flexiblebiomass

FlexibleBiomassPkg()

This class constrains metabolites of the biomass reaction and adjusts the objective values:

from modelseedpy.fbapkg import FlexibleBiomassPkg
flexbio = FlexibleBiomassPkg(model)

• model cobra.core.model.Model: the CobraKBase model that will be constrained. The conversion from standard COBRA models to CobraKBase models is facilitated by the cobrakbase package.

build_package()

The drain reactions are created through this function:

flexbio.build_package(parameters)

• parameters dict: The parameters that govern how the constraints be created and implemented into the model. The only require key:value entry is specifying the bio_rxn_id of the biomass reaction. The default dictionary

{
           "flex_coefficient":0.75,
           "use_rna_class":[-0.75,0.75],
           "use_dna_class":[-0.75,0.75],
           "use_protein_class":[-0.75,0.75],
           "use_energy_class":[-0.1,0.1],
}

can be supplanted in the parameters argument by listing the key to be changed with the new value.

Accessible content

The FlexibleBiomassPkg class contains a couple of accessible content that may be useful for subsequent post-processing or troubleshooting:

• model cobra.core.model.Model: The cobrakbase model that possesses the implemented drain reactions.

• variables & parameters dict: Dictionaries of the linear programming variables and simulation parameters, respectively.