SBML2Modelica

SBML2Modelica translates models defined in System Biology Markup Language (SBML) Version 3 Level 2 into Modelica to enable integration of biochemical network models into general-purpose simulation and co-simulation ecosystems for applications such as in silico clinical trials, pharmacological protocol simulation, and biomedical device evaluation within Virtual Physiological Human models.

Key Features:

• Translation Capability: Converts models from SBML Version 3 Level 2 into well-structured Modelica representations.
• Compliance and Reliability: Conforms to SBML Version 3 Level 2 standards and passes 96.47% of the SBML Test Suite Core while detecting and reporting unsupported construct combinations.
• Performance Evaluation: Experimental evaluations on 613 models from the BioModels database, including models with up to 5438 variables, demonstrate comparable performance of major open-source Modelica and FMU simulators to specialized SBML simulators.
• FMU Export and Co-simulation: Enables export of converted Modelica models as Functional Mock-Up Units (FMUs) for language-independent co-simulation and integration with heterogeneous model types.

Scientific Applications:

• In Silico Clinical Trials: Facilitates integration of biochemical models into simulations that predict drug interactions and pharmacological responses.
• Pharmacological Protocol Simulation: Supports simulation of pharmacological protocols and drug effects within larger multi-model environments.
• Biomedical Device Evaluation: Enables testing and analysis of biomedical devices within integrated simulation ecosystems.
• Virtual Physiological Human Integration: Supports incorporation of biochemical network models into Virtual Physiological Human modelling efforts.

Methodology:

Converts SBML Version 3 Level 2 models to Modelica and can export converted models as Functional Mock-Up Units (FMUs); compliance checked against the SBML Test Suite Core (96.47% pass reported); experimental evaluation performed on 613 BioModels database models (up to 5438 variables); unsupported SBML construct combinations are detected and signaled.