scientific-systems-biology

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.