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',
# ..."}