findCPcore - find ChokePoint reactions in genome-scale metabolic models

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

Table of Contents

• Install
• Maintainers
• Contributing
• License

Install

$ pip install findCPcore

Quickstart

Example 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()

Maintainers

@alexOarga

Contributing

Feel free to dive in! Open an issue or submit PRs.

Standard Readme follows the Contributor Covenant Code of Conduct.

License

GPL © Alex Oarga