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cobrapy

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About cobrapy

C

cobrapy

Performs constraint-based metabolic modeling

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.

View cobrapyAll AI Skills apps
Price
Free
Made by
k-dense-ai
Category
AI Skills
Website
github.com/k-dense-ai/scientific-agent-skills/cobrapy