cobrapy

1# COBRApy - Constraint-Based Reconstruction and Analysis
2 
3## When to use
4 
5Use for loading/building metabolic networks, optimizing their steady-state fluxes,
6knockout screens, medium design, feasible-space sampling, and gap-filling hypotheses.
7FBA is a constraint-based prediction; it does not infer kinetic rates or establish
8experimental growth, thermodynamic feasibility, or flux identifiability.
9 
10## Setup and reproducibility
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12Targets **cobra 0.32.1** (import `cobra`), checked against its released source and
13[current documentation](https://cobrapy.readthedocs.io/en/latest/).
14 
15```bash
16uv pip install "cobra==0.32.1"
17# Optional SciPy support for MATLAB I/O and array operations:
18uv pip install "cobra[array]==0.32.1"
19```
20 
21Plotting examples additionally require matplotlib, pandas, and seaborn. The
22`cobra[chrr]` extra supplies hopsy for the new CHRR sampler; that optional backend
23was documentation-reviewed, not executed in this refresh. In 0.32.1, `sample()`
24defaults to `method="auto"` (CHRR when hopsy is installed, otherwise OptGP).
25Choose the method explicitly to avoid environment-dependent changes.
26 
27Record model source/version/checksum, cobra and solver versions, objective,
28medium, bounds, tolerances, and any random seed with each analysis. GLPK handles
29the examples below; inspect `cobra.util.solver.solvers` before choosing an
30optional solver. Use `"hybrid"` for its HiGHS/OSQP interface when installed;
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