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references.bib
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@ -6,6 +6,7 @@
journaltitle = {The Register}, journaltitle = {The Register},
url = {https://resana.numerique.gouv.fr/public/document/consulter/3231705?slug=160133} url = {https://resana.numerique.gouv.fr/public/document/consulter/3231705?slug=160133}
} }
@article{gitorious, @article{gitorious,
title = {Code collaboration platform GitLab acquires rival Gitorious, will shut it down on June 1}, title = {Code collaboration platform GitLab acquires rival Gitorious, will shut it down on June 1},
author = {Andrii Degeler}, author = {Andrii Degeler},
@ -14,6 +15,7 @@
journaltitle = {The Next Web}, journaltitle = {The Next Web},
url = {https://thenextweb.com/news/gitlab-acquires-rival-gitorious-will-shut-june-1} url = {https://thenextweb.com/news/gitlab-acquires-rival-gitorious-will-shut-june-1}
} }
@article{googlecode, @article{googlecode,
title = {Google to close Google Code open source project hosting}, title = {Google to close Google Code open source project hosting},
author = {ARS Staff}, author = {ARS Staff},
@ -22,6 +24,7 @@
journaltitle = {ARS Technica}, journaltitle = {ARS Technica},
url = {https://arstechnica.com/information-technology/2015/03/google-to-close-google-code-open-source-project-hosting/} url = {https://arstechnica.com/information-technology/2015/03/google-to-close-google-code-open-source-project-hosting/}
} }
@article{elasticsearch, @article{elasticsearch,
title = {Elastic changes open-source license to monetize cloud-service use}, title = {Elastic changes open-source license to monetize cloud-service use},
author = {Steven Vaughan-Nichols}, author = {Steven Vaughan-Nichols},
@ -30,6 +33,7 @@
journaltitle = {ZD NET}, journaltitle = {ZD NET},
url = {https://www.zdnet.com/article/elastic-changes-open-source-license-to-monetize-cloud-service-use/} url = {https://www.zdnet.com/article/elastic-changes-open-source-license-to-monetize-cloud-service-use/}
} }
@misc{codeetlogiciel, @misc{codeetlogiciel,
title = {Science ouverte – codes et logiciels}, title = {Science ouverte – codes et logiciels},
author = {Pellegrini, François and Di Cosmo, Roberto and Romary, Laurent and Janik, Joanna and Hodenq, Sacha and Coutanson, Romane and Géroudet, Madeleine}, author = {Pellegrini, François and Di Cosmo, Roberto and Romary, Laurent and Janik, Joanna and Hodenq, Sacha and Coutanson, Romane and Géroudet, Madeleine},
@ -38,6 +42,7 @@
publisher = {ministère de l’Enseignement supérieur et de la Recherche}, publisher = {ministère de l’Enseignement supérieur et de la Recherche},
url = {https://www.ouvrirlascience.fr/science-ouverte-codes-et-logiciels/} url = {https://www.ouvrirlascience.fr/science-ouverte-codes-et-logiciels/}
} }
@article{akka, @article{akka,
title = {Lightbend: Open-source licensing con game or smart business move?}, title = {Lightbend: Open-source licensing con game or smart business move?},
author = {Steven Vaughan-Nichols}, author = {Steven Vaughan-Nichols},
@ -46,17 +51,18 @@
journaltitle = {ZD NET}, journaltitle = {ZD NET},
url = {https://www.zdnet.com/article/lightbend-open-source-licensing-con-game-or-smart-business-move/} url = {https://www.zdnet.com/article/lightbend-open-source-licensing-con-game-or-smart-business-move/}
} }
@misc{jecode, @misc{jecode,
TITLE = {{Je code : Les bonnes pratiques de d{\'e}veloppement logiciel}}, title = {{Je code : Les bonnes pratiques de d{\'e}veloppement logiciel}},
AUTHOR = {Ammour, Lila and Capp{\'e}, Olivier and Chaventre, Thierry and Dassas, Karin and Dexet, Marc and Moreau, Patrick and Mouton, C. and Souplet, Jean-Christophe}, author = {Ammour, Lila and Capp{\'e}, Olivier and Chaventre, Thierry and Dassas, Karin and Dexet, Marc and Moreau, Patrick and Mouton, C. and Souplet, Jean-Christophe},
URL = {https://hal.archives-ouvertes.fr/hal-02083801}, url = {https://hal.archives-ouvertes.fr/hal-02083801},
NOTE = {Guide de bonnes pratiques de d{\'e}veloppement logiciel {\`a} destination de la communaut{\'e} de l'enseignement sup{\'e}rieur et de la recherche.}, note = {Guide de bonnes pratiques de d{\'e}veloppement logiciel {\`a} destination de la communaut{\'e} de l'enseignement sup{\'e}rieur et de la recherche.},
YEAR = {2019}, year = {2019},
MONTH = Dec, month = Dec,
KEYWORDS = {r{\'e}seau DevLOG ; CNRS}, keywords = {r{\'e}seau DevLOG ; CNRS},
PDF = {https://hal.archives-ouvertes.fr/hal-02083801/file/20191202_plaquette_developpement_V1.1.pdf}, pdf = {https://hal.archives-ouvertes.fr/hal-02083801/file/20191202_plaquette_developpement_V1.1.pdf},
HAL_ID = {hal-02083801}, hal_id = {hal-02083801},
HAL_VERSION = {v1}, hal_version = {v1},
} }
@article{eclipsegitlab, @article{eclipsegitlab,
@ -112,6 +118,7 @@ abstract = {Software is the backbone of scientific computing. Yet, while we regu
biburl = {https://dblp.org/rec/books/daglib/0003337.bib}, biburl = {https://dblp.org/rec/books/daglib/0003337.bib},
bibsource = {dblp computer science bibliography, https://dblp.org} bibsource = {dblp computer science bibliography, https://dblp.org}
} }
@article{bestpracticesscientificcomputing, @article{bestpracticesscientificcomputing,
doi = {10.1371/journal.pbio.1001745}, doi = {10.1371/journal.pbio.1001745},
author = {Wilson, Greg and Aruliah, D. A. and Brown, C. Titus and Chue Hong, Neil P. and Davis, Matt and Guy, Richard T. and Haddock, Steven H. D. and Huff, Kathryn D. and Mitchell, Ian M. and Plumbley, Mark D. and Waugh, Ben and White, Ethan P. and Wilson, Paul}, author = {Wilson, Greg and Aruliah, D. A. and Brown, C. Titus and Chue Hong, Neil P. and Davis, Matt and Guy, Richard T. and Haddock, Steven H. D. and Huff, Kathryn D. and Mitchell, Ian M. and Plumbley, Mark D. and Waugh, Ben and White, Ethan P. and Wilson, Paul},
@ -128,25 +135,25 @@ abstract = {Software is the backbone of scientific computing. Yet, while we regu
} }
@InProceedings{githubinpublications, @InProceedings{githubinpublications,
author="Escamilla, Emily author = {Escamilla, Emily
and Klein, Martin and Klein, Martin
and Cooper, Talya and Cooper, Talya
and Rampin, Vicky and Rampin, Vicky
and Weigle, Michele C. and Weigle, Michele C.
and Nelson, Michael L.", and Nelson, Michael L.},
editor="Silvello, Gianmaria editor = {Silvello, Gianmaria
and Corcho, Oscar and Corcho, Oscar
and Manghi, Paolo and Manghi, Paolo
and Di Nunzio, Giorgio Maria and Di Nunzio, Giorgio Maria
and Golub, Koraljka and Golub, Koraljka
and Ferro, Nicola and Ferro, Nicola
and Poggi, Antonella", and Poggi, Antonella},
title="The Rise of GitHub in Scholarly Publications", title = {The Rise of GitHub in Scholarly Publications},
booktitle="Linking Theory and Practice of Digital Libraries", booktitle = {Linking Theory and Practice of Digital Libraries},
year="2022", year = {2022},
publisher="Springer International Publishing", publisher = {Springer International Publishing},
address="Cham", address = {Cham},
pages="187--200", pages = {187--200},
abstract="The definition of scholarly content has expanded to include the data and source code that contribute to a publication. While major archiving efforts to preserve conventional scholarly content, typically in PDFs (e.g., LOCKSS, CLOCKSS, Portico), are underway, no analogous effort has yet emerged to preserve the data and code referenced in those PDFs, particularly the scholarly code hosted online on Git Hosting Platforms (GHPs). Similarly, the Software Heritage Foundation is working to archive public source code, but there is value in archiving the issue threads, pull requests, and wikis that provide important context to the code while maintaining their original URLs. In current implementations, source code and its ephemera are not preserved, which presents a problem for scholarly projects where reproducibility matters. To understand and quantify the scope of this issue, we analyzed the use of GHP URIs in the arXiv and PMC corpora from January 2007 to December 2021. In total, there were 253,590 URIs to GitHub, SourceForge, Bitbucket, and GitLab repositories across the 2.66 million publications in the corpora. We found that GitHub, GitLab, SourceForge, and Bitbucket were collectively linked to 160 times in 2007 and 76,746 times in 2021. In 2021, one out of five publications in the arXiv corpus included a URI to GitHub. The complexity of GHPs like GitHub is not amenable to conventional Web archiving techniques. Therefore, the growing use of GHPs in scholarly publications points to an urgent and growing need for dedicated efforts to archive their holdings in order to preserve research code and its scholarly ephemera.", abstract = {The definition of scholarly content has expanded to include the data and source code that contribute to a publication. While major archiving efforts to preserve conventional scholarly content, typically in PDFs (e.g., LOCKSS, CLOCKSS, Portico), are underway, no analogous effort has yet emerged to preserve the data and code referenced in those PDFs, particularly the scholarly code hosted online on Git Hosting Platforms (GHPs). Similarly, the Software Heritage Foundation is working to archive public source code, but there is value in archiving the issue threads, pull requests, and wikis that provide important context to the code while maintaining their original URLs. In current implementations, source code and its ephemera are not preserved, which presents a problem for scholarly projects where reproducibility matters. To understand and quantify the scope of this issue, we analyzed the use of GHP URIs in the arXiv and PMC corpora from January 2007 to December 2021. In total, there were 253,590 URIs to GitHub, SourceForge, Bitbucket, and GitLab repositories across the 2.66 million publications in the corpora. We found that GitHub, GitLab, SourceForge, and Bitbucket were collectively linked to 160 times in 2007 and 76,746 times in 2021. In 2021, one out of five publications in the arXiv corpus included a URI to GitHub. The complexity of GHPs like GitHub is not amenable to conventional Web archiving techniques. Therefore, the growing use of GHPs in scholarly publications points to an urgent and growing need for dedicated efforts to archive their holdings in order to preserve research code and its scholarly ephemera.},
isbn="978-3-031-16802-4" isbn = {978-3-031-16802-4}
} }