The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update
Linelle Ann L Abueg
(1)
,
Enis Afgan
(2)
,
Olivier Allart
(3)
,
Ahmed Awan
(2)
,
Wendi Bacon
(4)
,
Dannon Baker
(2)
,
Madeline Bassetti
(5)
,
Bérénice Batut
(6, 7)
,
Matthias Bernt
(8)
,
Daniel Blankenberg
(9)
,
Aureliano Bombarely
(10)
,
Anthony Bretaudeau
(11, 6)
,
Catherine Bromhead
(12)
,
Melissa Burke
(13)
,
Patrick Capon
(12)
,
Martin Čech
(14)
,
María Chavero-Díez
(15)
,
John Chilton
(14)
,
Tyler Collins
(2)
,
Frederik Coppens
(16, 17)
,
Nate Coraor
(4)
,
Gianmauro Cuccuru
(18)
,
Fabio Cumbo
(9)
,
John Davis
(2)
,
Paul de Geest
(19)
,
Willem de Koning
(20)
,
Martin Demko
(21)
,
Assunta Desanto
(14)
,
José Manuel Domínguez Begines
(22)
,
Maria Doyle
(23)
,
Bert Droesbeke
(16, 19)
,
Anika Erxleben-Eggenhofer
(22)
,
Melanie Föll
(22)
,
Giulio Formenti
(1)
,
Anne Fouilloux
(24)
,
Rendani Gangazhe
(22)
,
Tanguy Genthon
(25)
,
Jeremy Goecks
(26)
,
Alejandra Beltran
(27)
,
Nuwan Goonasekera
(12)
,
Nadia Goué
(28)
,
Timothy Griffin
(29)
,
Björn Grüning
(22)
,
Aysam Guerler
(2)
,
Sveinung Gundersen
(30)
,
Ove Johan Ragnar Gustafsson
(12)
,
Christina Hall
(12)
,
Thomas Harrop
(12)
,
Helge Hecht
(21)
,
Alireza Heidari
(22)
,
Tillman Heisner
(22)
,
Florian Heyl
(31)
,
Saskia Hiltemann
(22, 32)
,
Hans-Rudolf Hotz
(32)
,
Cameron Hyde
(5)
,
Pratik Jagtap
(29)
,
Julia Jakiela
(33)
,
James Johnson
(29)
,
Jayadev Joshi
(9)
,
Marie Jossé
(34)
,
Khaled Jum’ah
(35)
,
Matúš Kalaš
(36)
,
Katarzyna Kamieniecka
(35)
,
Tunc Kayikcioglu
(22)
,
Markus Konkol
(37)
,
Leonid Kostrykin
(38)
,
Natalie Kucher
(2)
,
Anup Kumar
(22)
,
Mira Kuntz
(22)
,
Delphine Lariviere
(14)
,
Ross Lazarus
(39)
,
Yvan Le Bras
(25)
,
Gildas Le Corguillé
(40)
,
Justin Lee
(41, 5)
,
Simone Leo
(42)
,
Leandro Liborio
(27, 43)
,
Romane Libouban
(11)
,
David López Tabernero
(22)
,
Lucille Lopez-Delisle
(44)
,
Laila Los
(22)
,
Alexandru Mahmoud
(45)
,
Igor Makunin
(46)
,
Pierre Marin
(7)
,
Subina Mehta
(29)
,
Winnie Mok
(12)
,
Pablo Moreno
(47)
,
François Morier-Genoud
(44)
,
Stephen Mosher
(2)
,
Teresa Müller
(22)
,
Engy Nasr
(22)
,
Anton Nekrutenko
(14)
,
Tiffanie Nelson
(13, 48)
,
Asime Oba
(49)
,
Alexander Ostrovsky
(2)
,
Polina Polunina
(22)
,
Krzysztof Poterlowicz
(35)
,
Elliott Price
(21)
,
Gareth Price
(46, 5)
,
Helena Rasche
(20)
,
Bryan Raubenolt
(50)
,
Coline Royaux
(51)
,
Luke Sargent
(52)
,
Michelle Savage
(2)
,
Volodymyr Savchenko
(44)
,
Denys Savchenko
(53)
,
Michael Schatz
(2)
,
Pauline Seguineau
(25)
,
Beatriz Serrano-Solano
(54)
,
Nicola Soranzo
(55)
,
Sanjay Kumar Srikakulam
(22)
,
Keith Suderman
(2)
,
Anna Syme
(12)
,
Marco Antonio Tangaro
(56)
,
Jonathan Tedds
(57)
,
Mehmet Tekman
(22)
,
Anil Thanki
(58)
,
Michael Uhl
(22)
,
Marius van den Beek
(14)
,
Deepti Varshney
(22)
,
Jenn Vessio
(2)
,
Pavankumar Videm
(22)
,
Greg von Kuster
(14)
,
Gregory Watson
(59)
,
Natalie Whitaker-Allen
(2)
,
Uwe Winter
(13, 12)
,
Martin Wolstencroft
(35)
,
Federico Zambelli
(10)
,
Paul Zierep
(22)
,
Rand Zoabi
(22)
1
Rockefeller University [New York]
2 JHU - Johns Hopkins University
3 AARNet - Australia's Academic and Research Network
4 OU - The Open University [Milton Keynes]
5 QCIF - Queensland Cyber Infrastructure Foundation [St Lucia]
6 IFB-CORE - Institut Français de Bioinformatique
7 AuBi - Plateforme Auvergne Bioinformatique
8 Institut für Informatik [Leipzig]
9 Cleveland Clinic
10 UNIMI - Università degli Studi di Milano = University of Milan
11 Plateforme bioinformatique GenOuest [Rennes]
12 University of Melbourne
13 Australian Biocommons
14 Penn State - Pennsylvania State University
15 BSC-CNS - Barcelona Supercomputing Center - Centro Nacional de Supercomputacion
16 UGENT - Universiteit Gent = Ghent University = Université de Gand
17 VIB [Belgium]
18 HumanTechnopole [Milan]
19 VIB - Vlaams Instituut voor Biotechnologie [Ghent, Belgique]
20 Erasmus MC - Erasmus University Medical Center [Rotterdam]
21 MUNI - Masaryk University [Brno]
22 Albert-Ludwigs-Universität Freiburg = University of Freiburg
23 UL - University of Limerick
24 Simula Research Laboratory [OSLO]
25 Muséum National d'Histoire Naturelle [Concarneau]
26 H. Lee Moffitt Cancer Center and Research Institute
27 STFC - Science and Technology Facilities Council
28 Université de Clermont-Ferrand
29 UMN - University of Minnesota System
30 UiO - University of Oslo
31 DKFZ - German Cancer Research Center - Deutsches Krebsforschungszentrum [Heidelberg]
32 FMI - Friedrich Miescher Institute for Biomedical Research
33 Edin. - University of Edinburgh
34 Data Terra - Unité Mixte Data Terra
35 University of Bradford
36 UiB - University of Bergen
37 52° North Spatial Information Research
38 Universität Heidelberg [Heidelberg] = Heidelberg University
39 Galaxy Project
40 SBR - Station biologique de Roscoff = Roscoff Marine Station
41 JCU - James Cook University
42 CRS4 - Center for Advanced Studies, Research and Development in Sardinia
43 RAL - STFC Rutherford Appleton Laboratory
44 EPFL - Ecole Polytechnique Fédérale de Lausanne
45 HMS - Harvard Medical School [Boston]
46 UQ [All campuses : Brisbane, Dutton Park Gatton, Herston, St Lucia and other locations] - The University of Queensland
47 AstraZeneca [Cambridge, UK]
48 Griffith University [Brisbane]
49 University of Maiduguri
50 Lerner Research Institute [Cleveland, OH, USA]
51 SU - Sorbonne Université
52 OHSU - Oregon Health and Science University [Portland]
53 UPCité - Université Paris Cité
54 EMBL Heidelberg
55 Earlham Institute [Norwich]
56 CNR - National Research Council of Italy | Consiglio Nazionale delle Ricerche
57 ELIXIR Hub [Cambridge]
58 EMBL-EBI - European Bioinformatics Institute [Hinxton]
59 ORNL - Oak Ridge National Laboratory [Oak Ridge]
2 JHU - Johns Hopkins University
3 AARNet - Australia's Academic and Research Network
4 OU - The Open University [Milton Keynes]
5 QCIF - Queensland Cyber Infrastructure Foundation [St Lucia]
6 IFB-CORE - Institut Français de Bioinformatique
7 AuBi - Plateforme Auvergne Bioinformatique
8 Institut für Informatik [Leipzig]
9 Cleveland Clinic
10 UNIMI - Università degli Studi di Milano = University of Milan
11 Plateforme bioinformatique GenOuest [Rennes]
12 University of Melbourne
13 Australian Biocommons
14 Penn State - Pennsylvania State University
15 BSC-CNS - Barcelona Supercomputing Center - Centro Nacional de Supercomputacion
16 UGENT - Universiteit Gent = Ghent University = Université de Gand
17 VIB [Belgium]
18 HumanTechnopole [Milan]
19 VIB - Vlaams Instituut voor Biotechnologie [Ghent, Belgique]
20 Erasmus MC - Erasmus University Medical Center [Rotterdam]
21 MUNI - Masaryk University [Brno]
22 Albert-Ludwigs-Universität Freiburg = University of Freiburg
23 UL - University of Limerick
24 Simula Research Laboratory [OSLO]
25 Muséum National d'Histoire Naturelle [Concarneau]
26 H. Lee Moffitt Cancer Center and Research Institute
27 STFC - Science and Technology Facilities Council
28 Université de Clermont-Ferrand
29 UMN - University of Minnesota System
30 UiO - University of Oslo
31 DKFZ - German Cancer Research Center - Deutsches Krebsforschungszentrum [Heidelberg]
32 FMI - Friedrich Miescher Institute for Biomedical Research
33 Edin. - University of Edinburgh
34 Data Terra - Unité Mixte Data Terra
35 University of Bradford
36 UiB - University of Bergen
37 52° North Spatial Information Research
38 Universität Heidelberg [Heidelberg] = Heidelberg University
39 Galaxy Project
40 SBR - Station biologique de Roscoff = Roscoff Marine Station
41 JCU - James Cook University
42 CRS4 - Center for Advanced Studies, Research and Development in Sardinia
43 RAL - STFC Rutherford Appleton Laboratory
44 EPFL - Ecole Polytechnique Fédérale de Lausanne
45 HMS - Harvard Medical School [Boston]
46 UQ [All campuses : Brisbane, Dutton Park Gatton, Herston, St Lucia and other locations] - The University of Queensland
47 AstraZeneca [Cambridge, UK]
48 Griffith University [Brisbane]
49 University of Maiduguri
50 Lerner Research Institute [Cleveland, OH, USA]
51 SU - Sorbonne Université
52 OHSU - Oregon Health and Science University [Portland]
53 UPCité - Université Paris Cité
54 EMBL Heidelberg
55 Earlham Institute [Norwich]
56 CNR - National Research Council of Italy | Consiglio Nazionale delle Ricerche
57 ELIXIR Hub [Cambridge]
58 EMBL-EBI - European Bioinformatics Institute [Hinxton]
59 ORNL - Oak Ridge National Laboratory [Oak Ridge]
Bérénice Batut
- Fonction : Auteur
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- IdHAL : berenice-batut
- ORCID : 0000-0001-9852-1987
- IdRef : 184297370
Anthony Bretaudeau
- Fonction : Auteur
- PersonId : 1688
- IdHAL : anthony-bretaudeau
- ORCID : 0000-0003-0914-2470
- IdRef : 253128358
Björn Grüning
- Fonction : Auteur
- PersonId : 784034
- ORCID : 0000-0002-3079-6586
Anton Nekrutenko
- Fonction : Auteur
- PersonId : 778921
- ORCID : 0000-0002-5987-8032
Gareth Price
- Fonction : Auteur correspondant
Coline Royaux
- Fonction : Auteur
- PersonId : 1247363
- ORCID : 0000-0003-4308-5617
- IdRef : 281931410
Résumé
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.
Domaines
Bio-informatique [q-bio.QM]| Origine | Fichiers éditeurs autorisés sur une archive ouverte |
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