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

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

doi:10.1093/nar/gkac247

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

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

Research output: Contribution to journal › Article › peer-review

265 Scopus citations

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.

Original language	English (US)
Pages (from-to)	W345-W351
Journal	Nucleic acids research
Volume	50
Issue number	W1
DOIs	https://doi.org/10.1093/nar/gkac247
State	Published - Jul 5 2022

ASJC Scopus subject areas

Genetics

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10.1093/nar/gkac247

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Afgan, E., Nekrutenko, A., Grüning, B. A., Blankenberg, D., Goecks, J., Schatz, M. C., Ostrovsky, A. E., Mahmoud, A., Lonie, A. J., Syme, A., Fouilloux, A., Bretaudeau, A., Kumar, A., Eschenlauer, A. C., Desanto, A. D., Guerler, A., Serrano-Solano, B., Batut, B., Grüning, B. A., ... Briggs, P. J. (2022). The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update. Nucleic acids research, 50(W1), W345-W351. https://doi.org/10.1093/nar/gkac247

Afgan, E, Nekrutenko, A, Grüning, BA, Blankenberg, D, Goecks, J, Schatz, MC, Ostrovsky, AE, Mahmoud, A, Lonie, AJ, Syme, A, Fouilloux, A, Bretaudeau, A, Kumar, A, Eschenlauer, AC, Desanto, AD, Guerler, A, Serrano-Solano, B, Batut, B, Grüning, BA, Langhorst, BW, Carr, B, Raubenolt, BA, Hyde, CJ, Bromhead, CJ, Barnett, CB, Royaux, C, Gallardo, C, Blankenberg, D, Fornika, DJ, Baker, D, Bouvier, D, Clements, D, De Lima Morais, DA, Tabernero, DL, Lariviere, D, Nasr, E, Afgan, E, Zambelli, F, Heyl, F, Psomopoulos, F, Coppens, F, Price, GR, Cuccuru, G, Corguillé, GL, Von Kuster, G, Akbulut, GG, Rasche, H, Hans-Rudolf, H, Eguinoa, I, Makunin, I, Ranawaka, IJ, Taylor, JP, Joshi, J, Hillman-Jackson, J, Chilton, JM, Kamali, K, Suderman, K, Poterlowicz, K, Yvan, LB, Lopez-Delisle, L, Sargent, L, Bassetti, ME, Tangaro, MA, Van Den Beek, M, Cech, M, Bernt, M, Fahrner, M, Tekman, M, Föll, MC, Schatz, MC, Crusoe, MR, Roncoroni, M, Kucher, N, Coraor, N, Stoler, N, Rhodes, N, Soranzo, N, Pinter, N, Goonasekera, NA, Moreno, PA, Videm, P, Melanie, P, Mandreoli, P, Jagtap, PD, Gu, Q, Weber, RJM, Lazarus, R, Vorderman, RHP, Hiltemann, S, Golitsynskiy, S, Garg, S, Bray, SA, Gladman, SL, Leo, S, Mehta, SP, Griffin, TJ, Jalili, V, Yves, V, Wen, V, Nagampalli, VK, Bacon, WA, De Koning, W, Maier, W & Briggs, PJ 2022, 'The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update', Nucleic acids research, vol. 50, no. W1, pp. W345-W351. https://doi.org/10.1093/nar/gkac247

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

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.",

author = "Enis Afgan and Anton Nekrutenko and Gr{\"u}ning, {Bj{\'o}rn A.} and Daniel Blankenberg and Jeremy Goecks and Schatz, {Michael C.} and Ostrovsky, {Alexander E.} and Alexandru Mahmoud and Lonie, {Andrew J.} and Anna Syme and Anne Fouilloux and Anthony Bretaudeau and Anup Kumar and Eschenlauer, {Arthur C.} and Desanto, {Assunta D.} and Aysam Guerler and Beatriz Serrano-Solano and B{\'e}r{\'e}nice Batut and Gr{\"u}ning, {Bj{\"o}rn A.} and Langhorst, {Bradley W.} and Bridget Carr and Raubenolt, {Bryan A.} and Hyde, {Cameron J.} and Bromhead, {Catherine J.} and Barnett, {Christopher B.} and Coline Royaux and Crist{\'o}bal Gallardo and Daniel Blankenberg and Fornika, {Daniel J.} and Dannon Baker and Dave Bouvier and Dave Clements and {De Lima Morais}, {David A.} and Tabernero, {D. L.} and Delphine Lariviere and Engy Nasr and Enis Afgan and Federico Zambelli and Florian Heyl and Fotis Psomopoulos and Frederik Coppens and Price, {Gareth R.} and Gianmauro Cuccuru and Corguill{\'e}, {Gildas Le} and {Von Kuster}, Greg and Akbulut, {Gulsum Gudukbay} and Helena Rasche and Hotz Hans-Rudolf and Ignacio Eguinoa and Igor Makunin and Ranawaka, {Isuru J.} and Taylor, {James P.} and Jayadev Joshi and Jennifer Hillman-Jackson and Chilton, {John M.} and Kaivan Kamali and Keith Suderman and Krzysztof Poterlowicz and Yvan, {Le Bras} and Lucille Lopez-Delisle and Luke Sargent and Bassetti, {Madeline E.} and Tangaro, {Marco Antonio} and {Van Den Beek}, Marius and Martin Cech and Matthias Bernt and Matthias Fahrner and Mehmet Tekman and F{\"o}ll, {Melanie C.} and Schatz, {Michael C.} and Crusoe, {Michael R.} and Miguel Roncoroni and Natalie Kucher and Nate Coraor and Nicholas Stoler and Nick Rhodes and Nicola Soranzo and Niko Pinter and Goonasekera, {Nuwan A.} and Moreno, {Pablo A.} and Pavankumar Videm and Petera Melanie and Pietro Mandreoli and Jagtap, {Pratik D.} and Qiang Gu and Weber, {Ralf J.M.} and Ross Lazarus and Vorderman, {Ruben H.P.} and Saskia Hiltemann and Sergey Golitsynskiy and Shilpa Garg and Bray, {Simon A.} and Gladman, {Simon L.} and Simone Leo and Mehta, {Subina P.} and Griffin, {Timothy J.} and Vahid Jalili and Vandenbrouck Yves and Victor Wen and Nagampalli, {Vijay K.} and Bacon, {Wendi A.} and {De Koning}, Willem and Wolfgang Maier and Briggs, {Peter J.}",

note = "Publisher Copyright: {\textcopyright} 2022 The Author(s). Published by Oxford University Press on behalf of Nucleic Acids Research.",

year = "2022",

month = jul,

day = "5",

doi = "10.1093/nar/gkac247",

language = "English (US)",

volume = "50",

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TY - JOUR

T1 - The Galaxy platform for accessible, reproducible and collaborative biomedical analyses

T2 - 2022 update

AU - Afgan, Enis

AU - Nekrutenko, Anton

AU - Grüning, Bjórn A.

AU - Blankenberg, Daniel

AU - Goecks, Jeremy

AU - Schatz, Michael C.

AU - Ostrovsky, Alexander E.

AU - Mahmoud, Alexandru

AU - Lonie, Andrew J.

AU - Syme, Anna

AU - Fouilloux, Anne

AU - Bretaudeau, Anthony

AU - Kumar, Anup

AU - Eschenlauer, Arthur C.

AU - Desanto, Assunta D.

AU - Guerler, Aysam

AU - Serrano-Solano, Beatriz

AU - Batut, Bérénice

AU - Grüning, Björn A.

AU - Langhorst, Bradley W.

AU - Carr, Bridget

AU - Raubenolt, Bryan A.

AU - Hyde, Cameron J.

AU - Bromhead, Catherine J.

AU - Barnett, Christopher B.

AU - Royaux, Coline

AU - Gallardo, Cristóbal

AU - Blankenberg, Daniel

AU - Fornika, Daniel J.

AU - Baker, Dannon

AU - Bouvier, Dave

AU - Clements, Dave

AU - De Lima Morais, David A.

AU - Tabernero, D. L.

AU - Lariviere, Delphine

AU - Nasr, Engy

AU - Afgan, Enis

AU - Zambelli, Federico

AU - Heyl, Florian

AU - Psomopoulos, Fotis

AU - Coppens, Frederik

AU - Price, Gareth R.

AU - Cuccuru, Gianmauro

AU - Corguillé, Gildas Le

AU - Von Kuster, Greg

AU - Akbulut, Gulsum Gudukbay

AU - Rasche, Helena

AU - Hans-Rudolf, Hotz

AU - Eguinoa, Ignacio

AU - Makunin, Igor

AU - Ranawaka, Isuru J.

AU - Taylor, James P.

AU - Joshi, Jayadev

AU - Hillman-Jackson, Jennifer

AU - Chilton, John M.

AU - Kamali, Kaivan

AU - Suderman, Keith

AU - Poterlowicz, Krzysztof

AU - Yvan, Le Bras

AU - Lopez-Delisle, Lucille

AU - Sargent, Luke

AU - Bassetti, Madeline E.

AU - Tangaro, Marco Antonio

AU - Van Den Beek, Marius

AU - Cech, Martin

AU - Bernt, Matthias

AU - Fahrner, Matthias

AU - Tekman, Mehmet

AU - Föll, Melanie C.

AU - Schatz, Michael C.

AU - Crusoe, Michael R.

AU - Roncoroni, Miguel

AU - Kucher, Natalie

AU - Coraor, Nate

AU - Stoler, Nicholas

AU - Rhodes, Nick

AU - Soranzo, Nicola

AU - Pinter, Niko

AU - Goonasekera, Nuwan A.

AU - Moreno, Pablo A.

AU - Videm, Pavankumar

AU - Melanie, Petera

AU - Mandreoli, Pietro

AU - Jagtap, Pratik D.

AU - Gu, Qiang

AU - Weber, Ralf J.M.

AU - Lazarus, Ross

AU - Vorderman, Ruben H.P.

AU - Hiltemann, Saskia

AU - Golitsynskiy, Sergey

AU - Garg, Shilpa

AU - Bray, Simon A.

AU - Gladman, Simon L.

AU - Leo, Simone

AU - Mehta, Subina P.

AU - Griffin, Timothy J.

AU - Jalili, Vahid

AU - Yves, Vandenbrouck

AU - Wen, Victor

AU - Nagampalli, Vijay K.

AU - Bacon, Wendi A.

AU - De Koning, Willem

AU - Maier, Wolfgang

AU - Briggs, Peter J.

PY - 2022/7/5

Y1 - 2022/7/5

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AB - 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.

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ER -

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

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ASJC Scopus subject areas

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