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Metabolic Study Planner

Turns a vague metabolic modelling topic into a concrete, feasible FBA study plan before code is written.

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

What it does

When an agent is asked to do a metabolic flux analysis or systems-biology paper, this skill makes it first plan the study: pick an organism, a metabolic model (from the BiGG database), a condition, a perturbation, the metrics and figures, and a testable claim. It also scores the idea for feasibility and writes a short study card before generating any simulation code. It is a planning aid for constraint-based metabolic modelling, not a tool that runs experiments by itself.

Great for

  • Researchers or students starting a computational metabolism project who have a broad topic but no concrete organism or hypothesis
  • Metabolic engineers who want a structured knockout-screen or yield-analysis plan for a product such as succinate or ethanol
  • Users running AutoResearchClaw who need hypotheses tied to a named model and analysis

Skip it if

  • Wet-lab or clinical decisions: the outputs are in-silico predictions from genome-scale models and are not validated biology, and drug-target claims need experimental follow-up
  • Users who already have a defined model and question and only need code: the sibling skills gsmm-builder, fba-simulator and flux-analyzer are a better fit
  • Non-specialists without a basic understanding of FBA and COBRApy, since the plan uses dense domain terminology

Try asking

  • “Plan a publishable metabolic engineering study to increase succinate production in E. coli using BiGG models”
  • “Suggest an essentiality and drug-target analysis for M. tuberculosis with a concrete model and metrics”
  • “Design a nutrient phase-map study comparing aerobic and anaerobic growth in yeast”
  • “Write a study_card.md for a knockout strategy project before generating COBRApy code”
Step-by-step guide: how to use Metabolic Study PlannerInstall, 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.

    metabolic-study-planner.zip
  2. 2

    Add it to your agent

    Claude Code (all projects)

    mkdir -p ~/.claude/skills && unzip metabolic-study-planner.zip -d ~/.claude/skills/

    Claude Code / Agent SDK (this project only)

    mkdir -p .claude/skills && unzip metabolic-study-planner.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

  • Give the agent a concrete organism or product if you have one; otherwise let it use the listed defaults, with E. coli recommended for a first run
  • Review the feasibility score and study card before accepting code generation, since model choice strongly affects the result
  • Treat generated claims as hypotheses to check against literature and experiments, not as established findings

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.