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FBA Metabolic Simulator

Runs flux balance analysis and gene/reaction knockout simulations on metabolic models using COBRApy

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

What it does

This skill teaches an AI agent to run constraint-based simulations on a metabolic model of an organism, such as predicting growth rate, how fluxes (rates of chemical reactions) are distributed, and which genes or reactions are essential. It walks the agent through standard FBA, parsimonious FBA, flux variability analysis, loopless FBA, single gene and reaction knockouts, and comparing carbon sources, then saves results as CSV and JSON files. It is meant to be used after a model has been built and validated by other tools.

Great for

  • Systems biology students learning constraint-based modelling with COBRApy
  • Researchers who already have a validated genome-scale metabolic model and want quick simulations
  • Developers building a pipeline that runs standard COBRApy analyses and exports results

Skip it if

  • Users without an existing COBRApy model, since the skill starts from a model file and does not build one (the skill references a separate model-building skill that is not included here)
  • Clinical or medical decisions, because the outputs are simulation predictions that need expert biological validation

Try asking

  • “Run FBA on my E. coli model and export the flux distribution to CSV”
  • “Find which genes are essential for growth using single gene deletions”
  • “Compare growth rates on glucose, fructose, acetate, glycerol and succinate”
  • “Run flux variability analysis at 90% of maximum growth and list rigid reactions”
Step-by-step guide: how to use FBA Metabolic SimulatorInstall, first run, examples, tips and FAQs

Install in 3 steps

  1. 1

    Download the skill

    The ZIP contains the 1 original files, the MIT licence and an attribution note.

    fba-simulator.zip
  2. 2

    Add it to your agent

    Claude Code (all projects)

    mkdir -p ~/.claude/skills && unzip fba-simulator.zip -d ~/.claude/skills/

    Claude Code / Agent SDK (this project only)

    mkdir -p .claude/skills && unzip fba-simulator.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

  • Provide a model file that has already been validated, and check that exchange reaction IDs such as EX_glc__D_e match your model before running the carbon source comparison.
  • Note that the example code references wt_growth, pfba_solution and loopless_sol from earlier steps, so run the steps in order or ask the agent to keep variables across steps.
  • Review the generated code before running it, since it writes files to the working directory and runs Python scripts on your model.

What's inside

  • SKILL.md

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.