Recent advances in biomedical simulations: a manifesto for model engineering
Open accessAbstract
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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References 43 · Cited by 20
Research works printed but not linked: 2
- [37]Hoehndorf R Dumontier M Gennari JH: Formalizing Systems Biology Models with Biomedical Ontologies. Systems Biology. 2011. PMC3170340 21835028
- [39]Sauro HM: Jarnac: A System for Interactive Metabolic Analysis. In: Hofmeyr JHS, Rohwer JM, Snoep JL, editors, Animating the Cellular Map: Proceedings of the 9th International Meeting on BioThermoKinetics Stellenbosch University Press. 2000 Reference Source
- Authors
- Hellerstein, J. L., Gu, S., Choi, K., & Sauro, H. M.
- Affiliations
- University of Washington (US)
- Corresponding author
- Hellerstein, Joseph L.
- Venue
- F1000Research
- Publisher
- F1000 Research Ltd
- Published
- 2019-03-05
- Volume
- 8
- Pages
- 261
- ISSN
- 2046-1402 (ISSN-L)
- PMC
- PMC6406177
- OpenAlex
- W2920140146
- Cited by
- 20
- References
- 43
- Citations by year
- 2026: 1 · 2023: 6 · 2022: 2 · 2021: 7 · 2020: 2 · 2019: 2
- FWCI
- 0.57
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- F1000Research (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- Alfred P. Sloan Foundation (2013-10-29)
- NIAID (HHSN266200500021C)
- Gordon and Betty Moore Foundation (3835)
- NIH (GM123032, U01HL122199, P41EB023912, GM081070)
- Topics
- Social Sciences › Decision Sciences › Information Systems and Management › Scientific Computing and Data Management
- Social Sciences › Decision Sciences › Management Science and Operations Research › Simulation Techniques and Applications
- Physical Sciences › Computer Science › Computational Theory and Mathematics › Modeling and Simulation Systems
- Keywords
- biomedical simulation, model engineering, software engineering practices, requirements engineering, simulation design, version control, error detection, simulation-based testing, disease modeling
- MeSH terms
- Computer Simulation, Software Design, Biomedical Research
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