Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.
---
name: cobrapy
description: Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.
license: GPL-2.0 license
allowed-tools: Read Write Edit Bash
compatibility: Requires Python 3.9+ (cobra 0.30+ dropped 3.8). Install with uv pip install. GLPK (swiglpk) is the default solver; CPLEX/Gurobi optional. load_model fetches from bundled data, BiGG, or BioModels (network required for remote models).
metadata: {"version": "1.1", "skill-author": "K-Dense Inc."}
---
# 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… load the full skill through Skill Me