Modular assembly of dynamic models in systems biology.

It is widely acknowledged that the construction of large-scale dynamic models in systems biology requires complex modelling problems to be broken up into more manageable pieces. To this end, both modelling and software frameworks are required to enable modular modelling. While there has been consist...

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Autores principales:	Michael Pan, Peter J Gawthrop, Joseph Cursons, Edmund J Crampin
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/4688ffc01167458e8271b1474bd0ae27
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id	oai:doaj.org-article:4688ffc01167458e8271b1474bd0ae27
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spelling	oai:doaj.org-article:4688ffc01167458e8271b1474bd0ae272021-12-02T19:57:42ZModular assembly of dynamic models in systems biology.1553-734X1553-735810.1371/journal.pcbi.1009513https://doaj.org/article/4688ffc01167458e8271b1474bd0ae272021-10-01T00:00:00Zhttps://doi.org/10.1371/journal.pcbi.1009513https://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358It is widely acknowledged that the construction of large-scale dynamic models in systems biology requires complex modelling problems to be broken up into more manageable pieces. To this end, both modelling and software frameworks are required to enable modular modelling. While there has been consistent progress in the development of software tools to enhance model reusability, there has been a relative lack of consideration for how underlying biophysical principles can be applied to this space. Bond graphs combine the aspects of both modularity and physics-based modelling. In this paper, we argue that bond graphs are compatible with recent developments in modularity and abstraction in systems biology, and are thus a desirable framework for constructing large-scale models. We use two examples to illustrate the utility of bond graphs in this context: a model of a mitogen-activated protein kinase (MAPK) cascade to illustrate the reusability of modules and a model of glycolysis to illustrate the ability to modify the model granularity.Michael PanPeter J GawthropJoseph CursonsEdmund J CrampinPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 17, Iss 10, p e1009513 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Michael Pan Peter J Gawthrop Joseph Cursons Edmund J Crampin Modular assembly of dynamic models in systems biology.
description	It is widely acknowledged that the construction of large-scale dynamic models in systems biology requires complex modelling problems to be broken up into more manageable pieces. To this end, both modelling and software frameworks are required to enable modular modelling. While there has been consistent progress in the development of software tools to enhance model reusability, there has been a relative lack of consideration for how underlying biophysical principles can be applied to this space. Bond graphs combine the aspects of both modularity and physics-based modelling. In this paper, we argue that bond graphs are compatible with recent developments in modularity and abstraction in systems biology, and are thus a desirable framework for constructing large-scale models. We use two examples to illustrate the utility of bond graphs in this context: a model of a mitogen-activated protein kinase (MAPK) cascade to illustrate the reusability of modules and a model of glycolysis to illustrate the ability to modify the model granularity.
format	article
author	Michael Pan Peter J Gawthrop Joseph Cursons Edmund J Crampin
author_facet	Michael Pan Peter J Gawthrop Joseph Cursons Edmund J Crampin
author_sort	Michael Pan
title	Modular assembly of dynamic models in systems biology.
title_short	Modular assembly of dynamic models in systems biology.
title_full	Modular assembly of dynamic models in systems biology.
title_fullStr	Modular assembly of dynamic models in systems biology.
title_full_unstemmed	Modular assembly of dynamic models in systems biology.
title_sort	modular assembly of dynamic models in systems biology.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/4688ffc01167458e8271b1474bd0ae27
work_keys_str_mv	AT michaelpan modularassemblyofdynamicmodelsinsystemsbiology AT peterjgawthrop modularassemblyofdynamicmodelsinsystemsbiology AT josephcursons modularassemblyofdynamicmodelsinsystemsbiology AT edmundjcrampin modularassemblyofdynamicmodelsinsystemsbiology
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Modular assembly of dynamic models in systems biology.

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