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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

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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.

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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.