COBRApy Bioinformatics

About

COBRApy is a specialized skill for Claude Code designed to handle complex metabolic modeling tasks using Python-based COBRA methodologies. It enables researchers and developers to manage genome-scale metabolic models, execute Flux Balance Analysis (FBA), perform Flux Variability Analysis (FVA), and conduct comprehensive gene knockout studies. Whether you are predicting cellular growth rates, optimizing metabolic pathways for bio-production, or analyzing metabolic flux distributions, this skill provides the necessary patterns and best practices for robust bioinformatics analysis and SBML model integration.

Key Features

• Flux Variability Analysis (FVA) with loopless and optimality constraints
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• Gene and reaction deletion studies for essentiality screening
• Flux Balance Analysis (FBA) and Parsimonious FBA simulations
• SBML, JSON, and YAML metabolic model management
• Flux sampling and phenotype production envelope calculations

Use Cases

• Identifying essential genes and potential targets for metabolic engineering
• Designing optimized growth media and minimal media for specific organisms
• Simulating microbial growth and metabolic flux under varying environmental conditions