The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update

作者：The Galaxy Community, Linelle Ann L Abueg, Enis Afgan, Olivier Allart, Ahmed Awan, Wendi Bacon, Dannon Baker, Madeline E. Bassetti, Bérénice Batut, Matthias Bernt, Daniel Blankenberg, Aureliano Bombarely, Anthony Bretaudeau, Catherine Bromhead, Melissa L. Burke, Patrick K. Capon, Martin Čech, María Chavero-Diez, John Chilton, Tyler J Collins, Frederik Coppens, Nate Coraor, Gianmauro Cuccuru, Fabio Cumbo, John Davis, Paul F De Geest, Willem de Koning, Martin Demko, Assunta D DeSanto, José Manuel Domínguez Begines, Maria Doyle, Bert Droesbeke, Anika Erxleben-Eggenhofer, Melanie Christine Föll, Giulio Formenti, Anne Fouilloux, Rendani Gangazhe, Tanguy Genthon, Jeremy Goecks, Alejandra N Gonzalez Beltran, Nuwan Goonasekera, Nadia Goué, Timothy J. Griffin, Björn Grüning, Aysam Guerler, Sveinung Gundersen, Ove Gustafsson, Christina Hall, Thomas W.R. Harrop, Helge Hecht, Alireza Heidari, Tillman Heisner, Florian Heyl, Saskia Hiltemann, Hans-Rudolf Hotz, Cameron Hyde, Pratik Jagtap, Julia Jakiela, James E. Johnson, Jayadev Joshi, Marie Jossé, Khaled Jumah, Matúš Kalaš, Katarzyna Kamieniecka, Tunc Kayikcioglu, Markus Konkol, Leonid Kostrykin, Natalie Kucher, Anup Kumar, Mira Kuntz, Delphine Larivière, Ross Lazarus, Yvan Le Bras, Gildas Le Corguillé, Justin Lee, Simone Leo, Leandro Liborio, Romane Libouban, David López Tabernero, Lucille Lopez‐Delisle, Laila S Los, Alexandru Mahmoud, Igor V. Makunin, Pierre Marin, Subina Mehta, Winnie Mok, Pablo Moreno, François Antoine Morier-Genoud, Stephen Mosher, Teresa Müller, Engy Nasr, Anton Nekrutenko, Tiffanie M. Nelson, Asime J Oba, Alexander Ostrovsky, Polina V Polunina, Krzysztof Poterlowicz, Elliott J. Price, Gareth Price, Helena Rasche, Bryan Raubenolt, Coline Royaux, Luke Sargent, Michelle Savage, V. Savchenko, Denys Savchenko, Michael C. Schatz, Pauline Seguineau, Beatriz Serrano‐Solano, Nicola Soranzo, Sanjay Kumar Srikakulam, Keith Suderman, Anna Syme, M. A. Tangaro, Jonathan Tedds, Mehmet Tekman, Wai Cheng Thang, Anil S. Thanki, Michaël Uhl, Marius van den Beek, Deepti Varshney, Jenn Vessio, Pavankumar Videm, Greg Von Kuster, Gregory R. Watson, Natalie Whitaker-Allen, Uwe Winter, Martin Wolstencroft, Federico Zambelli, Paul Zierep, Rand Zoabi · 发表于：Nucleic Acids Research · 年份：2024 · DOI：10.1093/nar/gkae410 · 被引用次数：936 · 研究领域：Scientific Computing and Data Management、Research Data Management Practices、Advanced Data Storage Technologies

Galaxy (https://galaxyproject.org) is deployed globally, predominantly through free-to-use services, supporting user-driven research that broadens in scope each year. Users are attracted to public Galaxy services by platform stability, tool and reference dataset diversity, training, support and integration, which enables complex, reproducible, shareable data analysis. Applying the principles of user experience design (UXD), has driven improvements in accessibility, tool discoverability through Galaxy Labs/subdomains, and a redesigned Galaxy ToolShed. Galaxy tool capabilities are progressing in two strategic directions: integrating general purpose graphical processing units (GPGPU) access for cutting-edge methods, and licensed tool support. Engagement with global research consortia is being increased by developing more workflows in Galaxy and by resourcing the public Galaxy services to run them. The Galaxy Training Network (GTN) portfolio has grown in both size, and accessibility, through learning paths and direct integration with Galaxy tools that feature in training courses. Code development continues in line with the Galaxy Project roadmap, with improvements to job scheduling and the user interface. Environmental impact assessment is also helping engage users and developers, reminding them of their role in sustainability, by displaying estimated CO2 emissions generated by each Galaxy job.