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

Cited by Lee Sonogan

What is Systems Biology? – Systems Biology Initiative

Abstract by Christopher Schölzel,Valeria Blesius,Gernot Ernst &Andreas Dominik 

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.

Publication: npj Systems Biology and Applications (Peer-Reviewed Journal)

Pub Date: 3 June 2021 Doi:

Keywords: Cardiology, Computer Modelling, Programming Language (Plenty more sections, figures and references in this article)

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