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

Bartholomew Jardine¹, Gary M Raymond¹, James B Bassingthwaighte¹

¹Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA.

|July 18, 2017

Summary

This summary is machine-generated.

The Modular Program Constructor (MPC) simplifies complex physiological modeling by automatically generating code from existing modules. This open-source Java tool accelerates multi-scale model development and hypothesis testing.

Keywords:

JSim multi-scale modeling physiological modeling reproducibility systems biology uncertainty quantification

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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.