Simulating a Model¶
Complete COBRAkbase models can be simulated through a multitude of FBA methods, and a subset of community methods. Individual and community COBRAkbase models can initially be constrained for various biochemical and physical processes.
Constraints¶
Elemental uptake¶
The total uptake of specific elements can be constrained through the ElementUptakePkg package:
from modelseedpy.fbapkg import ElementUptakePkg
eleup = ElementUptakePkg(model)
eleup.build_package(element_limits)
The package applies uptake limits for any elemental symbol (values and keys of the element_limits dictionary, respectively) to a given model.
Reaction Thermodynamics¶
The thermodynamic free energy of each reaction, and variable formation energies of each metabolite, can be constrained through the FullThermoPkg package:
from modelseedpy.fbapkg import FullThermoPkg
tfa = FullThermoPkg(model)
tfa.build_package(parameters)
The package applies free energy constraints for all reactions in a given model, based upon the free energy data in the ModelSEED Database. The user must specify the "modelseed_db_path" `` in the argument (*parameters* ``dict). The user is also able to redefine default values through parameters, which is detailed in the respective API documentation.
An example of FullThermoPkg is available here .
Community member growth rates¶
The growth rate of community members can be constrained with a kinetic rate constant through the CommKineticPkg package:
from modelseedpy.community import CommKineticPkg
commkin = CommKineticPkg(model)
commkin.build_package(kinetic_coef)
The package applies the kinetic coefficient (kinetic_coef float) to the biomass reaction of each species in a given community model.
FBA Methods¶
COBRAkbase models, either with or without additional constraints, can be simulated through a few FBA processes. A broad example of FBA in ModelSEEDpy is available here .
Bilevel¶
reactionuse¶
dFBA¶
metabofba¶
The MetaboFBA Package forces flux through observed metabolites in metabolomics data. An example is available here .
Flexible Biomass¶
The FlexibleBiomass Package enables the coefficients on a biomass reaction to vary. An example is available here .
Media Scan¶
The Media Scan Package concisely tests numerous media for a single model. An example is available here .
Community Methods¶
COBRAkbase community models, either with or without additional constraints, can be simulated through a few packages.
MSCommunity¶
The MSCommunity package is an original package from ModelSEEDpy that resolves metabolite-level cross-feeding and provides a concise API for numerous constraints and FBA methods:
from modelseedpy.community import MSCommunity
mscom = MSCommunity(model, names=[], abundances=None, pfba = True, lp_filename = None)
solution = mscom.run(media = None, pfba = True)
A community COBRA model is passed to the package with a list of the community members, which are indexed sequentially according to their community number. The abundances of the community members can be provided in relative or absolute terms (values & keys, respectively, in abdundances dict). The community can then be simulated in an arbitrary KBase media, where None specifies a complete media.
Community cross-feeding is calculated through the compute_interactions interactions function:
cross_feeding_df = mscom.compute_interactions(solution = None, threshold=1)
An FBA solution, such as that from mscom.run, is parsed to determine the cross-feeding interactions of the community that surpass a flux threshold (threshold int). The function returns a Pandas DataFrame , which conveniently permits user manipulation of the data.