PROTO-PLASM: parallel language for adaptive and scalable modelling of biosystems

Area of Science:

• Computational Biology
• Biophysics
• Systems Biology

Background:

• Developing predictive computational models for biological systems is complex.
• Existing platforms often lack integrated multiscale geometric and multiphysics simulation capabilities.
• There is a need for flexible, combinable modeling frameworks.

Purpose of the Study:

• Introduce PROTO-PLASM, a novel computational environment for biosystem modeling.
• Demonstrate the platform's capabilities in multiscale geometric modeling and multiphysics simulations.
• Explore the potential for patient-specific modeling through symbolic combination of components.

Main Methods:

• Development of a computational framework including a language, model library, IDE, and parallel engine.
• Focus on symbolic description of model geometry and parallel simulation support.
• Integration with established formats like CellML and SBML for behavioral functions.

Main Results:

• Successful construction of a schematic heart model as a functional example.
• Demonstration of PROTO-PLASM's core functionalities for model creation and simulation.
• Discussion of multiscale challenges in geometric and physical modeling.

Conclusions:

• PROTO-PLASM provides a foundational framework for executable, combinable, and customizable biosystem models.
• The platform facilitates predictive understanding via multiscale geometric and multiphysics simulations.
• Future development aims to enhance patient-specific computational modeling capabilities.