ArticleNPJ systems biology and applications2021
Characteristics of mathematical modeling languages that facilitate model reuse in systems biology: a software engineering perspective.
Article in NPJ systems biology and applications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Computational modelling of cardiovascular pathophysiology to risk stratify commercial spaceflight.Nature reviews. Cardiology · 2024Review
- Biology System Description Language (BiSDL): a modeling language for the design of multicellular synthetic biological systems.BMC bioinformatics · 2024Article
- Scalable reaction network modeling with automatic validation of consistency in Event-B.Scientific reports · 2022Article
- Characteristics of mathematical modeling languages that facilitate model reuse in systems biology: a software engineering perspective.NPJ systems biology and applications · 2021Article
- Hierarchical semantic composition of biosimulation models using bond graphs.PLoS computational biology · 2021Article
- Constructing and analysing dynamic models with modelbase v1.2.3: a software update.BMC bioinformatics · 2021Article
- Article
- An Understandable, Extensible, and Reusable Implementation of the Hodgkin-Huxley Equations Using Modelica.Frontiers in physiology · 2020Article
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Authors and funding
4 authors.
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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.
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Registered trials
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