Interfaces

CobraPy

ReFramed supports conversion of its models from and to CobraPy models. This allows users to take full advantage of all the features present in both packages.

You can load a model in ReFramed and simulate it with CobraPy:

> from reframed import load_cbmodel, to_cobrapy

> rf_model = load_cbmodel("e_coli_core.xml")
> cb_model = to_cobrapy(rf_model)
> cb_model.optimize()

Optimal solution with objective value 0.874

You can load a model with CobraPy and simulate it with ReFramed:

> from cobra.io import read_sbml_model
> from reframed import from_cobrapy, FBA

> cb_model = read_sbml_model("e_coli_core.xml")
> rf_model = from_cobrapy(cb_model)
> FBA(rf_model)

Objective: 0.8739215069684306
Status: Optimal

Escher

If you are using Jupyter notebooks, you can easily visualize flux distributions using Escher.

The following will start the Escher widget inside a Jupyter notebook cell:

> from reframed import fluxes2escher
> sol = pFBA(model)
> fluxes2escher(sol.values)

You can also specify which Escher map to use and send additional arguments directly to the Escher API:

> fluxes2escher(sol.values, map_name='e_coli_core.Core metabolism')

> fluxes2escher(sol.values, hide_secondary_metabolites=True)