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Sim2Ls: FAIR simulation workflows and data
Just like the scientific data they generate, simulation workflows for research should be findable, accessible, interoperable, and reusable (FAIR). However, while significant progress has been made towards FAIR data, the majority of science and engineering workflows used in research remain poorly doc...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8912189/ https://www.ncbi.nlm.nih.gov/pubmed/35271613 http://dx.doi.org/10.1371/journal.pone.0264492 |
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author | Hunt, Martin Clark, Steven Mejia, Daniel Desai, Saaketh Strachan, Alejandro |
author_facet | Hunt, Martin Clark, Steven Mejia, Daniel Desai, Saaketh Strachan, Alejandro |
author_sort | Hunt, Martin |
collection | PubMed |
description | Just like the scientific data they generate, simulation workflows for research should be findable, accessible, interoperable, and reusable (FAIR). However, while significant progress has been made towards FAIR data, the majority of science and engineering workflows used in research remain poorly documented and often unavailable, involving ad hoc scripts and manual steps, hindering reproducibility and stifling progress. We introduce Sim2Ls (pronounced simtools) and the Sim2L Python library that allow developers to create and share end-to-end computational workflows with well-defined and verified inputs and outputs. The Sim2L library makes Sim2Ls, their requirements, and their services discoverable, verifies inputs and outputs, and automatically stores results in a globally-accessible simulation cache and results database. This simulation ecosystem is available in nanoHUB, an open platform that also provides publication services for Sim2Ls, a computational environment for developers and users, and the hardware to execute runs and store results at no cost. We exemplify the use of Sim2Ls using two applications and discuss best practices towards FAIR simulation workflows and associated data. |
format | Online Article Text |
id | pubmed-8912189 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-89121892022-03-11 Sim2Ls: FAIR simulation workflows and data Hunt, Martin Clark, Steven Mejia, Daniel Desai, Saaketh Strachan, Alejandro PLoS One Research Article Just like the scientific data they generate, simulation workflows for research should be findable, accessible, interoperable, and reusable (FAIR). However, while significant progress has been made towards FAIR data, the majority of science and engineering workflows used in research remain poorly documented and often unavailable, involving ad hoc scripts and manual steps, hindering reproducibility and stifling progress. We introduce Sim2Ls (pronounced simtools) and the Sim2L Python library that allow developers to create and share end-to-end computational workflows with well-defined and verified inputs and outputs. The Sim2L library makes Sim2Ls, their requirements, and their services discoverable, verifies inputs and outputs, and automatically stores results in a globally-accessible simulation cache and results database. This simulation ecosystem is available in nanoHUB, an open platform that also provides publication services for Sim2Ls, a computational environment for developers and users, and the hardware to execute runs and store results at no cost. We exemplify the use of Sim2Ls using two applications and discuss best practices towards FAIR simulation workflows and associated data. Public Library of Science 2022-03-10 /pmc/articles/PMC8912189/ /pubmed/35271613 http://dx.doi.org/10.1371/journal.pone.0264492 Text en https://creativecommons.org/publicdomain/zero/1.0/This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 (https://creativecommons.org/publicdomain/zero/1.0/) public domain dedication. |
spellingShingle | Research Article Hunt, Martin Clark, Steven Mejia, Daniel Desai, Saaketh Strachan, Alejandro Sim2Ls: FAIR simulation workflows and data |
title | Sim2Ls: FAIR simulation workflows and data |
title_full | Sim2Ls: FAIR simulation workflows and data |
title_fullStr | Sim2Ls: FAIR simulation workflows and data |
title_full_unstemmed | Sim2Ls: FAIR simulation workflows and data |
title_short | Sim2Ls: FAIR simulation workflows and data |
title_sort | sim2ls: fair simulation workflows and data |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8912189/ https://www.ncbi.nlm.nih.gov/pubmed/35271613 http://dx.doi.org/10.1371/journal.pone.0264492 |
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