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Toward practical transparent verifiable and long-term reproducible research using Guix
Reproducibility crisis urge scientists to promote transparency which allows peers to draw same conclusions after performing identical steps from hypothesis to results. Growing resources are developed to open the access to methods, data and source codes. Still, the computational environment, an inter...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9532446/ https://www.ncbi.nlm.nih.gov/pubmed/36195618 http://dx.doi.org/10.1038/s41597-022-01720-9 |
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author | Vallet, Nicolas Michonneau, David Tournier, Simon |
author_facet | Vallet, Nicolas Michonneau, David Tournier, Simon |
author_sort | Vallet, Nicolas |
collection | PubMed |
description | Reproducibility crisis urge scientists to promote transparency which allows peers to draw same conclusions after performing identical steps from hypothesis to results. Growing resources are developed to open the access to methods, data and source codes. Still, the computational environment, an interface between data and source code running analyses, is not addressed. Environments are usually described with software and library names associated with version labels or provided as an opaque container image. This is not enough to describe the complexity of the dependencies on which they rely to operate on. We describe this issue and illustrate how open tools like Guix can be used by any scientist to share their environment and allow peers to reproduce it. Some steps of research might not be fully reproducible, but at least, transparency for computation is technically addressable. These tools should be considered by scientists willing to promote transparency and open science. |
format | Online Article Text |
id | pubmed-9532446 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-95324462022-10-06 Toward practical transparent verifiable and long-term reproducible research using Guix Vallet, Nicolas Michonneau, David Tournier, Simon Sci Data Article Reproducibility crisis urge scientists to promote transparency which allows peers to draw same conclusions after performing identical steps from hypothesis to results. Growing resources are developed to open the access to methods, data and source codes. Still, the computational environment, an interface between data and source code running analyses, is not addressed. Environments are usually described with software and library names associated with version labels or provided as an opaque container image. This is not enough to describe the complexity of the dependencies on which they rely to operate on. We describe this issue and illustrate how open tools like Guix can be used by any scientist to share their environment and allow peers to reproduce it. Some steps of research might not be fully reproducible, but at least, transparency for computation is technically addressable. These tools should be considered by scientists willing to promote transparency and open science. Nature Publishing Group UK 2022-10-04 /pmc/articles/PMC9532446/ /pubmed/36195618 http://dx.doi.org/10.1038/s41597-022-01720-9 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Article Vallet, Nicolas Michonneau, David Tournier, Simon Toward practical transparent verifiable and long-term reproducible research using Guix |
title | Toward practical transparent verifiable and long-term reproducible research using Guix |
title_full | Toward practical transparent verifiable and long-term reproducible research using Guix |
title_fullStr | Toward practical transparent verifiable and long-term reproducible research using Guix |
title_full_unstemmed | Toward practical transparent verifiable and long-term reproducible research using Guix |
title_short | Toward practical transparent verifiable and long-term reproducible research using Guix |
title_sort | toward practical transparent verifiable and long-term reproducible research using guix |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9532446/ https://www.ncbi.nlm.nih.gov/pubmed/36195618 http://dx.doi.org/10.1038/s41597-022-01720-9 |
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