cobrapy

SUMMARY

What it does

This skill provides procedural knowledge for constraint-based metabolic modeling using COBRApy. It enables loading, building, and exporting genome-scale metabolic models (SBML, JSON, YAML), running flux balance analysis (FBA), parsimonious FBA, flux variability analysis (FVA), flux sampling, gene and reaction deletion studies, growth media optimization, production envelope analysis, and gap-filling. It includes workflows for model management, context-manager-based temporary modifications, and best practices for solver selection and parallelization. The skill is designed for systems biology research and metabolic engineering, requiring Python 3.9+ and the cobra library (version 0.31.1).