COBRApy — Constraint-Based Metabolic Modeling

Overview

COBRApy is a Python package for constraint-based reconstruction and analysis (COBRA) of genome-scale metabolic models. It provides flux balance analysis (FBA), flux variability analysis (FVA), gene and reaction knockout screens, flux sampling, production envelopes, gapfilling, and media optimization on SBML-format metabolic networks.

When to Use

• Predicting microbial growth rates under different nutrient conditions (FBA)
• Identifying essential genes or reactions via single and double knockout screens
• Determining flux ranges and alternative optimal solutions (FVA)
• Sampling feasible flux distributions to characterize metabolic flexibility
• Designing minimal growth media or optimizing carbon sources
• Computing production envelopes for metabolic engineering targets
• Gapfilling incomplete draft models using a universal reaction database
• For kinetic modeling or dynamic ODE-based models, use Tellurium instead
• For pathway visualization on metabolic maps, use Escher instead

Prerequisites