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COBRApy Metabolic Modeling

Equips Claude Code to run FBA, FVA, knockout screens, and flux sampling on genome-scale metabolic models with COBRApy.

Data & AnalyticsAdvanced★ 33,030⑂ 3,248AI score 8/10Last updated: Aug 9, 2026

What it does

Teaches Claude to drive COBRApy, the constraint-based reconstruction and analysis library, with accurate up-to-date syntax.

  • Model I/O: SBML, JSON, YAML; load_model for textbook, iJO1366, iML1515 and more
  • Simulation: FBA, pFBA, geometric FBA, FVA (including loopless)
  • Design analysis: single/double gene and reaction deletions, production envelopes
  • Media design: editing model.medium, computing minimal_medium
  • Flux sampling (OptGP/ACHR) with sample validation, gapfilling, building models from scratch
  • Solver notes (GLPK default, hybrid/HIGHS, optional CPLEX/Gurobi) plus troubleshooting tips

It emphasizes the context-manager pattern (with model:) so temporary edits revert automatically.

Who it's for

  • Systems biology and metabolic engineering researchers or grad students
  • Bioengineers screening strain designs and production pathways
  • Anyone bitten by API changes across cobra 0.29–0.31
  • Teams needing a reproducible FBA pipeline fast

Example uses

  1. Essential gene screen: "Run single_gene_deletion on the textbook model and export genes with growth < 0.01 to CSV."
  2. Anaerobic growth prediction: "In iML1515 set O2 uptake to 0 with 10 mmol/gDW/h glucose, then report growth rate and secretion fluxes."
  3. Acetate production limits: "Compute the EX_ac_e production envelope over glucose and oxygen and plot it with matplotlib."

· · · Install guide · · ·

Install in the Claude app (no terminal)
  1. Download the ZIP with the button below.
  2. In Claude, open Settings → Capabilities and turn on 'Code execution and file creation'. (one time)
  3. Go to Customize → Skills → + → 'Upload a skill' and upload the ZIP.
↓ Download ZIP
Install in Claude Code

Let Claude do it — paste this into Claude Code

Install the skill I found on Claude Skill Mart.
Copy the skills/cobrapy folder from the GitHub repo K-Dense-AI/scientific-agent-skills into my ~/.claude/skills/cobrapy/.
When it's done, tell me in one line what this skill can do.

Install with a command instead

git clone https://github.com/K-Dense-AI/scientific-agent-skills.git && mkdir -p ~/.claude/skills && cp -r scientific-agent-skills/skills/cobrapy ~/.claude/skills/

⚠ This is a third-party skill. Check the source repository before installing.

  1. Open a terminal and confirm Python 3.9+ is available: python3 --version
  2. Install COBRApy: uv pip install "cobra==0.31.1" (or pip install "cobra==0.31.1" if you don't use uv)
  3. Clone the skill repository: git clone https://github.com/K-Dense-AI/scientific-agent-skills.git
  4. Copy the skill into Claude Code's skills folder: mkdir -p ~/.claude/skills && cp -r scientific-agent-skills/skills/cobrapy ~/.claude/skills/
  5. Restart Claude Code and verify cobrapy appears in your skill list.
  6. Try a prompt like "Load the textbook model and compute growth rate with FBA" to trigger the skill.
  7. Genome-scale models such as iML1515 are fetched over the network, so the first run may take a while.
View source on GitHub ↗License: MIT