A python-based implementation for the context-specific metabolic model extraction methods from Vlassis et al. 2014
Project description
pyfastcore
A python implementation of the context-specific model extraction method FastCore by Vlassis et al. (2014)
- Vlassis, N., Pacheco, M. P., & Sauter, T. (2014). PLoS Computational Biology, 10(1) [Full Article]
INSTALATION
You can install pyfastcore using:
python setup.py install
of via pip:
pip install pyfastcore
USAGE EXAMPLE
from cobra.test import create_test_model
from pyfastcore import Fastcore
# Loading a toy model of E. coli from cobra.test package
model = create_test_model('textbook')
# Define the list of core reactions
core_reactions = ['Biomass_Ecoli_core', 'ATPM']
# Setting the penalty of exchange fluxes to 0
penalties = {}
for r in model.exchanges:
penalties[r.id] = 0
# Creating a fastcore solver instnace
fc_builder = Fastcore(model, core_reactions,
penalties=penalties,
default_penalty=10,
debug_mode=True)
# Rnunning fastcore
fc_builder.fast_core()
# checking the list of reaction in the consistent network found
consistent_subnetwork = fc_builder.consistent_subnetwork
print("Consistent subnetworksize set size", len(consistent_subnetwork))
print("Context specific core:")
print(consistent_subnetwork)
# creating a cobra model for the consistent network found
print(f"Building context-specific model for {model.id}")
cs_model = fc_builder.build_context_specific_model()
# Running and FBA using subnetwork model
print("Running FBA on CS-model")
sol = cs_model.optimize()
print(cs_model.summary())
Citation
If you use this package cite:
- Ponce-De-Leon, M. et al. (2015) Consistency Analysis of Genome-Scale Models of Bacterial Metabolism: A Metamodel Approach. PloS one, 10, e0143626.
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