Cobrapy

If you're doing metabolic modeling or systems biology work, this is the standard Python library for constraint-based analysis. It handles genome-scale models in SBML format, runs flux balance analysis (FBA), flux variability analysis (FVA), and gene knockout screens. The skill covers loading bundled models like E. coli core or pulling from BiGG, running optimizations with different solvers (GLPK comes bundled, CPLEX and Gurobi are optional), and doing flux sampling for uncertainty analysis. Gapfilling support helps fix infeasible models. It uses optlang under the hood for the LP solver interface, so switching between GLPK and commercial solvers is straightforward. Solid for metabolic engineering and predicting cellular phenotypes.

Install to Claude Code

npx -y skills add k-dense-ai/scientific-agent-skills --skill cobrapy --agent claude-code