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COBRApy Metabolic Modeling

Guides Claude through constraint-based metabolic modeling with COBRApy: FBA, FVA, knockouts, media design and flux sampling.

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

What it does

  • Provides a version-pinned playbook for COBRApy (cobra 0.31.1) covering the full constraint-based modeling workflow.
  • Model I/O (SBML, JSON, YAML), component inspection, FBA, pFBA and geometric FBA.
  • FVA including loopless mode, single/double gene and reaction deletion screens, minimal media computation, OptGP/ACHR flux sampling, production envelopes, gapfilling and building models from scratch.
  • Adds practical guidance on context managers for temporary changes, solver choice (GLPK/hybrid/CPLEX/Gurobi) and troubleshooting infeasible or unbounded solutions.

Who it's for

  • Systems biology and metabolic engineering researchers or graduate students
  • Teams doing in silico strain design and knockout screening
  • Anyone analyzing genome-scale models (iML1515, iJO1366, e_coli_core) reproducibly

Examples

  1. "Predict growth on the textbook model and list active fluxes" → load_model + optimize workflow.
  2. "Find essential genes in E. coli" → single_gene_deletion filtered at growth < 0.01.
  3. "Plot an acetate production envelope under anaerobic conditions" → edit model.medium, run production_envelope, plot with matplotlib.

· · · Install guide · · ·

Try it now, no install

Paste this into Claude to use the skill without installing anything.

Read the instructions in this file and follow them to help me:
https://raw.githubusercontent.com/K-Dense-AI/scientific-agent-skills/HEAD/skills/cobrapy/SKILL.md

What I want: (describe your task here)

If Claude can't open the link, open it yourself and paste the contents instead.

↓ If it works for you, download the ZIP below and install it. Then it runs on its own — no pasting each time.

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 in your working directory.
  2. Clone the repository: git clone https://github.com/K-Dense-AI/scientific-agent-skills.git
  3. Create the skills directory: mkdir -p ~/.claude/skills
  4. Copy just this skill: cp -r scientific-agent-skills/skills/cobrapy ~/.claude/skills/
  5. Install the library in your Python environment: uv pip install "cobra==0.31.1" (Python 3.9+ required).
  6. Restart Claude Code and ask something like "use the cobrapy skill to run FBA on the textbook model" to trigger it.
View source on GitHub ↗License: MIT