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

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.

SUBMITTER: Forrest J

PROVIDER: S-EPMC10551222 | biostudies-literature | 2023 Oct

REPOSITORIES: biostudies-literature

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

Forrest Joshua J Rajagopal Vijay V Stumpf Michael P H MPH Pan Michael M

Bioinformatics (Oxford, England) 20231001 10

<h4>Summary</h4>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.<h4>Availability and imple ...[more]

PMID: 37725363

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