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Flux Analyzer for Metabolic Models

Turns FBA metabolic model outputs into gene essentiality, phase plane, sampling and pathway figures

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

What it does

This skill teaches an agent how to analyse flux balance analysis (FBA) results, which are predictions of how a microbe or other organism uses its metabolic network to grow. Once installed, the agent can write and run Python code (using the COBRApy library) to find genes and reactions whose removal stops growth, map how growth changes with nutrient supply, sample the range of feasible metabolic flows, summarise activity by pathway, list likely secreted products, and produce publication-style PDF and PNG figures. It is aimed at turning numbers from a metabolic model into biological interpretation.

Great for

  • Systems biology or metabolic engineering researchers who already have a COBRA-compatible model and FBA output
  • Students learning constraint-based metabolic modelling who want worked examples
  • Pipelines (such as the ColliderAgent-style biology workflow referenced) that need a flux analysis stage

Skip it if

  • People without a metabolic model or FBA results: the skill analyses existing outputs and does not build models from scratch
  • Clinical or safety-critical decisions: the outputs are model predictions, not experimental evidence, and the essentiality cutoff (5% of wild-type growth) is a convention that may not fit every organism
  • Running on large genome-scale models without planning: double gene deletions over many genes and 1000-sample flux sampling can be slow and compute-heavy

Try asking

  • “Find which genes are essential for growth in my E. coli model and export a CSV of results”
  • “Plot a phenotypic phase plane of growth versus glucose and oxygen uptake”
  • “Run flux sampling with 1000 samples and make a violin plot of central carbon metabolism reactions”
  • “Summarise total absolute flux by metabolic subsystem and list the top secreted products”
Step-by-step guide: how to use Flux Analyzer for Metabolic ModelsInstall, 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.

    flux-analyzer.zip
  2. 2

    Add it to your agent

    Claude Code (all projects)

    mkdir -p ~/.claude/skills && unzip flux-analyzer.zip -d ~/.claude/skills/

    Claude Code / Agent SDK (this project only)

    mkdir -p .claude/skills && unzip flux-analyzer.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

  • Check that reaction IDs (such as EX_glc__D_e and the biomass reaction ID) match your model before running, since the example uses an E. coli iJO1366 identifier
  • Reduce the gene set or sample count first to test runtime, and review the generated code before executing it on your own files
  • Treat results as hypotheses from a model and validate key findings experimentally or against the literature

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.