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

Abueg, L.A.L.; Afgan, E.; Allart, O.; Awan, A.H.; Bacon, W.A.; Baker, D.; Bassetti, M.; Batut, B.; Bernt, M.; Blankenberg, D.; Bombarely, A.; Bretaudeau, A.; Bromhead, C.J.; Burke, M.L.; Capon, P.K.; Čech, M.; Chavero-Diez, M.; Chilton, J.M.; Collins, T.J.; Coppens, F.; Coraor, N.; Cuccuru, G.; Cumbo, F.; Davis, J.; De Geest, P.F.; de Koning, W.; Demko, M.; DeSanto, A.; Domínguez Begines, J.M.; Doyle, M.A.; Droesbeke, B.; Erxleben-Eggenhofer, A.; Föll, M.C.; Formenti, G.; Fouilloux, A.; Gangazhe, R.; Genthon, T.; Goecks, J.; Gonzalez Beltran, A.N.; Goonasekera, N.A.; Goué, N.; Griffin, T.J.; Grüning, B.A.; Guerler, A.; Gundersen, S.; Gustafsson, O.J.R.; Hall, C.; Harrop, T.W.; Hecht, H.; Heidari, A.; Heisner, T.; Heyl, F.; Hiltemann, S.; Hotz, H.; Hyde, C.J.; Jagtap, P.D.; Jakiela, J.; Johnson, J.E.; Joshi, J.; Jossé, M.; Jum'ah, Khaled; Kalaš, M.; Kamieniecka, Katarzyna; Kayikcioglu, T.; Konkol, M.; Kostrykin, L.; Kucher, N.; Kumar, A.; Kuntz, M.; Lariviere, D.; Lazarus, R.; Le Bras, Y.; Le Corguillé, G.; Lee, J.; Leo, S.; Liborio, L.; Libouban, R.; López Tabernero, D.; Lopez-Delisle, L.; Los, L.S.; Mahmoud, A.; Makunin, I.; Marin, P.; Mehta, S.; Mok, W.; Moreno, P.A.; Morier-Genoud, F.; Mosher, S.; Müller, T.; Nasr, E.; Nekrutenko, A.; Nelson, T.M.; Oba, A.J.; Ostrovsky, A.; Polunina, P.V.; Poterlowicz, Krzysztof; Price, E.J.; Price, G.R.; Rasche, H.; Raubenolt, B.; Royaux, C.; Sargent, L.; Savage, M.T.; Savchenko, V.; Savchenko, D.; Schatz, M.C.; Seguineau, P.; Serrano-Solano, B.; Soranzo, N.; Srikakulam, S.K.; Suderman, K.; Syme, A.E.; Tangaro, M.A.; Tedds, J.A.; Tekman, M.; Thang, W.C.; Thanki, A.S.; Uhl, M.; van den Beek, M.; Varshney, D.; Vessio, J.; Videm, P.; Von Kuster, G.; Watson, G.R.; Whitaker-Allen, N.; Winter, U.; Wolstencroft, Martin; Zambelli, F.; Zierep, P.; Zoabi, R.

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Publication date

2024-07-05

Author

Abueg, L.A.L.
Afgan, E.
Allart, O.
Awan, A.H.
Bacon, W.A.
Baker, D.
Bassetti, M.
Batut, B.
Bernt, M.
Blankenberg, D.

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Keyword

Galaxy platform
Data analysis
User experience design (UXD)
Galaxy Training Network (GTN)

Rights

© The Author(s) 2024. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

Peer-Reviewed

Yes

Open Access status

openAccess

Accepted for publication

2024-05-02

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Abstract

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.

URI

http://hdl.handle.net/10454/19918

Version

Published version

Citation

Abueg LAL, Afgan E, Allart O et al (2024) The Galaxy platform for accessible, reproduciable, and collaborative data analyses: 2024 update. Nucleic Acids Research. 52(W1): W83-W94.

Link to Version of Record

https://doi.org/10.1093/nar/gkae410

Type

Article

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Life Sciences Publications