Standards, dissemination, and best practices in systems biology

Shin, Janis; Porubsky, Veronica; Carothers, James; Sauro, Herbert M.

doi:10.1016/j.copbio.2023.102922

Standards, dissemination, and best practices in systems biology

Journal Article · Fri Mar 31 00:00:00 EDT 2023 · Current Opinion in Biotechnology

DOI:https://doi.org/10.1016/j.copbio.2023.102922· OSTI ID:2418702

Shin, Janis ^[1]; Porubsky, Veronica ^[2]; Carothers, James ^[2]; Sauro, Herbert M. ^[2]

Univ. of Washington, Seattle, WA (United States); Univ. of Washington, Seattle, WA (United States)
Univ. of Washington, Seattle, WA (United States)

In this study, the reproducibility of scientific research is crucial to the success of the scientific method. Here, we review the current best practices when publishing mechanistic models in systems biology. We recommend, where possible, to use software engineering strategies such as testing, verification, validation, documentation, versioning, iterative development, and continuous integration. In addition, adhering to the Findable, Accessible, Interoperable, and Reusable modeling principles allows other scientists to collaborate and build off of each other’s work. Existing standards such as Systems Biology Markup Language, CellML, or Simulation Experiment Description Markup Language can greatly improve the likelihood that a published model is reproducible, especially if such models are deposited in well-established model repositories. Where models are published in executable programming languages, the source code and their data should be published as open-source in public code repositories together with any documentation and testing code. For complex models, we recommend container-based solutions where any software dependencies and the run-time context can be easily replicated.

View Accepted Manuscript (DOE)

Research Organization:: Univ. of Washington, Seattle, WA (United States)

Sponsoring Organization:: National Institutes of Health (NIH); National Science Foundation (NSF); USDOE Office of Energy Efficiency and Renewable Energy (EERE)

Grant/Contract Number:: EE0008927

OSTI ID:: 2418702

Journal Information:: Current Opinion in Biotechnology, Journal Name: Current Opinion in Biotechnology Journal Issue: C Vol. 81; ISSN 0958-1669

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

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Standards, dissemination, and best practices in systems biology

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