Systems Biology Simulation Core Library

Systems Biology Simulation Core Library implements interpretation and numerical solution of Systems Biology Markup Language (SBML) models formulated as ordinary differential equations (ODEs) to simulate and analyze dynamical biochemical networks involving metabolites, genes, and fluxes.

Key Features:

• Efficient Algorithm: Implements an algorithm tailored to solve SBML models represented as ODEs, addressing SBML-specific complexity and special cases.
• Comprehensive Preprocessing: Performs preprocessing to derive the precise mathematical form of SBML-encoded models for accurate numerical solution.
• Flexible Reference Implementation: Provides a Java reference implementation with an interface hierarchy and support for a wide array of numerical solvers to define custom differential-equation systems.
• Extensive Testing and Validation: Validated using the entire SBML Test Suite and all models from the BioModels Database.

Scientific Applications:

• Dynamic simulation of SBML models: Enables simulation of SBML-encoded dynamical systems to study time-dependent behavior of biochemical networks.
• Metabolic pathway analysis: Supports ODE-based modeling and simulation of metabolic pathways and flux dynamics.
• Gene regulatory network modeling: Facilitates modeling of gene regulatory mechanisms using SBML-formulated ODEs.
• Time-course analysis of metabolites, genes, and fluxes: Handles high-dimensional time-course data for metabolites, genes, and fluxes within ODE-based SBML models.

Methodology:

Formal representation of the mathematical structure of SBML models enabling precise interpretation and numerical solution of ordinary differential equations (ODEs), implemented in Java with a modular interface hierarchy.