Toward practical transparent verifiable and long-term reproducible research using Guix
Abstract 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,...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2022-10-01
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| Series: | Scientific Data |
| Online Access: | https://doi.org/10.1038/s41597-022-01720-9 |
| _version_ | 1797996174991425536 |
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| author | Nicolas Vallet David Michonneau Simon Tournier |
| author_facet | Nicolas Vallet David Michonneau Simon Tournier |
| author_sort | Nicolas Vallet |
| collection | DOAJ |
| description | Abstract 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. |
| first_indexed | 2024-04-11T10:13:19Z |
| format | Article |
| id | doaj.art-da7e7c2847ed45ada5ad97d82cb94d6a |
| institution | Directory Open Access Journal |
| issn | 2052-4463 |
| language | English |
| last_indexed | 2024-04-11T10:13:19Z |
| publishDate | 2022-10-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Data |
| spelling | doaj.art-da7e7c2847ed45ada5ad97d82cb94d6a2022-12-22T04:30:03ZengNature PortfolioScientific Data2052-44632022-10-01911910.1038/s41597-022-01720-9Toward practical transparent verifiable and long-term reproducible research using GuixNicolas Vallet0David Michonneau1Simon Tournier2Université de ParisUniversité de ParisUniversité de Paris, INSERM US53, CNRS UAR 2030, Saint Louis Research InstituteAbstract 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.https://doi.org/10.1038/s41597-022-01720-9 |
| spellingShingle | Nicolas Vallet David Michonneau Simon Tournier Toward practical transparent verifiable and long-term reproducible research using Guix Scientific Data |
| 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 |
| url | https://doi.org/10.1038/s41597-022-01720-9 |
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