7. Refine model with FVA

contrabass can generate a new model in which the flux bounds of the reactions have been updated with the values obtained in the computation of FVA . In this way the model can receive a different topology and the number of chokepoints, essential reactions or dead reactions, among others, can vary. The pseudocode of this operation is presented below:

7.1. Pseudocode

• Update model flux bounds with Flux Variability Analysis

function update_flux_bounds_with_fva(model, fraction_of_optmimum_growth)
    max_fva, min_fva = flux_variability_analysis(model, fraction_of_optmimum_growth)
    for reaction in model
        reaction.upper_flux_bound = max_fva[reaction]
        reaction.lower_flux_bound = min_fva[reaction]
    return model

7.2. Command

Apart from computing vulnerabilities and generating reports, CONTRABASS can also produce a new model with refined fluxes (procedure explained above). This can be achieved with command:

$ contrabass new-model fva-constrained MODEL.xml

Alternatively a new model can be generated refined with FVA and with DEMs removed after.

$ contrabass new-model fva-constrained-without-dem MODEL.xml

.

Note that the previous command is equivalent as first constraining the model with FVA (running command contrabass new-model fva-constrained) and then removing DEM on the output model (running command contrabass new-model without-dem):

$ contrabass new-model fva-constrained MODEL.xml
$ mv output.xml MODEL_FVA.xml
$ contrabass new-model without-dem MODEL_FVA.xml