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

Forrest, J.; Rajagopal, V.; Stumpf, M. P. H.; Pan, M.

2023-04-25 systems biology
10.1101/2023.04.23.537337 bioRxiv
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SummaryBondGraphs.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, multi-scale, multi-physics, and BondGraphs.jl is compatible with the Julia modelling ecosystem. Availability and ImplementationBondGraphs.jl is freely available under the MIT license. Source code and documentation can be found at https://github.com/jedforrest/BondGraphs.jl. Contactpan.m@unimelb.edu.au, mstumpf@unimelb.edu.au Supplementary informationSupplementary data are available at Bioinformatics online.

Published in Bioinformatics (predicted rank #1) · training set

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