SBMLsimulator

SBMLsimulator performs dynamic simulation and heuristic parameter estimation of biochemical models encoded in the Systems Biology Markup Language (SBML) to calibrate models against experimentally obtained time series data.

Key Features:

• SBML simulation: Performs time-course simulation of biochemical models encoded in SBML using the Systems Biology Simulation Core Library.
• Heuristic optimization (EvA2): Incorporates the nature-inspired EvA2 framework for heuristic parameter optimization.
• Parameter estimation: Calibrates complex biochemical reaction systems by identifying parameter sets that fit experimental time series data.
• Benchmarking: The simulation core has been benchmarked against the SBML Test Suite and all models from the Biomodels.net database.
• SBML support via JSBML: Uses the JSBML library to parse and handle SBML model files.
• Java implementation: Implemented in Java for integration with Java-based simulation and optimization libraries.

Scientific Applications:

• Parameter calibration of biochemical networks: Estimating uncertain kinetic parameters in biochemical reaction systems from experimental time series data.
• Dynamic model simulation: Running time-course simulations of SBML-encoded biochemical models for hypothesis testing and analysis.
• Model validation and benchmarking: Validating simulation accuracy through comparison with the SBML Test Suite and models from the Biomodels.net database.
• Exploration of complex parameter spaces: Applying heuristic optimization to search large or multimodal parameter landscapes in systems biology models.

Methodology:

Implemented in Java using JSBML to load SBML models, integrating the Systems Biology Simulation Core Library for simulation and EvA2 for heuristic parameter optimization; benchmarking performed against the SBML Test Suite and models from the Biomodels.net database.