsFile: name of tab delimited file with metabolite bounds

format: ‘%s %f %f’ i.e. abbreviation lowerBound upperBound

rxnBoundsFile: name of tab delimited file with reaction bounds

format: ‘%s %f %f’ i.e. abbreviation lowerBound upperBound

OUTPUT:

model: structure with fileds:

• model.concMin(j)

• model.concMax(j)

• model.lb

• model.ub