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Genome-Scale Metabolic Model Builder

Builds or loads metabolic network models in COBRApy and exports them as validated JSON files

Source Download skill
Repository
aiming-lab/AutoResearchClaw
Stars
14,802
Licence
MIT
Files
3 files

What it does

This skill teaches an AI agent how to create or load a genome-scale metabolic model, a structured map of the chemical reactions in a living organism, using the COBRApy Python library. Once installed, the agent can load published models such as E. coli iJO1366 from the BIGG database, build small toy models from scratch, set growth medium limits, set a biomass objective, and save the result as JSON or SBML files for later flux analysis. It also includes reference notes on naming conventions and common failure modes.

Great for

  • Computational biology students learning flux balance analysis
  • Researchers who want an agent to scaffold a COBRApy workflow
  • Developers building metabolic modelling pipelines

Skip it if

  • Clinical or diagnostic decisions, since the models are simplified research tools and the skill provides no validation against experimental data
  • Users without Python and COBRApy experience who expect a finished analysis with no review, because the generated code needs checking

Try asking

  • “Load the iJO1366 E. coli model from BIGG and report its reaction and gene counts”
  • “Build a toy glycolysis model from scratch and save it as JSON”
  • “Set an M9 minimal glucose medium on my model and check whether it is feasible”
  • “Export my COBRApy model to SBML and JSON files in an output folder”
Step-by-step guide: how to use Genome-Scale Metabolic Model BuilderInstall, first run, examples, tips and FAQs

Install in 3 steps

  1. 1

    Download the skill

    The ZIP contains the 3 original files, the MIT licence and an attribution note.

    gsmm-builder.zip
  2. 2

    Add it to your agent

    Claude Code (all projects)

    mkdir -p ~/.claude/skills && unzip gsmm-builder.zip -d ~/.claude/skills/

    Claude Code / Agent SDK (this project only)

    mkdir -p .claude/skills && unzip gsmm-builder.zip -d .claude/skills/

    Claude apps (web/desktop): Settings → Capabilities → Skills → Upload skill, and choose the ZIP.

  3. 3

    Ask for the task

    No special command needed — the agent reads the skill's description and loads it when your request matches. Try one of the prompts above.

Get better results

  • Start from a curated BIGG model rather than the toy template when you need results that reflect a real organism
  • Check solution status after optimizing, since infeasible results usually mean a missing exchange reaction or a closed medium
  • Review the templates/minimal_model.py script before running it, and run it in a sandbox or virtual environment

What's inside

  • references/cobra_reference.md
  • SKILL.md
  • templates/minimal_model.py

Redistributed unmodified from aiming-lab/AutoResearchClaw under the MIT licence. The assessment was drafted with AI from the skill's files on 2026-10-29. Skills can instruct your agent to run code — read SKILL.md and any scripts before installing.