Cargando…

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...

Descripción completa

Detalles Bibliográficos
Autores principales: Vallet, Nicolas, Michonneau, David, Tournier, Simon
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2022
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
_version_ 1784802118516867072
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
work_keys_str_mv AT valletnicolas towardpracticaltransparentverifiableandlongtermreproducibleresearchusingguix
AT michonneaudavid towardpracticaltransparentverifiableandlongtermreproducibleresearchusingguix
AT tourniersimon towardpracticaltransparentverifiableandlongtermreproducibleresearchusingguix