BondGraphs.jl: composable energy-based modelling in systems biology

Joshua Forrest; Vijay Rajagopal; Michael P H Stumpf; Michael Pan

doi:10.1093/bioinformatics/btad578

BondGraphs.jl: composable energy-based modelling in systems biology

Bioinformatics. 2023 Oct 3;39(10):btad578. doi: 10.1093/bioinformatics/btad578.

Authors

Joshua Forrest^{1

2

3}, Vijay Rajagopal^{3

4

5}, Michael P H Stumpf^{1

2

6

7}, Michael Pan²

Affiliations

¹ School of BioSciences, University of Melbourne, Parkville, Australia.
² School of Mathematics and Statistics, University of Melbourne, Parkville, Australia.
³ Department of Biomedical Engineering, University of Melbourne, Parkville, Australia.
⁴ Baker Department of Cardiometabolic Health, University of Melbourne, Parkville, Australia.
⁵ The Graeme Clark Institute, University of Melbourne, Parkville, Australia.
⁶ Melbourne Integrative Genomics, University of Melbourne, Parkville, Australia.
⁷ ARC Centre of Excellence for the Mathematical Analysis of Cellular Systems, University of Melbourne, Parkville, Australia.

Abstract

Summary: BondGraphs.jl is a Julia implementation of bond graphs. Bond graphs provide a modelling framework that describes energy flow through a physical system and by construction enforce thermodynamic constraints. The framework is widely used in engineering and has recently been shown to be a powerful approach for modelling biology. Models are mutable, hierarchical, multiscale, and multiphysics, and BondGraphs.jl is compatible with the Julia modelling ecosystem.

Availability and implementation: BondGraphs.jl is freely available under the MIT license. Source code and documentation can be found at https://github.com/jedforrest/BondGraphs.jl.

Grants and funding

University of Melbourne