The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update

Enis Afgan; Anton Nekrutenko; Bjórn Grüning; Daniel Blankenberg; Jeremy Goecks; Michael Schatz; Alexander Ostrovsky; Alexandru Mahmoud; Andrew Lonie; Anna Syme; Anne Fouilloux; Anthony Bretaudeau; Anton Nekrutenko; Anup Kumar; Arthur Eschenlauer; Assunta Desanto; Aysam Guerler; Beatriz Serrano-Solano; Bérénice Batut; Björn Grüning; Bradley Langhorst; Bridget Carr; Bryan Raubenolt; Cameron Hyde; Catherine Bromhead; Christopher Barnett; Coline Royaux; Cristóbal Gallardo; Daniel Blankenberg; Daniel Fornika; Dannon Baker; Dave Bouvier; Dave Clements; David de Lima Morais; David Lopez Tabernero; Delphine Lariviere; Engy Nasr; Enis Afgan; Federico Zambelli; Florian Heyl; Fotis Psomopoulos; Frederik Coppens; Gareth Price; Gianmauro Cuccuru; Gildas Le Corguillé; Greg von Kuster; Gulsum Gudukbay Akbulut; Helena Rasche; Hans-Rudolf Hotz; Ignacio Eguinoa; Igor Makunin; Isuru Ranawaka; James Taylor; Jayadev Joshi; Jennifer Hillman-Jackson; Jeremy Goecks; John Chilton; Kaivan Kamali; Keith Suderman; Krzysztof Poterlowicz; Yvan Le Bras; Lucille Lopez-Delisle; Luke Sargent; Madeline Bassetti; Marco Antonio Tangaro; Marius van den Beek; Martin Čech; Matthias Bernt; Matthias Fahrner; Mehmet Tekman; Melanie Föll; Mélanie Pétéra; Michael Schatz; Michael Crusoe; Miguel Roncoroni; Natalie Kucher; Nate Coraor; Nicholas Stoler; Nick Rhodes; Nicola Soranzo; Niko Pinter; Nuwan Goonasekera; Pablo Moreno; Pavankumar Videm; Pietro Mandreoli; Pratik Jagtap; Qiang Gu; Ralf Weber; Ross Lazarus; Ruben Vorderman; Saskia Hiltemann; Sergey Golitsynskiy; Shilpa Garg; Simon Bray; Simon Gladman; Simone Leo; Subina Mehta; Timothy Griffin; Vahid Jalili; Vandenbrouck Yves; Victor Wen; Vijay Nagampalli; Wendi Bacon; Willem de Koning; Wolfgang Maier; Peter Briggs

doi:10.1093/nar/gkac247

Journal Articles Nucleic Acids Research Year : 2022

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update

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Enis Afgan

Function : Author

Anton Nekrutenko

Function : Author

Bjórn Grüning

Function : Author

Daniel Blankenberg

Function : Author

Jeremy Goecks

Function : Author

Michael Schatz

Function : Author

Alexander Ostrovsky

Function : Author

Alexandru Mahmoud

Function : Author

Andrew Lonie

Function : Author

Anna Syme

Function : Author

Anne Fouilloux

Function : Author

Anthony Bretaudeau

Function : Author

Institut de Génétique, Environnement et Protection des Plantes

Anton Nekrutenko

Function : Author

Anup Kumar

Function : Author

Arthur Eschenlauer

Function : Author

Assunta Desanto

Function : Author

Aysam Guerler

Function : Author

Beatriz Serrano-Solano

Function : Author

Bérénice Batut

Function : Author

Björn Grüning

Function : Author

Bradley Langhorst

Function : Author

Bridget Carr

Function : Author

Bryan Raubenolt

Function : Author

Cameron Hyde

Function : Author

Catherine Bromhead

Function : Author

Christopher Barnett

Function : Author

Coline Royaux

Function : Author

Cristóbal Gallardo

Function : Author

Daniel Blankenberg

Function : Author

Daniel Fornika

Function : Author

Dannon Baker

Function : Author

Dave Bouvier

Function : Author

Dave Clements

Function : Author

David de Lima Morais

Function : Author

David Lopez Tabernero

Function : Author

Delphine Lariviere

Function : Author

Engy Nasr

Function : Author

Enis Afgan

Function : Author

Federico Zambelli

Function : Author

Florian Heyl

Function : Author

Fotis Psomopoulos

Function : Author

Frederik Coppens

Function : Author

Gareth Price

Function : Author

Gianmauro Cuccuru

Function : Author

Gildas Le Corguillé

Function : Author

Greg von Kuster

Function : Author

Gulsum Gudukbay Akbulut

Function : Author

Helena Rasche

Function : Author

Hans-Rudolf Hotz

Function : Author

Ignacio Eguinoa

Function : Author

Igor Makunin

Function : Author

Isuru Ranawaka

Function : Author

James Taylor

Function : Author

Jayadev Joshi

Function : Author

Jennifer Hillman-Jackson

Function : Author

Jeremy Goecks

Function : Author

John Chilton

Function : Author

Kaivan Kamali

Function : Author

Keith Suderman

Function : Author

Krzysztof Poterlowicz

Function : Author

Yvan Le Bras

Function : Author
PersonId : 184303
IdHAL : yvan-le-bras
ORCID : 0000-0002-8504-068X
IdRef : 150878001

Lucille Lopez-Delisle

Function : Author

Luke Sargent

Function : Author

Madeline Bassetti

Function : Author

Marco Antonio Tangaro

Function : Author

Marius van den Beek

Function : Author

Martin Čech

Function : Author

Matthias Bernt

Function : Author

Matthias Fahrner

Function : Author

Mehmet Tekman

Function : Author

Melanie Föll

Function : Author

Mélanie Pétéra

Function : Author
PersonId : 742819
IdHAL : melanie-petera

Plateforme Exploration du Métabolisme

Michael Schatz

Function : Author

Michael Crusoe

Function : Author

Miguel Roncoroni

Function : Author

Natalie Kucher

Function : Author

Nate Coraor

Function : Author

Nicholas Stoler

Function : Author

Nick Rhodes

Function : Author

Nicola Soranzo

Function : Author

Niko Pinter

Function : Author

Nuwan Goonasekera

Function : Author

Pablo Moreno

Function : Author

Pavankumar Videm

Function : Author

Pietro Mandreoli

Function : Author

Pratik Jagtap

Function : Author

Qiang Gu

Function : Author

Ralf Weber

Function : Author

Ross Lazarus

Function : Author

Ruben Vorderman

Function : Author

Saskia Hiltemann

Function : Author

Sergey Golitsynskiy

Function : Author

Shilpa Garg

Function : Author

Simon Bray

Function : Author

Simon Gladman

Function : Author

Simone Leo

Function : Author

Subina Mehta

Function : Author

Timothy Griffin

Function : Author

Vahid Jalili

Function : Author

Vandenbrouck Yves

Function : Author

Victor Wen

Function : Author

Vijay Nagampalli

Function : Author

Wendi Bacon

Function : Author

Willem de Koning

Function : Author

Wolfgang Maier

Function : Author

Peter Briggs

Function : Author

Abstract

Abstract Galaxy is a mature, browser accessible workbench for scientific computing. It enables scientists to share, analyze and visualize their own data, with minimal technical impediments. A thriving global community continues to use, maintain and contribute to the project, with support from multiple national infrastructure providers that enable freely accessible analysis and training services. The Galaxy Training Network supports free, self-directed, virtual training with >230 integrated tutorials. Project engagement metrics have continued to grow over the last 2 years, including source code contributions, publications, software packages wrapped as tools, registered users and their daily analysis jobs, and new independent specialized servers. Key Galaxy technical developments include an improved user interface for launching large-scale analyses with many files, interactive tools for exploratory data analysis, and a complete suite of machine learning tools. Important scientific developments enabled by Galaxy include Vertebrate Genome Project (VGP) assembly workflows and global SARS-CoV-2 collaborations.

Domains

Biochemistry, Molecular Biology

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2022_Galaxy Company_Nucleic_Acids_Res.pdf (1.75 Mo)

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https://hal.inrae.fr/hal-04053853

Submitted on : Friday, March 31, 2023-2:40:27 PM

Last modification on : Friday, July 12, 2024-3:29:01 AM

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hal-04053853 , version 1 (31-03-2023)

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HAL Id : hal-04053853 , version 1
DOI : 10.1093/nar/gkac247
PUBMED : 35446428
WOS : 000784263500001

Cite

Enis Afgan, Anton Nekrutenko, Bjórn Grüning, Daniel Blankenberg, Jeremy Goecks, et al.. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update. Nucleic Acids Research, 2022, 50 (W1), pp.W345-W351. ⟨10.1093/nar/gkac247⟩. ⟨hal-04053853⟩

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The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update

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