scientific-systems-biology

Coordinate ODE simulations, flux balance analysis, and GRN inference with SBML and database integrations.

3|1|Updated Feb 11, 2026

Search Tags:#modeling #fba #systems-biology #grn #ode #sbml

Ready to run

npx skills add https://github.com/nahisaho/satori --skill scientific-systems-biology

💬 Prompt for ChatGPT / Claude Chat▼

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

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Systematic pipelines for quantitative systems biology modeling, unifying dynamic ODE models, flux balance analysis, GRN inference, and parameter estimation with access to BioModels, Reactome, KEGG, and BiGG.

Core Features & Use Cases

Dynamic modeling of biological pathways with ODE-based models.
Metabolic flux analysis (FBA/pFBA) for network-wide metabolism.
Gene regulatory network inference from expression data.
Integrated access to BioModels, Reactome, KEGG, BiGG for model retrieval and data.
Parameter estimation and sensitivity analysis to quantify uncertainty.
Use Case: Build end-to-end pipelines from model retrieval to simulation, parameter fitting, and reporting.

Quick Start

Load an SBML model, run a time-course simulation, and report key results.

Frequently Asked Questions about scientific-systems-biology

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

FAQPage Schema

How do I run dynamic ODE simulations on an SBML model?▼

To run dynamic ODE simulations, you can load an SBML model into this pipeline and execute time-course simulations to model biological pathways and report key dynamic results.

What is the best way to perform flux balance analysis on metabolic networks?▼

Flux balance analysis is performed using the pipeline's integrated FBA and pFBA capabilities to analyze network-wide metabolism and quantify metabolic flux distributions.

Can I retrieve models from BioModels and KEGG for systems biology modeling?▼

Yes, you can retrieve models and biological data directly from BioModels, Reactome, KEGG, and BiGG databases to build and support your quantitative systems biology pipelines.

How does gene regulatory network inference from expression data work?▼

Gene regulatory network inference works by processing expression data through the pipeline to identify and map regulatory interactions within the biological system.

Do I need parameter estimation tools for sensitivity analysis in SBML projects?▼

You need parameter estimation and sensitivity analysis capabilities to quantify uncertainty in SBML-based projects, both of which are integrated into this modeling pipeline.

What databases are supported for model retrieval in systems biology pipelines?▼

The pipeline supports integrated access to BioModels, Reactome, KEGG, and BiGG databases for systematic model retrieval and data integration in systems biology projects.