Welcome to cobrapy-bigg-client’s documentation!

This project provides a bridge between BiGG Models and cobrapy. It allows you to retrieve entities from the database as cobrapy objects.

Examples

List available models

from cobrapy_bigg_client import client
models = client.list_models()

Returns:

  bigg_id metabolites reactions genes organism
0 e_coli_core 72 95 137 Escherichia coli str. K-12 substr. MG1655
1 iAB_RBC_283 342 469 346 Homo sapiens
2 iAF1260 1668 2382 1261 Escherichia coli str. K-12 substr. MG1655
3 iAF1260b 1668 2388 1261 Escherichia coli str. K-12 substr. MG1655
4 iAF692 628 690 692 Methanosarcina barkeri str. Fusar
.

Retrieve a model from the database

from cobrapy_bigg_client import client
# save it as a file
client.download_model("e_coli_core")  #  writes the file in the current folder
# get a cobra model
model = client.download_model("e_coli_core", save=False)
type(model)  # => cobra.core.model.Model

Analyse a reaction

from cobrapy_bigg_client import client
model = client.download_model("e_coli_core", save=False)

reaction = model.reaction.ACALD

db_reaction = client.get_reaction(reaction)
db_reaction = client.get_reaction(reaction.id)  # it also works with id

type(db_reaciton)  # => cobra.core.reaction.Reaction

db_reaction.annotation

# Returns:
# {'models_containing_reaction': ['iJN746',
#   'iS_1188',
#   'iECW_1372',
#   'iNF517',
#   'iPC815',
#   'iRC1080',
#   'iEcolC_1368',
#   'iECP_1309',
#  ..."}

Indices and tables