Dynamicfba

dynamicFBA(model, substrateRxns, initConcentrations, initBiomass, timeStep, nSteps, plotRxns, exclUptakeRxns)[source]

Performs dynamic FBA simulation using the static optimization approach

USAGE

[concentrationMatrix, excRxnNames, timeVec, biomassVec] = dynamicFBA (model, substrateRxns, initConcentrations, initBiomass, timeStep, nSteps, plotRxns, exclUptakeRxns)

INPUTS

  • model – COBRA model structure

  • substrateRxns – List of exchange reaction names for substrates initially in the media that may change (e.g. not h2o or co2)

  • initConcentrations – Initial concentrations of substrates (in the same structure as substrateRxns)

  • initBiomass – Initial biomass (must be non zero)

  • timeStep – Time step size

  • nSteps – Maximum number of time steps

OPTIONAL INPUTS

  • plotRxns – Reactions to be plotted (Default = {‘EX_glc(e)’, ‘EX_ac(e)’, ‘EX_for(e)’})

  • exclUptakeRxns – List of uptake reactions whose substrate concentrations do not change (Default = {‘EX_co2(e)’, ‘EX_o2(e)’, ‘EX_h2o(e)’, ‘EX_h(e)’})

OUTPUTS

  • concentrationMatrix – Matrix of extracellular metabolite concentrations

  • excRxnNames – Names of exchange reactions for the EC metabolites

  • timeVec – Vector of time points

  • biomassVec – Vector of biomass values

If no initial concentration is given for a substrate that has an open uptake in the model (i.e. model.lb < 0) the concentration is assumed to be high enough to not be limiting. If the uptake rate for a nutrient is calculated to exceed the maximum uptake rate for that nutrient specified in the model and the max uptake rate specified is > 0, the maximum uptake rate specified in the model is used instead of the calculated uptake rate.

Note

The dynamic FBA method implemented in this function is essentially the same as the method described in [Varma, A., and B. O. Palsson. Appl. Environ. Microbiol. 60:3724 (1994)]. This function does not implement the dynamic FBA using dynamic optimization approach described in [Mahadevan, R. et al. Biophys J, 83:1331-1340 (2003)].