Experimentaldata

• Ecoli
• Alberty2006
• Transport
• Metaboliteconcentrations

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 Concentration units in Molar

• 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