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. ## Installation and Requirements ```bash uv pip install 'cobra>=0.29,<0.32' ``` **Requirements:** Python 3.8+; depends on optlang and a solver (GLPK ships by default via swiglpk; CPLEX/Gurobi optional). Optional for plots: matplotlib, seaborn, pandas (pandas is already a hard dependency). Flux sampling and parallel deletions use multiprocessing. > **Bundled model names.** `load_model` only recognizes three bundled aliases: `"textbook"` (the E. coli core model, `e_coli_core`), `"iJO1366"` (full E. coli genome-scale), and `"salmonella"`. Any other identifier (e.g. `"ecoli"`, `"e_coli_core"`) is not a bundled alias and triggers a remote lookup against BiGG/BioModels, which requires network access and may fail. Use `read_sbml_model("path.xml")` for your own models. ## Core Capabilities COBRApy provides comprehensive tools organized into several key areas: ### 1. Model Management Load existing models from repositories or files: ```python from cobra.io import load_model # Load bundled test models model = load_model("textbook") # E. coli core model model = load_model("iJO1366") # Full E. ...