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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...

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Autores principales: Hunt, Martin, Clark, Steven, Mejia, Daniel, Desai, Saaketh, Strachan, Alejandro
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2022
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.
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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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