cobrapy-metabolic-modeling
Constraint-based (COBRA) analysis of genome-scale metabolic models: FBA, FVA, knockouts, flux sampling, production envelopes, gapfilling, media optimization. Use for strain design, essential gene ID, flux analysis. For kinetic modeling use tellurium; for visualization use Escher.
npx skills add BioTender-max/awesome-bio-agent-skills --skill cobrapy-metabolic-modeling --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# COBRApy — Constraint-Based Metabolic Modeling ## Overview COBRApy is a Python package for constraint-based reconstruction and analysis (COBRA) of genome-scale metabolic models. It provides flux balance analysis (FBA), flux variability analysis (FVA), gene and reaction knockout screens, flux sampling, production envelopes, gapfilling, and media optimization on SBML-format metabolic networks. ## When to Use - Predicting microbial growth rates under different nutrient conditions (FBA) - Identifying essential genes or reactions via single and double knockout screens - Determining flux ranges and alternative optimal solutions (FVA) - Sampling feasible flux distributions to characterize metabolic flexibility - Designing minimal growth media or optimizing carbon sources - Computing production envelopes for metabolic engineering targets - Gapfilling incomplete draft models using a universal reaction database - For **kinetic modeling** or **dynamic ODE-based models**, use Tellurium instead - For **pathway visualization** on metabolic maps, use Escher instead ## Prerequisites - **Python packages**: `cobra` (includes GLPK solver), `numpy`, `pandas` - **Optional solvers**: CPLEX or Gurobi (f
- Overview
- When to Use
- Prerequisites
- Quick Start
- Core API
- 1. Model I/O
- 2. Model Structure and Components
- 3. Flux Balance Analysis (FBA)
- 4. Flux Variability Analysis (FVA)
- 5. Gene and Reaction Deletions
- 6. Growth Media and Minimal Media
- 7. Flux Sampling
- 8. Production Envelopes and Gapfilling
- Key Concepts
pip install cobra
What does the cobrapy-metabolic-modeling skill do?
Constraint-based (COBRA) analysis of genome-scale metabolic models: FBA, FVA, knockouts, flux sampling, production envelopes, gapfilling, media optimization. Use for strain design, essential gene ID, flux analysis. For kinetic modeling use tellurium; for visualization use Escher.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill cobrapy-metabolic-modeling --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.