vivarium.library.cobra_fba module

class vivarium.library.cobra_fba.CobraFBA(config={})

Bases: object

This class provides an interface to cobra FBA. It can load in BiGG models (http://bigg.ucsd.edu/models) if provided a model_path to a saved JSON BiGG model, or load in a novel model specified by stoichiometry, reversibility, and objective.

TODO (Eran) – MOMA option is provided, but has not yet been tested.

cobra_configuration

constrain_flux(bounds={})

add externally imposed constraints

constrain_reaction_bounds(bounds={})

external_reactions()

get_reaction_bounds(reactions=[])

get_reactions(reactions=[])

internal_reactions()

objective_value()

optimize()

reaction_ids()

read_exchange_fluxes()

removes the prefix from exchange reactions keys, leaving only the external molecule id

read_exchange_reactions()

leaves the prefix in exchange reactions keys

read_fluxes(molecules)

read_internal_fluxes()

regulate_flux(reactions)

regulate flux based on True/False activity values for each id in reactions dictionary

set_exchange_bounds(bounds={})

apply new_bounds for the defined molecules. reset unincluded molecules to their exchange_bounds.

class vivarium.library.cobra_fba.JsonFBA(path)

Bases: object

vivarium.library.cobra_fba.build_model(stoichiometry, reversible, objective, external_molecules, default_upper_bound=1000)

vivarium.library.cobra_fba.extract_model(model)

TODO – where do demands and sinks go? demands = model.demands sinks = model.sinks

# boundary reactions include exchanges, demands, sinks boundary = model.boundary boundary_reactions = [reaction.id for reaction in boundary]

vivarium.library.cobra_fba.swap_synonyms(model)

vivarium.library.cobra_fba.test_canonical()

vivarium.library.cobra_fba.test_demo()

vivarium.library.cobra_fba.test_fba()

vivarium.library.cobra_fba.test_minimal()