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Recent advances in biomedical simulations: a manifesto for model engineering

Biomedical simulations are widely used to understand disease, engineer cells, and model cellular processes. In this article, we explore how to improve the quality of biomedical simulations by developing simulation models using tools and practices employed in software engineering. We refer to this di...

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Detalles Bibliográficos
Autores principales: Hellerstein, Joseph L., Gu, Stanley, Choi, Kiri, Sauro, Herbert M.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: F1000 Research Limited 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6406177/
https://www.ncbi.nlm.nih.gov/pubmed/30881691
http://dx.doi.org/10.12688/f1000research.15997.1
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author Hellerstein, Joseph L.
Gu, Stanley
Choi, Kiri
Sauro, Herbert M.
author_facet Hellerstein, Joseph L.
Gu, Stanley
Choi, Kiri
Sauro, Herbert M.
author_sort Hellerstein, Joseph L.
collection PubMed
description Biomedical simulations are widely used to understand disease, engineer cells, and model cellular processes. In this article, we explore how to improve the quality of biomedical simulations by developing simulation models using tools and practices employed in software engineering. We refer to this direction as model engineering. Not all techniques used by software engineers are directly applicable to model engineering, and so some adaptations are required. That said, we believe that simulation models can benefit from software engineering practices for requirements, design, and construction as well as from software engineering tools for version control, error checking, and testing. Here we survey current efforts to improve simulation quality and discuss promising research directions for model engineering.
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spelling pubmed-64061772019-03-15 Recent advances in biomedical simulations: a manifesto for model engineering Hellerstein, Joseph L. Gu, Stanley Choi, Kiri Sauro, Herbert M. F1000Res Review Biomedical simulations are widely used to understand disease, engineer cells, and model cellular processes. In this article, we explore how to improve the quality of biomedical simulations by developing simulation models using tools and practices employed in software engineering. We refer to this direction as model engineering. Not all techniques used by software engineers are directly applicable to model engineering, and so some adaptations are required. That said, we believe that simulation models can benefit from software engineering practices for requirements, design, and construction as well as from software engineering tools for version control, error checking, and testing. Here we survey current efforts to improve simulation quality and discuss promising research directions for model engineering. F1000 Research Limited 2019-03-05 /pmc/articles/PMC6406177/ /pubmed/30881691 http://dx.doi.org/10.12688/f1000research.15997.1 Text en Copyright: © 2019 Hellerstein JL et al. http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Review
Hellerstein, Joseph L.
Gu, Stanley
Choi, Kiri
Sauro, Herbert M.
Recent advances in biomedical simulations: a manifesto for model engineering
title Recent advances in biomedical simulations: a manifesto for model engineering
title_full Recent advances in biomedical simulations: a manifesto for model engineering
title_fullStr Recent advances in biomedical simulations: a manifesto for model engineering
title_full_unstemmed Recent advances in biomedical simulations: a manifesto for model engineering
title_short Recent advances in biomedical simulations: a manifesto for model engineering
title_sort recent advances in biomedical simulations: a manifesto for model engineering
topic Review
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6406177/
https://www.ncbi.nlm.nih.gov/pubmed/30881691
http://dx.doi.org/10.12688/f1000research.15997.1
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