The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update
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ABUEG, Linelle Ann L.; Enis AFGAN; Olivier ALLART; Ahmed H. A. WAN; W. Endi A. BACON; Dannon BAKER; Madeline BASSETTI; Berenice BATUT; Matthias BERNT; Daniel BLANKENBERG; Aureliano BOMBARELY; Anthony BRETAUDEAU; Catherine J. BROMHEAD; Melissa L. BURKE; Patrick K. CAPON; Martin CECH; Maria CHAVERO-DIEZ; John M. CHILTON; Tyler J. COLLINS; Frederik COPPENS; Nate CORAOR; Gianmauro CUCCURU; Fabio CUMBO; John DAVIS; F. Paul DE GEEST; Willem DE KONING; Martin DEMKO ORCID; Assunta DESANTO; Jose Manuel Dominguez BEGINES; Maria A. DOYLE; Bert DROESBEKE; Anika ERXLEBEN-EGGENHOFER; Melanie C. FOLL; Giulio FORMENTI; Anne FOUILLOUX; Rendani GANGAZHE; Tanguy GENTHON; Jeremy GOECKS; Alejandra N. Gonzalez BELTRAN; Nuwan A. GOONASEKERA; Nadia GOUE; Timothy J. GRIFFIN; Bjorn A. GRUNING; Aysam GUERLER; Sveinung GUNDERSEN; Ove Johan Ragnar GUSTAFSSON; Christina HALL; Thomas W. HARROP; Helge HECHT; Alireza HEIDARI; Tillman HEISNER; Florian HEYL; Saskia HILTEMANN; Hans-Rudolf HOTZ; Cameron J. HYDE; Pratik D. JAGTAP; Julia JAKIELA; James E. JOHNSON; Jayadev JOSHI; Marie JOSSE; Khaled JUM'AH; Matus KALAS; Katarzyna KAMIENIECKA; Tunc KAYIKCIOGLU; Markus KONKOL; Leonid KOSTRYKIN; Natalie KUCHER; Anup KUMAR; Mira KUNTZ; Delphine LARIVIERE; Ross LAZARUS; Yvan LE BRAS; Gildas LE CORGUILLE; Justin LEE; Simone LEO; Leandro LIBORIO; Romane LIBOUBAN; David Lopez TABERNERO; Lucille LOPEZ-DELISLE; Laila S. LOS; Alexandru MAHMOUD; Igor MAKUNIN; Pierre MARIN; Subina MEHTA; Winnie MOK; Pablo A. MORENO; Francois MORIER-GENOUD; Stephen MOSHER; Teresa MUELLER; Engy NASR; Anton NEKRUTENKO; Tiffanie M. NELSON; Asime J. OBA; Alexander OSTROVSKY; Polina V. POLUNINA; Krzysztof POTERLOWICZ; Elliott James PRICE; Gareth R. PRICE; Helena RASCHE; Bryan RAUBENOLT; Coline ROYAUX; Luke SARGENT; Michelle T. SAVAGE; Volodymyr SAVCHENKO; Denys SAVCHENKO; Michael C. SCHATZ; Pauline SEGUINEAU; Beatriz SERRANO-SOLANO; Nicola SORANZO; Sanjay Kumar SRIKAKULAM; Keith SUDERMAN; Anna E. SYME; Marco Antonio TANGARO; Jonathan A. T. EDDS; Mehmet T. EKMAN; Wai Cheng THANG; Anil S. THANKI; Michael UHL; Marius VAN DEN BEEK; Deepti VARSHNEY; Jenn VESSIO; Pavankumar VIDEM; Von Kuster GREG; Gregory R. WATSON; Natalie WHITAKER-ALLEN; Uwe WINTER; Martin WOLSTENCROFT; Federico ZAMBELLI; Paul ZIEREP a Rand ZOABI
Vydání
Nucleic acids research, Oxford, Oxford University Press, 2024, 0305-1048
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.
ABUEG, Linelle Ann L.; Enis AFGAN; Olivier ALLART; Ahmed H. A. WAN; W. Endi A. BACON; Dannon BAKER; Madeline BASSETTI; Berenice BATUT; Matthias BERNT; Daniel BLANKENBERG; Aureliano BOMBARELY; Anthony BRETAUDEAU; Catherine J. BROMHEAD; Melissa L. BURKE; Patrick K. CAPON; Martin CECH; Maria CHAVERO-DIEZ; John M. CHILTON; Tyler J. COLLINS; Frederik COPPENS; Nate CORAOR; Gianmauro CUCCURU; Fabio CUMBO; John DAVIS; F. Paul DE GEEST; Willem DE KONING; Martin DEMKO; Assunta DESANTO; Jose Manuel Dominguez BEGINES; Maria A. DOYLE; Bert DROESBEKE; Anika ERXLEBEN-EGGENHOFER; Melanie C. FOLL; Giulio FORMENTI; Anne FOUILLOUX; Rendani GANGAZHE; Tanguy GENTHON; Jeremy GOECKS; Alejandra N. Gonzalez BELTRAN; Nuwan A. GOONASEKERA; Nadia GOUE; Timothy J. GRIFFIN; Bjorn A. GRUNING; Aysam GUERLER; Sveinung GUNDERSEN; Ove Johan Ragnar GUSTAFSSON; Christina HALL; Thomas W. HARROP; Helge HECHT; Alireza HEIDARI; Tillman HEISNER; Florian HEYL; Saskia HILTEMANN; Hans-Rudolf HOTZ; Cameron J. HYDE; Pratik D. JAGTAP; Julia JAKIELA; James E. JOHNSON; Jayadev JOSHI; Marie JOSSE; Khaled JUM'AH; Matus KALAS; Katarzyna KAMIENIECKA; Tunc KAYIKCIOGLU; Markus KONKOL; Leonid KOSTRYKIN; Natalie KUCHER; Anup KUMAR; Mira KUNTZ; Delphine LARIVIERE; Ross LAZARUS; Yvan LE BRAS; Gildas LE CORGUILLE; Justin LEE; Simone LEO; Leandro LIBORIO; Romane LIBOUBAN; David Lopez TABERNERO; Lucille LOPEZ-DELISLE; Laila S. LOS; Alexandru MAHMOUD; Igor MAKUNIN; Pierre MARIN; Subina MEHTA; Winnie MOK; Pablo A. MORENO; Francois MORIER-GENOUD; Stephen MOSHER; Teresa MUELLER; Engy NASR; Anton NEKRUTENKO; Tiffanie M. NELSON; Asime J. OBA; Alexander OSTROVSKY; Polina V. POLUNINA; Krzysztof POTERLOWICZ; Elliott James PRICE; Gareth R. PRICE; Helena RASCHE; Bryan RAUBENOLT; Coline ROYAUX; Luke SARGENT; Michelle T. SAVAGE; Volodymyr SAVCHENKO; Denys SAVCHENKO; Michael C. SCHATZ; Pauline SEGUINEAU; Beatriz SERRANO-SOLANO; Nicola SORANZO; Sanjay Kumar SRIKAKULAM; Keith SUDERMAN; Anna E. SYME; Marco Antonio TANGARO; Jonathan A. T. EDDS; Mehmet T. EKMAN; Wai Cheng THANG; Anil S. THANKI; Michael UHL; Marius VAN DEN BEEK; Deepti VARSHNEY; Jenn VESSIO; Pavankumar VIDEM; Von Kuster GREG; Gregory R. WATSON; Natalie WHITAKER-ALLEN; Uwe WINTER; Martin WOLSTENCROFT; Federico ZAMBELLI; Paul ZIEREP a Rand ZOABI. The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update. Nucleic acids research. Oxford: Oxford University Press, 2024, roč. 52, W1, s. "W83"-"W94", 12 s. ISSN 0305-1048. Dostupné z: https://doi.org/10.1093/nar/gkae410.
@article{2484659, author = {Abueg, Linelle Ann L. and Afgan, Enis and Allart, Olivier and Wan, Ahmed H. A. and Bacon, W. Endi A. and Baker, Dannon and Bassetti, Madeline and Batut, Berenice and Bernt, Matthias and Blankenberg, Daniel and Bombarely, Aureliano and Bretaudeau, Anthony and Bromhead, Catherine J. and Burke, Melissa L. and Capon, Patrick K. and Cech, Martin and ChaveroandDiez, Maria and Chilton, John M. and Collins, Tyler J. and Coppens, Frederik and Coraor, Nate and Cuccuru, Gianmauro and Cumbo, Fabio and Davis, John and De Geest, F. Paul and de Koning, Willem and Demko, Martin and DeSanto, Assunta and Begines, Jose Manuel Dominguez and Doyle, Maria A. and Droesbeke, Bert and ErxlebenandEggenhofer, Anika and Foll, Melanie C. and Formenti, Giulio and Fouilloux, Anne and Gangazhe, Rendani and Genthon, Tanguy and Goecks, Jeremy and Beltran, Alejandra N. Gonzalez and Goonasekera, Nuwan A. and Goue, Nadia and Griffin, Timothy J. and Gruning, Bjorn A. and Guerler, Aysam and Gundersen, Sveinung and Gustafsson, Ove Johan Ragnar and Hall, Christina and Harrop, Thomas W. and Hecht, Helge and Heidari, Alireza and Heisner, Tillman and Heyl, Florian and Hiltemann, Saskia and Hotz, HansandRudolf and Hyde, Cameron J. and Jagtap, Pratik D. and Jakiela, Julia and Johnson, James E. and Joshi, Jayadev and Josse, Marie and Jum'ah, Khaled and Kalas, Matus and Kamieniecka, Katarzyna and Kayikcioglu, Tunc and Konkol, Markus and Kostrykin, Leonid and Kucher, Natalie and Kumar, Anup and Kuntz, Mira and Lariviere, Delphine and Lazarus, Ross and Le Bras, Yvan and Le Corguille, Gildas and Lee, Justin and Leo, Simone and Liborio, Leandro and Libouban, Romane and Tabernero, David Lopez and LopezandDelisle, Lucille and Los, Laila S. and Mahmoud, Alexandru and Makunin, Igor and Marin, Pierre and Mehta, Subina and Mok, Winnie and Moreno, Pablo A. and MorierandGenoud, Francois and Mosher, Stephen and Mueller, Teresa and Nasr, Engy and Nekrutenko, Anton and Nelson, Tiffanie M. and Oba, Asime J. and Ostrovsky, Alexander and Polunina, Polina V. and Poterlowicz, Krzysztof and Price, Elliott James and Price, Gareth R. and Rasche, Helena and Raubenolt, Bryan and Royaux, Coline and Sargent, Luke and Savage, Michelle T. and Savchenko, Volodymyr and Savchenko, Denys and Schatz, Michael C. and Seguineau, Pauline and SerranoandSolano, Beatriz and Soranzo, Nicola and Srikakulam, Sanjay Kumar and Suderman, Keith and Syme, Anna E. and Tangaro, Marco Antonio and Edds, Jonathan A. T. and Ekman, Mehmet T. and Thang, Wai Cheng and Thanki, Anil S. and Uhl, Michael and van den Beek, Marius and Varshney, Deepti and Vessio, Jenn and Videm, Pavankumar and Greg, Von Kuster and Watson, Gregory R. and WhitakerandAllen, Natalie and Winter, Uwe and Wolstencroft, Martin and Zambelli, Federico and Zierep, Paul and Zoabi, Rand}, article_location = {Oxford}, article_number = {W1}, doi = {https://doi.org/10.1093/nar/gkae410}, keywords = {GPGPU; Galaxy; tools; Galaxy Toolshed}, language = {eng}, issn = {0305-1048}, journal = {Nucleic acids research}, title = {The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update}, url = {https://academic.oup.com/nar/article/52/W1/W83/7676834?login=false}, volume = {52}, year = {2024} }
TY - JOUR ID - 2484659 AU - Abueg, Linelle Ann L. - Afgan, Enis - Allart, Olivier - Wan, Ahmed H. A. - Bacon, W. Endi A. - Baker, Dannon - Bassetti, Madeline - Batut, Berenice - Bernt, Matthias - Blankenberg, Daniel - Bombarely, Aureliano - Bretaudeau, Anthony - Bromhead, Catherine J. - Burke, Melissa L. - Capon, Patrick K. - Cech, Martin - Chavero-Diez, Maria - Chilton, John M. - Collins, Tyler J. - Coppens, Frederik - Coraor, Nate - Cuccuru, Gianmauro - Cumbo, Fabio - Davis, John - De Geest, F. Paul - de Koning, Willem - Demko, Martin - DeSanto, Assunta - Begines, Jose Manuel Dominguez - Doyle, Maria A. - Droesbeke, Bert - Erxleben-Eggenhofer, Anika - Foll, Melanie C. - Formenti, Giulio - Fouilloux, Anne - Gangazhe, Rendani - Genthon, Tanguy - Goecks, Jeremy - Beltran, Alejandra N. Gonzalez - Goonasekera, Nuwan A. - Goue, Nadia - Griffin, Timothy J. - Gruning, Bjorn A. - Guerler, Aysam - Gundersen, Sveinung - Gustafsson, Ove Johan Ragnar - Hall, Christina - Harrop, Thomas W. - Hecht, Helge - Heidari, Alireza - Heisner, Tillman - Heyl, Florian - Hiltemann, Saskia - Hotz, Hans-Rudolf - Hyde, Cameron J. - Jagtap, Pratik D. - Jakiela, Julia - Johnson, James E. - Joshi, Jayadev - Josse, Marie - Jum'ah, Khaled - Kalas, Matus - Kamieniecka, Katarzyna - Kayikcioglu, Tunc - Konkol, Markus - Kostrykin, Leonid - Kucher, Natalie - Kumar, Anup - Kuntz, Mira - Lariviere, Delphine - Lazarus, Ross - Le Bras, Yvan - Le Corguille, Gildas - Lee, Justin - Leo, Simone - Liborio, Leandro - Libouban, Romane - Tabernero, David Lopez - Lopez-Delisle, Lucille - Los, Laila S. - Mahmoud, Alexandru - Makunin, Igor - Marin, Pierre - Mehta, Subina - Mok, Winnie - Moreno, Pablo A. - Morier-Genoud, Francois - Mosher, Stephen - Mueller, Teresa - Nasr, Engy - Nekrutenko, Anton - Nelson, Tiffanie M. - Oba, Asime J. - Ostrovsky, Alexander - Polunina, Polina V. - Poterlowicz, Krzysztof - Price, Elliott James - Price, Gareth R. - Rasche, Helena - Raubenolt, Bryan - Royaux, Coline - Sargent, Luke - Savage, Michelle T. - Savchenko, Volodymyr - Savchenko, Denys - Schatz, Michael C. - Seguineau, Pauline - Serrano-Solano, Beatriz - Soranzo, Nicola - Srikakulam, Sanjay Kumar - Suderman, Keith - Syme, Anna E. - Tangaro, Marco Antonio - Edds, Jonathan A. T. - Ekman, Mehmet T. - Thang, Wai Cheng - Thanki, Anil S. - Uhl, Michael - van den Beek, Marius - Varshney, Deepti - Vessio, Jenn - Videm, Pavankumar - Greg, Von Kuster - Watson, Gregory R. - Whitaker-Allen, Natalie - Winter, Uwe - Wolstencroft, Martin - Zambelli, Federico - Zierep, Paul - Zoabi, Rand PY - 2024 TI - The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update JF - Nucleic acids research VL - 52 IS - W1 SP - "W83"-"W94" EP - "W83"-"W94" PB - Oxford University Press SN - 03051048 KW - GPGPU KW - Galaxy KW - tools KW - Galaxy Toolshed UR - https://academic.oup.com/nar/article/52/W1/W83/7676834?login=false N2 - 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. ER -
ABUEG, Linelle Ann L.; Enis AFGAN; Olivier ALLART; Ahmed H. A. WAN; W. Endi A. BACON; Dannon BAKER; Madeline BASSETTI; Berenice BATUT; Matthias BERNT; Daniel BLANKENBERG; Aureliano BOMBARELY; Anthony BRETAUDEAU; Catherine J. BROMHEAD; Melissa L. BURKE; Patrick K. CAPON; Martin CECH; Maria CHAVERO-DIEZ; John M. CHILTON; Tyler J. COLLINS; Frederik COPPENS; Nate CORAOR; Gianmauro CUCCURU; Fabio CUMBO; John DAVIS; F. Paul DE GEEST; Willem DE KONING; Martin DEMKO; Assunta DESANTO; Jose Manuel Dominguez BEGINES; Maria A. DOYLE; Bert DROESBEKE; Anika ERXLEBEN-EGGENHOFER; Melanie C. FOLL; Giulio FORMENTI; Anne FOUILLOUX; Rendani GANGAZHE; Tanguy GENTHON; Jeremy GOECKS; Alejandra N. Gonzalez BELTRAN; Nuwan A. GOONASEKERA; Nadia GOUE; Timothy J. GRIFFIN; Bjorn A. GRUNING; Aysam GUERLER; Sveinung GUNDERSEN; Ove Johan Ragnar GUSTAFSSON; Christina HALL; Thomas W. HARROP; Helge HECHT; Alireza HEIDARI; Tillman HEISNER; Florian HEYL; Saskia HILTEMANN; Hans-Rudolf HOTZ; Cameron J. HYDE; Pratik D. JAGTAP; Julia JAKIELA; James E. JOHNSON; Jayadev JOSHI; Marie JOSSE; Khaled JUM'AH; Matus KALAS; Katarzyna KAMIENIECKA; Tunc KAYIKCIOGLU; Markus KONKOL; Leonid KOSTRYKIN; Natalie KUCHER; Anup KUMAR; Mira KUNTZ; Delphine LARIVIERE; Ross LAZARUS; Yvan LE BRAS; Gildas LE CORGUILLE; Justin LEE; Simone LEO; Leandro LIBORIO; Romane LIBOUBAN; David Lopez TABERNERO; Lucille LOPEZ-DELISLE; Laila S. LOS; Alexandru MAHMOUD; Igor MAKUNIN; Pierre MARIN; Subina MEHTA; Winnie MOK; Pablo A. MORENO; Francois MORIER-GENOUD; Stephen MOSHER; Teresa MUELLER; Engy NASR; Anton NEKRUTENKO; Tiffanie M. NELSON; Asime J. OBA; Alexander OSTROVSKY; Polina V. POLUNINA; Krzysztof POTERLOWICZ; Elliott James PRICE; Gareth R. PRICE; Helena RASCHE; Bryan RAUBENOLT; Coline ROYAUX; Luke SARGENT; Michelle T. SAVAGE; Volodymyr SAVCHENKO; Denys SAVCHENKO; Michael C. SCHATZ; Pauline SEGUINEAU; Beatriz SERRANO-SOLANO; Nicola SORANZO; Sanjay Kumar SRIKAKULAM; Keith SUDERMAN; Anna E. SYME; Marco Antonio TANGARO; Jonathan A. T. EDDS; Mehmet T. EKMAN; Wai Cheng THANG; Anil S. THANKI; Michael UHL; Marius VAN DEN BEEK; Deepti VARSHNEY; Jenn VESSIO; Pavankumar VIDEM; Von Kuster GREG; Gregory R. WATSON; Natalie WHITAKER-ALLEN; Uwe WINTER; Martin WOLSTENCROFT; Federico ZAMBELLI; Paul ZIEREP a Rand ZOABI. The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update. \textit{Nucleic acids research}. Oxford: Oxford University Press, 2024, roč.~52, W1, s.~''W83''-''W94'', 12 s. ISSN~0305-1048. Dostupné z: https://doi.org/10.1093/nar/gkae410.