COBRApy

COBRApy is a Data skill for Claude Code, published by K-Dense-AI in scientific-agent-skills.

33.5K stars3.3K forkson K-Dense-AI/scientific-agent-skillsAdded 2026/08/14Repository updated 2026/08/13

agent-skillsai-scientistbioinformaticschemoinformaticsclaudeclaude-skillsclaudecodeclinical-researchcomputational-biologydata-analysisdrug-discoverygenomicsmaterials-sciencemetabolomicsproteomicsscientific-computingscientific-visualization

Install in seconds

Install COBRApy

Copy COBRApy into your Claude Code skills folder. Run the command in your terminal, or review the source on GitHub before installing.

terminal

npx degit https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/cobrapy ~/.claude/skills/cobrapy

Requires Node.js. Downloads this skill only — not the rest of the repository — into your Claude Code skills folder.

Without Node.js

git clone https://github.com/K-Dense-AI/scientific-agent-skills.git

Clones the whole repository, then copy the skill’s own directory into your skills folder yourself.

In this catalog

Source file: skills/cobrapy/SKILL.md in K-Dense-AI/scientific-agent-skills
Installs to: ~/.claude/skills/cobrapy
Collection: One of 25 skills cataloged from this repository
Category: Data — 668 skills

What COBRApy does

COBRApy performs constraint-based metabolic modeling for systems biology, including FBA, FVA, gene knockouts, flux sampling, and SBML model handling. Use it when working with genome-scale metabolic models to simulate and optimize cellular metabolism or design metabolic engineering experiments.

COBRApy is cataloged under Data on DirSkills. COBRApy comes from a repository tagged agent-skills, ai-scientist, bioinformatics, chemoinformatics and claude.

Documentation

README

Excerpt

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. Repo: opencobra/cobrapy.

When to Use This Skill

This is the opening of the README. Read the full README on GitHub.

Frequently asked about COBRApy

What else does K-Dense-AI publish alongside COBRApy?
COBRApy is one of 25 skills that DirSkills catalogs from K-Dense-AI/scientific-agent-skills, the repository it ships in. Its siblings there include Adaptyv Bio Foundry API, Aeon and Analytical Method Validation. Each one is a separate skill with its own page in this directory, installs the same way COBRApy does, and is maintained by K-Dense-AI in that same repository. The rest of the collection is listed on the K-Dense-AI/scientific-agent-skills page.
How does COBRApy compare to other Data skills?
COBRApy ranks #47 by stars among the 668 Data skills in this catalog. The most-starred ones next to it are Benchmark Methodology, Jupyter Notebook and Solana. DirSkills ranks by the star count of the repository each skill ships in, so that order reflects how popular those repositories are rather than any review of COBRApy against them. Open each page to compare what they document and how they install.