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cobrapy — Claude Code skill: what it does, how to install

Guides COBRApy-based metabolic model analysis, from flux calculations and gene knockouts to media design and SBML checks.

Install into Claude Code · Skills CLI (Vercel) All methods and platforms ↓ 
npx skills add K-Dense-AI/scientific-agent-skills --skill cobrapy -a claude-code
Open on GitHub

What cobrapy does

This skill guides work with COBRApy metabolic models. It covers model loading and checks, flux balance analysis, parsimonious flux analysis, flux variability analysis, gene knockouts, media design, feasible-flux sampling, gap filling, and SBML validation.

It requires Python 3.9+ and the cobra package. Its examples target cobra 0.32.1; GLPK needs swiglpk, while commercial solvers require separate installation and licensing. Downloading remote models needs network access, but bundled textbook models can run offline.

FBA produces a constraint-based prediction, not proof of experimental growth or kinetic rates. Treat that as a reason to review formulas, charges, boundary reactions, and to record the model version, solver settings, medium, and bounds used for each analysis.

What it helps with

  • calculate fluxes in a metabolic network
  • compare FBA, pFBA, and FVA results
  • screen gene knockouts for growth effects
  • derive a minimal growth medium
  • validate an SBML model before analysis

Example prompts for the agent

  • "Load my SBML model and run FBA with the GLPK solver."
  • "Run FVA for PFK, FBA, and PGI."
  • "Screen gene knockouts and separate failed solves from low-growth results."

How to install cobrapy

1Skills CLI (Vercel)

npx skills add K-Dense-AI/scientific-agent-skills --skill cobrapy -a claude-code

2Manually: put the files in place

~/.claude/skills/cobrapy/SKILL.md

Copy the whole skill folder; for one project use .claude/skills/cobrapy/

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Questions about cobrapy

How do I install cobrapy in Claude Code?

Run npx skills add K-Dense-AI/scientific-agent-skills --skill cobrapy -a claude-code, then run npx skills add K-Dense-AI/scientific-agent-skills --skill cobrapy -a claude-code again. The skill file is at ~/.claude/skills/cobrapy/SKILL.md.

What does the cobrapy skill do?

It guides constraint-based metabolic modelling with COBRApy, including flux analysis, variability analysis, gene knockouts, media work, and SBML validation. It also covers gap-filling hypotheses and sampling feasible fluxes.

What does cobrapy require?

It requires Python 3.9+ and cobra. GLPK uses swiglpk, and remote model downloads need network access.

See also

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