fullthermopkg

FullThermoPkg()

This class applies and simulates rigorous thermodynamic constraints upon COBRA models:

from modelseedpy.fbapkg import FullThermoPkg
tfa = FullThermoPkg(model)

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

build_package()

A cobrakbase model is simulated with the parameterized kinetics data over the defined time and conditions:

tfa.build_package(parameters, verbose = True)

• parameters dict: specifies simulations parameters in base metric units – e.g. Molar, Kilojoules per mol, and Kelvins – that are used to populate the FBA simulation. The default concentrations,

{
           "cpd00067_c0":[0.0000001,0.0000001],
           "cpd00007_c0":[1E-07,8.2E-06],
           "cpd00011_c0":[1E-08,0.0014],
           "cpd00067_e0":[3.16228E-07,3.16228E-07],
           "cpd00009_e0":[0.056,0.056],
           "cpd00048_e0":[0.0030,0.0030],
           "cpd00013_e0":[0.019,0.019],
           "cpd00971_e0":[0.16,0.16],
           "cpd00205_e0":[0.022,0.022],
           "cpd10515_e0":[0.062,0.062],
           "cpd00011_e0":[0.00010,0.00010],
           "cpd00007_e0":[8.2E-06,8.2E-06],
           "cpd00027_e0":[0.020,0.020]
}

and compartment potentials (the extracellular environment is 0 by definition to facilitate community modeling),

{
           "e0":0,
           "c0":-160
}

are supplanted by specified parameters

{
           "default_max_conc":0.02,
           "default_min_conc":0.000001,
           "default_max_error":5,
           "custom_concentrations":{},
           "custom_deltaG_error":{},
           "compartment_potential":{},
           "temperature":298,
           "filter":null,
           "infeasible_model": false,
           "dgbin":false
}

that can be adjusted through the parameters argument. The only required key in parameters that must be provided by the user is the modelseed_db_path that enables the import of the ModelSEED Database.

• verbose bool: specifies whether simulation details and calculations will be printed, which is valuable for troubleshooting.

Accessible content

Several objects within the FullThermo class may be useful for subsequent post-processing or troubleshooting of the simulation results:

• model cobra.core.model.Model: The cobrakbase model, with the corresponding constraints, that is simulated.

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

• pkgmgr modelseedpy.fbapkg.mspackagemanager.MSPackageManager: The collection of associated classes that are used in the FullThermo package.