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

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