| Title: |
The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update |
| Authors: |
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-Díez, 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.-R.; 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.M.; 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, M.; Zambelli, F.; Zierep, P.; Zoabi, R. |
| Publication Year: |
2024 |
| Collection: |
Bradford Scholars@University of Bradford |
| Subject Terms: |
Galaxy platform |
| Description: |
Yes ; 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. ; NIH [U41 HG006620, U24 HG010263, U24 CA231877, U01 CA253481]; US National Science Foundation [1661497, 1758800, 2216612]; computational resources are provided by the Advanced Cyberinfrastructure Coordination Ecosystem (ACCESS-CI), Texas Advanced Computing Center, and the JetStream2 scientific cloud. Funding for open access charge: NIH. ELIXIR IS and Travel grants; EU Horizon Europe [HORIZON-INFRA-2021-EOSC-01-04, 101057388]; EU Horizon Europe under the Biodiversity, Circular Economy and Environment program (REA.B.3, BGE 101059492); German Federal Ministry of Education and Research, BMBF [031 A538A de.NBI-RBC]; ... |
| Document Type: |
article in journal/newspaper |
| File Description: |
application/pdf |
| Language: |
English |
| Relation: |
https://hdl.handle.net/10454/19930; https://doi.org/10.1093/nar/gkae410 |
| DOI: |
10.1093/nar/gkae410 |
| Availability: |
https://hdl.handle.net/10454/19930; https://doi.org/10.1093/nar/gkae410 |
| Rights: |
(c) 2024 The Authors. This is an Open Access article distributed under the Creative Commons CC-BY license (https://creativecommons.org/licenses/by/4.0/) ; CC-BY |
| Accession Number: |
edsbas.2CAB8E40 |
| Database: |
BASE |