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BondGraphs.jl: composable energy-based modelling in systems biology.
Joshua Forrest1,2,3, Vijay Rajagopal3,4,5, Michael P H Stumpf1,2,6,7
1School of BioSciences, University of Melbourne, Parkville, Australia.
Bioinformatics (Oxford, England)
|September 19, 2023
Summary
BondGraphs.jl is a new Julia package for bond graph modeling, a framework for analyzing energy flow in physical and biological systems. It offers a flexible and compatible approach for complex, multiphysics modeling.
Area of Science:
- Computational Biology
- Systems Engineering
- Multiphysics Modeling
Background:
- Bond graphs offer a robust framework for modeling energy flow in physical systems.
- This framework inherently enforces thermodynamic constraints.
- Recent research highlights its utility in biological system modeling.
Purpose of the Study:
- Introduce BondGraphs.jl, a Julia implementation of the bond graph modeling framework.
- Provide a tool for researchers in engineering and biology to model complex systems.
Main Methods:
- Developed as a Julia package, BondGraphs.jl leverages the language's capabilities for high-performance scientific computing.
- The implementation supports mutable, hierarchical, multiscale, and multiphysics models.
- Ensures compatibility with the broader Julia scientific modeling ecosystem.
Main Results:
- BondGraphs.jl provides a functional implementation of the bond graph methodology in Julia.
- The package facilitates the creation of complex, integrated models across different physical domains.
- Demonstrates the applicability of bond graph modeling to biological systems.
Conclusions:
- BondGraphs.jl is a valuable, freely available resource for multiphysics and multiscale modeling.
- It extends the application of bond graphs to biological systems, enhancing interdisciplinary research.
- The package integrates seamlessly with the Julia ecosystem, promoting efficient model development.
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