findCPcore is a Python tool for the computation of chokepoint reactions in genome-scale metabolic models. The tool allows the calculation of chokepoints taking into account only the topology of the metabolic network or also using its dynamic information.
The documentation can be found at readthedocs and can also be downloaded.
A command line application of the tool is provided at findCPcli.
You can also try it with Binder.
For citation purposes please refer to:
Oarga et al. "Growth Dependent Computation of Chokepoints in Metabolic Networks." International Conference on Computational Methods in Systems Biology. Springer, Cham, 2020. https://doi.org/10.1007/978-3-030-60327-4_6
$ pip install findCPcoreExample of network refinement and chokepoint computation:
from findCPcore import CobraMetabolicModel
model = CobraMetabolicModel("aureus.xml")
# update flux bounds with FVA
model.fva(update_flux=True)
# compute chokepoints
model.find_chokepoints()
# get chokepoints
model.chokepoints()Feel free to dive in! Open an issue or submit PRs.
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GPL © Alex Oarga