Semi-automated Modular Program Constructor for physiological modeling: Building cell and organ models

Area of Science:

• Computational Biology
• Systems Biology
• Physiological Modeling

Background:

• Developing complex physiological models is time-consuming due to the myriad simultaneous processes in biological systems.
• Manual model combination is error-prone and inefficient, hindering rapid hypothesis testing and multi-scale research.

Purpose of the Study:

• To introduce the Modular Program Constructor (MPC), an open-source Java utility designed to streamline the construction of complex physiological models.
• To provide a method for rapidly assembling and testing multi-scale models by automating code generation from modular components.

Main Methods:

• MPC utilizes JSim's Mathematical Modeling Language (MML) and embedded directives to construct larger models from smaller, existing ones.
• Code-generating algorithms within MPC take input from multiple models to produce new JSim-compatible model code.
• The system encodes and preserves module relationships, facilitating easy updates and substitutions for hypothesis testing.

Main Results:

• MPC significantly reduces the time and errors associated with building complex physiological models.
• The tool enables efficient multi-scale model development, allowing for rapid configuration and testing of numerous variants.
• Preservation of module information supports iterative refinement and hypothesis-driven model modification.

Conclusions:

• MPC offers a powerful, open-source solution for accelerating physiological model development and multi-scale research.
• The utility enhances the efficiency and accuracy of creating complex biological simulations by automating model assembly.
• MPC facilitates hypothesis testing by enabling quick module substitution and model variant management.