cobrapy-metabolic-modeling
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
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