Metabolic Study Planner

Overview

Use this skill before gsmm-builder, fba-simulator, and flux-analyzer when the project starts from a broad prompt such as "do a metabolic flux analysis paper" or "find a publishable idea in microbial metabolism".

The goal is to turn a vague topic into a concrete, executable, paper-shaped study plan:

organism + model + condition + perturbation + metric + figure set + claim

This is the MFA analogue of choosing a collider process and parameter scan before generating events.

Planning Inputs

Extract or infer the following:

Field	Examples
Biological scope	microbial metabolism, cancer metabolism, yeast fermentation, tuberculosis
Organism	E. coli, S. cerevisiae, human Recon3D, M. tuberculosis
Model source	BiGG ID, local SBML/JSON, manually constructed toy model
Objective	biomass, product secretion, ATP maintenance, dual objective
Condition	aerobic, anaerobic, carbon source, nutrient limitation
Perturbation	gene knockout, reaction knockout, medium swap, oxygen sweep
Target output	growth, product yield, essential genes, secretion profile
Paper type	mechanism hypothesis, metabolic engineering strategy, benchmark, reproduction

If the user provides no organism, start with one of these low-risk defaults:

Default	Model	Why
E. coli K-12	iJO1366 or core model	Fast, well curated, standard for FBA papers
S. cerevisiae	iMM904	Fermentation and product-yield studies
Human metabolism	Recon3D	Disease metabolism, but larger and harder
M. tuberculosis	iNJ661	Essentiality and drug-target hypotheses

Prefer E. coli for fully autonomous first runs because it is fast and interpretable.

Study Archetypes

Archetype A: Knockout Strategy for Product Overproduction

Use when the topic mentions metabolic engineering, bio-production, yield, or fermentation.