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scientific-metabolic-atlas

Query Metabolic Atlas REST API for metabolic reactions, metabolites, and compartments.

3|1|Updated Feb 11, 2026
Search Tags:#bioinformatics#network-analysis#flux-balance-analysis#metabolic-atlas#human-gem#metabolic-model#pathway-visualization
One-click install
npx skills add https://github.com/nahisaho/satori --skill scientific-metabolic-atlas
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: scientific-metabolic-atlas
Source: https://github.com/nahisaho/satori/tree/main/src/.github/skills/scientific-metabolic-atlas
Command: npx skills add https://github.com/nahisaho/satori --skill scientific-metabolic-atlas

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Metabolic Atlas enables programmable access to Human-GEM data; this skill automates searching for metabolic reactions, metabolites and compartments, and integrates flux analysis and network visualization to streamline GEM workflows.

Core Features & Use Cases

  • Search metabolic reactions, metabolites and compartments using the Metabolic Atlas REST API.
  • Build and visualize metabolic networks and prepare data for flux balance analysis.
  • Use cases: explore pathway connectivity in tissue-specific GEMs, identify hub metabolites, and prepare inputs for COBRA workflows.

Quick Start

Query glycolysis in Metabolic Atlas to retrieve reactions and metabolites and generate a simple network.

Frequently Asked Questions about scientific-metabolic-atlas

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I search metabolic reactions and metabolites in Human-GEM automatically?▼

You can search metabolic reactions and metabolites by automating queries through the Metabolic Atlas REST API, which replaces manual GEM curation by retrieving and normalizing data for tissue-specific models.

What is the best way to prepare flux balance analysis inputs from a metabolic atlas?▼

The best way to prepare flux balance analysis inputs is to query the Metabolic Atlas REST API to retrieve metabolic reactions and compartments, then parse and normalize the network data for COBRA workflows.

Can I use Metabolic Atlas data for genome-scale metabolic modeling workflows?▼

Yes, you can use Metabolic Atlas data for genome-scale metabolic modeling workflows by automating REST API queries to retrieve metabolic reactions, metabolites, and compartments across tissue-specific models.

How do I visualize pathway connectivity in tissue-specific GEMs?▼

To visualize pathway connectivity in tissue-specific GEMs, you query the Metabolic Atlas REST API to retrieve reactions and metabolites, then parse the network data to build and visualize metabolic networks.

Do I need REST API calls to retrieve metabolic compartments from Human-GEM?▼

Yes, retrieving metabolic compartments from Human-GEM requires REST API calls to automate the data queries, replacing manual GEM curation and delivering searchable, normalized results.

Why does manual GEM curation slow down metabolic network analysis?▼

Manual GEM curation slows down metabolic network analysis because it requires hand-searching reactions and metabolites, whereas automating Metabolic Atlas REST API queries delivers ready-to-analyze outputs instantly.

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