COBRApy - Constraint-Based Reconstruction and Analysis

When to use

Use for loading/building metabolic networks, optimizing their steady-state fluxes, knockout screens, medium design, feasible-space sampling, and gap-filling hypotheses. FBA is a constraint-based prediction; it does not infer kinetic rates or establish experimental growth, thermodynamic feasibility, or flux identifiability.

Setup and reproducibility

Targets cobra 0.32.1 (import cobra), checked against its released source and current documentation.

uv pip install "cobra==0.32.1"
# Optional SciPy support for MATLAB I/O and array operations:
uv pip install "cobra[array]==0.32.1"

Plotting examples additionally require matplotlib, pandas, and seaborn. The cobra[chrr] extra supplies hopsy for the new CHRR sampler; that optional backend was documentation-reviewed, not executed in this refresh. In 0.32.1, sample() defaults to method="auto" (CHRR when hopsy is installed, otherwise OptGP). Choose the method explicitly to avoid environment-dependent changes.

Record model source/version/checksum, cobra and solver versions, objective, medium, bounds, tolerances, and any random seed with each analysis. GLPK handles the examples below; inspect cobra.util.solver.solvers before choosing an optional solver. Use "hybrid" for its HiGHS/OSQP interface when installed; the legacy "osqp" alias is deprecated. QP methods require a suitable backend. Start with processes=1; scripts using multiprocessing need a guarded entry point.

Workflow

1. Load, inspect, and validate a model

from cobra.io import load_model