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

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 power...

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Detalles Bibliográficos
Autores principales: Forrest, Joshua, Rajagopal, Vijay, Stumpf, Michael P H, Pan, Michael
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2023
Materias:
Applications Note
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10551222/
https://www.ncbi.nlm.nih.gov/pubmed/37725363
http://dx.doi.org/10.1093/bioinformatics/btad578
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author Forrest, Joshua
Rajagopal, Vijay
Stumpf, Michael P H
Pan, Michael
author_facet Forrest, Joshua
Rajagopal, Vijay
Stumpf, Michael P H
Pan, Michael
author_sort Forrest, Joshua
collection PubMed
description 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.
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spelling pubmed-105512222023-10-06 BondGraphs.jl: composable energy-based modelling in systems biology Forrest, Joshua Rajagopal, Vijay Stumpf, Michael P H Pan, Michael Bioinformatics Applications Note 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. Oxford University Press 2023-09-19 /pmc/articles/PMC10551222/ /pubmed/37725363 http://dx.doi.org/10.1093/bioinformatics/btad578 Text en © The Author(s) 2023. Published by Oxford University Press. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Applications Note
Forrest, Joshua
Rajagopal, Vijay
Stumpf, Michael P H
Pan, Michael
BondGraphs.jl: composable energy-based modelling in systems biology
title BondGraphs.jl: composable energy-based modelling in systems biology
title_full BondGraphs.jl: composable energy-based modelling in systems biology
title_fullStr BondGraphs.jl: composable energy-based modelling in systems biology
title_full_unstemmed BondGraphs.jl: composable energy-based modelling in systems biology
title_short BondGraphs.jl: composable energy-based modelling in systems biology
title_sort bondgraphs.jl: composable energy-based modelling in systems biology
topic Applications Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10551222/
https://www.ncbi.nlm.nih.gov/pubmed/37725363
http://dx.doi.org/10.1093/bioinformatics/btad578
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AT stumpfmichaelph bondgraphsjlcomposableenergybasedmodellinginsystemsbiology
AT panmichael bondgraphsjlcomposableenergybasedmodellinginsystemsbiology

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