Characteristics of mathematical modeling languages that facilitate model reuse in systems biology: a software engineering perspective

Abstract Reuse of mathematical models becomes increasingly important in systems biology as research moves toward large, multi-scale models composed of heterogeneous subcomponents. Currently, many models are not easily reusable due to inflexible or confusing code, inappropriate languages, or insuffic...

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Autores principales:	Christopher Schölzel, Valeria Blesius, Gernot Ernst, Andreas Dominik
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/1f0302591a794f1382cbf4ba57727b11
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spelling	oai:doaj.org-article:1f0302591a794f1382cbf4ba57727b112021-12-02T15:56:57ZCharacteristics of mathematical modeling languages that facilitate model reuse in systems biology: a software engineering perspective10.1038/s41540-021-00182-w2056-7189https://doaj.org/article/1f0302591a794f1382cbf4ba57727b112021-06-01T00:00:00Zhttps://doi.org/10.1038/s41540-021-00182-whttps://doaj.org/toc/2056-7189Abstract Reuse of mathematical models becomes increasingly important in systems biology as research moves toward large, multi-scale models composed of heterogeneous subcomponents. Currently, many models are not easily reusable due to inflexible or confusing code, inappropriate languages, or insufficient documentation. Best practice suggestions rarely cover such low-level design aspects. This gap could be filled by software engineering, which addresses those same issues for software reuse. We show that languages can facilitate reusability by being modular, human-readable, hybrid (i.e., supporting multiple formalisms), open, declarative, and by supporting the graphical representation of models. Modelers should not only use such a language, but be aware of the features that make it desirable and know how to apply them effectively. For this reason, we compare existing suitable languages in detail and demonstrate their benefits for a modular model of the human cardiac conduction system written in Modelica.Christopher SchölzelValeria BlesiusGernot ErnstAndreas DominikNature PortfolioarticleBiology (General)QH301-705.5ENnpj Systems Biology and Applications, Vol 7, Iss 1, Pp 1-20 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Christopher Schölzel Valeria Blesius Gernot Ernst Andreas Dominik Characteristics of mathematical modeling languages that facilitate model reuse in systems biology: a software engineering perspective
description	Abstract Reuse of mathematical models becomes increasingly important in systems biology as research moves toward large, multi-scale models composed of heterogeneous subcomponents. Currently, many models are not easily reusable due to inflexible or confusing code, inappropriate languages, or insufficient documentation. Best practice suggestions rarely cover such low-level design aspects. This gap could be filled by software engineering, which addresses those same issues for software reuse. We show that languages can facilitate reusability by being modular, human-readable, hybrid (i.e., supporting multiple formalisms), open, declarative, and by supporting the graphical representation of models. Modelers should not only use such a language, but be aware of the features that make it desirable and know how to apply them effectively. For this reason, we compare existing suitable languages in detail and demonstrate their benefits for a modular model of the human cardiac conduction system written in Modelica.
format	article
author	Christopher Schölzel Valeria Blesius Gernot Ernst Andreas Dominik
author_facet	Christopher Schölzel Valeria Blesius Gernot Ernst Andreas Dominik
author_sort	Christopher Schölzel
title	Characteristics of mathematical modeling languages that facilitate model reuse in systems biology: a software engineering perspective
title_short	Characteristics of mathematical modeling languages that facilitate model reuse in systems biology: a software engineering perspective
title_full	Characteristics of mathematical modeling languages that facilitate model reuse in systems biology: a software engineering perspective
title_fullStr	Characteristics of mathematical modeling languages that facilitate model reuse in systems biology: a software engineering perspective
title_full_unstemmed	Characteristics of mathematical modeling languages that facilitate model reuse in systems biology: a software engineering perspective
title_sort	characteristics of mathematical modeling languages that facilitate model reuse in systems biology: a software engineering perspective
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/1f0302591a794f1382cbf4ba57727b11
work_keys_str_mv	AT christopherscholzel characteristicsofmathematicalmodelinglanguagesthatfacilitatemodelreuseinsystemsbiologyasoftwareengineeringperspective AT valeriablesius characteristicsofmathematicalmodelinglanguagesthatfacilitatemodelreuseinsystemsbiologyasoftwareengineeringperspective AT gernoternst characteristicsofmathematicalmodelinglanguagesthatfacilitatemodelreuseinsystemsbiologyasoftwareengineeringperspective AT andreasdominik characteristicsofmathematicalmodelinglanguagesthatfacilitatemodelreuseinsystemsbiologyasoftwareengineeringperspective
_version_	1718385377425752064

Characteristics of mathematical modeling languages that facilitate model reuse in systems biology: a software engineering perspective

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