Description
cobrapy is an agent skill for constraint-based metabolic modelling with COBRApy. It covers loading and building metabolic networks, optimising their steady-state fluxes, and running knockout screens. It also covers medium design, sampling of the feasible flux space and gap-filling hypotheses. The methods named include flux balance analysis, parsimonious FBA, flux variability analysis, gene knockouts, flux sampling, growth media and production envelopes. The skill is careful about what the methods can show. Flux balance analysis is a constraint-based prediction. It does not infer kinetic rates, and it does not establish experimental growth, thermodynamic feasibility or flux identifiability. The skill targets cobra 0.32.1, which is imported as cobra, and it was checked against the released source and current documentation. The install command is uv pip install with cobra pinned to 0.32.1, and an optional extra adds SciPy support for MATLAB file input and output and array operations. It is part of the k-dense-ai scientific agent skills repository on GitHub, which has about 49,600 stars.…
Highlights
- Flux balance, parsimonious and variability analysis
- Gene knockout screens
- Medium design and growth media
- Flux sampling and gap filling
- Pinned to cobra 0.32.1
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cobrapy FAQ
What can it model?
Metabolic networks, including building and loading them, optimising steady-state fluxes, knockouts, medium design and sampling.
What are the limits of FBA?
The skill says flux balance analysis is a prediction that does not infer kinetic rates or establish experimental growth or thermodynamic feasibility.
Which version does it target?
cobra 0.32.1, which is imported as cobra.
Is there an optional extra?
Yes. An install with cobra[array] adds SciPy support for MATLAB I/O and array operations.
How do I install it?
Run npx skills add https://github.com/k-dense-ai/scientific-agent-skills --skill cobrapy, then uv pip install cobra==0.32.1.
Is it checked for security?
Its security audits show passes from Gen Agent Trust Hub, Socket and Snyk.
What are the best cobrapy alternatives?
Popular alternatives to cobrapy include gget, anndata and arboreto. See all cobrapy alternatives