Overview
cobrapy is an open-source data skill for Claude Code and compatible agents, published by K-Dense-AI. Its author describes it as: “Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.”. The project has 44k stars on GitHub and is available under the MIT license. Add it to your setup with `git clone https://github.com/K-Dense-AI/scientific-agent-skills ~/.claude/skills/cobrapy`.
What cobrapy does
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.
What’s inside
The SKILL.md for cobrapy is organised into these sections:
- 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
Installation
Add cobrapy to your agent with:
git clone https://github.com/K-Dense-AI/scientific-agent-skills ~/.claude/skills/cobrapyReview a skill’s source before installing it — skills can instruct your agent to run commands. This command comes from the skill’s public repository, which is the source of truth for setup steps. New to skills? Read how to install Claude Code skills.
Supported agents
Neither the skill nor its repository names a specific agent. It uses the SKILL.md format, which several agents can load — check the repository for any agent-specific requirements.
License
cobrapy is published under the MIT license.
Strengths
- Clear MIT license — safe to read and adapt within its terms
- Ships in K-Dense-AI/scientific-agent-skills, an established project with 43,503 GitHub stars
- Actively maintained — repository updated in the last 30 days
- Its repository gained 9,682 GitHub stars over the last 20 days
Author
Topics
Frequently asked questions
- What does cobrapy 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 cobrapy?
- Run git clone https://github.com/K-Dense-AI/scientific-agent-skills ~/.claude/skills/cobrapy in your agent, then reload your skills. Review the source at https://github.com/K-Dense-AI/scientific-agent-skills before installing.
- Is cobrapy free to use?
- Yes. cobrapy is free and open source under the MIT license, so you can read, run, and adapt it within that license's terms.
- Where does cobrapy come from?
- cobrapy ships inside K-Dense-AI/scientific-agent-skills, a repository that contains 42 catalogued skills in total. The repository's 43,503 GitHub stars apply to that whole collection, not to this skill on its own.