Basic usage

Loading and saving

ReFramed can load and save models SBML format. You optionally can use the flavor argument to indicate if the model uses the new fbc2 format (default) or the legacy cobra format.

from reframed import load_cbmodel
model = load_cbmodel('e_coli_core.xml', flavor='fbc2')

If you make any changes to the model, you can choose to save it in a different flavor.

from reframed import save_cbmodel
save_cbmodel(model, 'e_coli_core_modified.xml', flavor='cobra')

Model manipulation

Once you load a model you can easily access the model’s attributes and perform different kinds of operations using the model object.

You can quickly inspect your model by printing it:

> model

R_ACALD: M_acald_c + M_coa_c + M_nad_c <-> M_accoa_c + M_h_c + M_nadh_c
R_ACALDt: M_acald_e <-> M_acald_c
R_ACKr: M_ac_c + M_atp_c <-> M_actp_c + M_adp_c
R_ACONTa: M_cit_c <-> M_acon_C_c + M_h2o_c
R_ACONTb: M_acon_C_c + M_h2o_c <-> M_icit_c
(...)

The summary method also gives a quick overview of metabolites, compartments, and reactions:

> model.summary()

Metabolites:
c 52
e 20

Reactions:
enzymatic 48
transport 25
exchange 20
sink 0
other 2

You can also inspect particular metabolites and reactions.

> model.reactions.R_PGI

R_PGI: M_g6p_c <-> M_f6p_c

> model.metabolites.M_g6p_c

D-Glucose-6-phosphate

> model.reactions.R_TKT1.gpr

(G_b2465 or G_b2935)

You can easily make changes to a model. For instance, let’s change the maximum glucose uptake rate:

model.reactions.R_EX_glc_e.lb = -10

But for programmatic access, you may want to use reactions as a dictionary instead:

for reaction in model.reactions.values():
    reaction.lb = 0

You can easily add a new reactions to a model (optionally specifying flux bounds) :

model.add_reaction_from_str('R_abc: A + 0.5 B --> 2 C')
model.add_reaction_from_str('R_s2p: S <-> P [-10, 10]')

You can add ratio constraints:

model.add_ratio_constraint("R_PGI", "R_G6PDH", 1.5)

You can also remove reactions, metabolites, genes or compartments:

model.remove_reaction('R_PGI')
model.remove_metabolites(['M_h2o_c', 'M_h_c'])

There is a lot more you can try! Just take a look into the API.