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

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 docu...

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Vydáno v:NPJ systems biology and applications Ročník 7; číslo 1; s. 27 - 20
Hlavní autoři: Schölzel, Christopher, Blesius, Valeria, Ernst, Gernot, Dominik, Andreas
Médium: Journal Article
Jazyk:angličtina
Vydáno: London Nature Publishing Group UK 03.06.2021
Nature Publishing Group
Nature Portfolio
Témata:
631/553/1751
631/553/2695
692/4019
Bioinformatics
Biomedical and Life Sciences
Computational Biology/Bioinformatics
Computer Appl. in Life Sciences
Computer programs
Humans
Life Sciences
Mathematical models
Models, Biological
Models, Theoretical
Software
Software engineering
Systems Biology
ISSN:2056-7189, 2056-7189
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Shrnutí: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.
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ISSN:2056-7189
2056-7189
DOI:10.1038/s41540-021-00182-w