alterlab-cobrapy

# COBRApy - Constraint-Based Reconstruction and Analysis ## Overview COBRApy is a Python library for constraint-based reconstruction and analysis (COBRA) of metabolic models, essential for systems biology research. Work with genome-scale metabolic models, perform computational simulations of cellular metabolism, conduct metabolic engineering analyses, and predict phenotypic behaviors. ## When to Use This Skill Use this skill when the user wants to: - Load a genome-scale metabolic model (SBML/JSON/YAML) and simulate growth with FBA/pFBA. - Predict knockout phenotypes, essential genes, or minimal media. - Explore flux space with FVA, flux sampling, or production envelopes. - Build, gapfill, or curate a constraint-based model. ### Does NOT Trigger | Scenario | Use Instead | |----------|-------------| | Looking up a pathway or reaction annotation rather than simulating | `alterlab-kegg`, `alterlab-reactome` | | Enzyme kinetic parameters (kcat, Km) for a reaction | `alterlab-brenda` | | Graph analysis of the metabolic network (centrality, communities) rather than flux | `alterlab-networkx` | | Metabolomics measurements and their identification | `alterlab-metabolomics-wb`, `alterlab-hmdb` | | Multi-objective optimization that is not a flux-balance problem | `alterlab-pymoo` | ## Installation and Requirements ```bash uv pip install cobra # 0.32.x as of 2026-09 uv pip install 'cobra[array]' # scipy extra, for array-based model handling uv pip install 'cobra[...