cobrapy
Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.
npx skills add K-Dense-AI/scientific-agent-skills --skill cobrapy --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# COBRApy - Constraint-Based Reconstruction and Analysis ## Overview COBRApy is a Python library for constraint-based reconstruction and analysis (COBRA) of metabolic models, essential for systems biology research. Work with genome-scale metabolic models, perform computational simulations of cellular metabolism, conduct metabolic engineering analyses, and predict phenotypic behaviors. **Version note:** Examples target **cobra 0.31.1** on PyPI (import `cobra`). Docs: [cobrapy.readthedocs.io](https://cobrapy.readthedocs.io/en/latest/). Repo: [opencobra/cobrapy](https://github.com/opencobra/cobrapy). ## When to Use This Skill Use this skill when: - Loading, building, or exporting genome-scale metabolic models (SBML, JSON, YAML) - Running FBA, pFBA, FVA, or flux sampling on COBRA models - Performing gene or reaction knockout screens and production envelope analysis - Designing or optimizing growth media and exchange constraints - Gap-filling infeasible models or validating model consistency ## Installation ```bash uv pip install "cobra==0.31.1" ``` MATLAB model I/O (optional): ```bash uv pip install "cobra[array]==0.31.1" ``` COBRApy uses [optlang](https://optlang.readthedocs.io/) for
- Overview
- When to Use This Skill
- Installation
- Core Capabilities
- 1. Model Management
- 2. Model Structure and Components
- 3. Flux Balance Analysis (FBA)
- 4. Flux Variability Analysis (FVA)
- 5. Gene and Reaction Deletion Studies
- 6. Growth Media and Minimal Media
- 7. Flux Sampling
- 8. Production Envelopes
- 9. Gapfilling
- 10. Model Building
uv pip install "cobra==0.31.1" uv pip install "cobra[array]==0.31.1"
What does the cobrapy skill do?
Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.
How do I install it?
Run `npx skills add K-Dense-AI/scientific-agent-skills --skill cobrapy --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From K-Dense-AI/scientific-agent-skills, a repository with 32,619 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.