scientific-metabolic-modeling

Search, retrieve, and compare genome-scale metabolic models from BiGG Models and BioModels.

3|1|Updated Feb 11, 2026

Search Tags:#pathway-analysis #metabolic-modeling #sbml #genome-scale-model #bigg #biomodels

Ready to run

npx skills add https://github.com/nahisaho/satori --skill scientific-metabolic-modeling

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: scientific-metabolic-modeling
Source: https://github.com/nahisaho/satori/tree/main/src/.github/skills/scientific-metabolic-modeling
Command: npx skills add https://github.com/nahisaho/satori --skill scientific-metabolic-modeling

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

BiGG Models と BioModels を活用したゲノムスケール代謝モデルの検索・探索・解析パイプラインを提供する。

Core Features & Use Cases

Integrated GEM search and retrieval from BiGG Models and BioModels
Pathway-level exploration and flux analysis setup for cross-species comparisons
Use Case: compare metabolic networks across organisms to identify model gaps and target pathways

Quick Start

Use BiGG Models and BioModels through the pipeline to search for a model by organism and retrieve its details for downstream analysis.

Frequently Asked Questions about scientific-metabolic-modeling

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

FAQPage Schema

How do I search and compare genome-scale metabolic models across different organisms?▼

You can compare genome-scale metabolic models across organisms by searching and retrieving integrated data from BiGG Models and BioModels. This enables multi-species metabolic analyses to identify model gaps and target pathways for downstream experiments.

Can I retrieve SBML files and model reactions directly from BiGG and BioModels databases?▼

Yes, you can retrieve SBML files, model metadata, and reactions directly from the BiGG Models and BioModels APIs. This integration supports pulling genome-scale metabolic model components for cross-species comparisons and pathway exploration.

What is the best way to set up flux balance analysis preprocessing for metabolic pathways?▼

The best way to set up flux balance analysis preprocessing is by retrieving genome-scale metabolic models and exploring pathway-level reactions. You can search BiGG Models and BioModels to gather the necessary metabolic network data for your flux analysis setup.

Do I need API access to BiGG Models and BioModels for pathway analysis and model retrieval?▼

Yes, API access to BiGG Models and BioModels is required for pathway analysis and model retrieval. The pipeline depends on these APIs to search, retrieve, and compare genome-scale metabolic models and their associated SBML files.

How does cross-database metabolic modeling help identify gaps in metabolic networks?▼

Cross-database metabolic modeling helps identify gaps by integrating genome-scale models from BiGG and BioModels for multi-species comparisons. Comparing metabolic networks across organisms highlights missing reactions and target pathways in your models.