Galaxy (computational biology)

Galaxy
Galaxy
	Workflow for tuberculosis analysis
Developer(s)	Galaxy Community
Initial release	16 September 2005
Stable release	24.2 / January 2025
Repository	github.com/galaxyproject/galaxy
Written in	Python, JavaScript, TypeScript
Operating system	Unix-like
Platform	Linux, macOS
Available in	English
Type	Scientific workflow, data integration, analysis and data publishing
License	MIT and Academic Free License
Website	galaxyproject.org

Galaxy^[2] is an open-source scientific workflow system designed to make research accessible, reproducible, and transparent. Originally developed for computational biology, Galaxy has evolved into a domain-agnostic framework utilized across various scientific disciplines. Some examples include: data science,^[3] microbiology,^[4] medical research,^[5] neuroscience,^[6] virology^[7] and outbreak detection,^[8] food safety,^[9] wastewater tracking and antibiotic resistance,^[10] long-read^[11] and high-throughput^[12] genomic sequencing, bioinformatics,^[13] and other scientific disciplines.

For many computational biology processes, Galaxy accommodates scientists from newcomers to professionals. It supports code-free workflow development, GUI workflow visualization as well as command-line interface access, scheduled jobs, and cloud infrastructure management. It supports data persistence and data publishing to facilitate collaboration. The freely hosted services of UseGalaxy (United States, EU, and Australia) support a global community of over 500,000 registered users through the Galaxy Hub which holds events, an annual conference, and hundreds of free online tutorials at the Galaxy Training Network.

^ "Project Licenses". GitHub.
^ The Galaxy Community (20 May 2024). "The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update". Nucleic Acids Research. 52 (Web Server Issue): W83 – W94. doi:10.1093/nar/gkae410. PMC 11223835. PMID 38769056.
^ Pireddu, Luca; Leo, Simone; Soranzo, Nicola; Zanetti, Gianluigi (2014-09-20). "A Hadoop-Galaxy adapter for user-friendly and scalable data-intensive bioinformatics in Galaxy". Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics. BCB '14. New York, NY, USA: Association for Computing Machinery. pp. 184–191. doi:10.1145/2649387.2649429. ISBN 978-1-4503-2894-4.
^ Nasr, Engy; Amato, Pierre; Bhardwaj, Anshu; Blankenberg, Daniel; Brites, Daniela; Cumbo, Fabio; Do, Katherine; Ferrari, Emanuele; Griffin, Timothy J. (2024-12-27). "microGalaxy: A gateway to tools, workflows, and training for reproducible and FAIR analysis of microbial data". bioRxiv 10.1101/2024.12.23.629682.
^ Foschini, Maria P.; Morandi, Luca; Sanchez, Alejandro M.; Santoro, Angela; Mulè, Antonino; Zannoni, Gian Franco; Varga, Zsuzsanna; Moskovszky, Linda; Cucchi, Maria C.; Moelans, Cathy B.; Giove, Gianluca; van Diest, Paul J.; Masetti, Riccardo (2020-06-17). "Methylation Profile of X-Chromosome–Related Genes in Male Breast Cancer". Frontiers in Oncology. 10: 784. doi:10.3389/fonc.2020.00784. ISSN 2234-943X. PMC 7313421. PMID 32626651.
^ Mitolo, Micaela; Zoli, Matteo; Testa, Claudia; Morandi, Luca; Rochat, Magali Jane; Zaccagna, Fulvio; Martinoni, Matteo; Santoro, Francesca; Asioli, Sofia; Badaloni, Filippo; Conti, Alfredo; Sturiale, Carmelo; Lodi, Raffaele; Mazzatenta, Diego; Tonon, Caterina (2022-06-03). "Neuroplasticity Mechanisms in Frontal Brain Gliomas: A Preliminary Study". Frontiers in Neurology. 13. doi:10.3389/fneur.2022.867048. ISSN 1664-2295. PMC 9204970. PMID 35720068.
^ Lo, Chien-Chi; Shakya, Migun; Connor, Ryan; Davenport, Karen; Flynn, Mark; Gutiérrez, Adán Myers y; Hu, Bin; Li, Po-E; Jackson, Elais Player; Xu, Yan; Chain, Patrick S G (2022-05-13). "EDGE COVID-19: a web platform to generate submission-ready genomes from SARS-CoV-2 sequencing efforts". Bioinformatics. 38 (10): 2700–2704. doi:10.1093/bioinformatics/btac176. ISSN 1367-4803. PMC 9113274. PMID 35561186.
^ Bogaerts, Bert; Van Braekel, Julien; Van Uffelen, Alexander; D’aes, Jolien; Godfroid, Maxime; Delcourt, Thomas; Kelchtermans, Michael; Milis, Kato; Goeders, Nathalie; De Keersmaecker, Sigrid C. J.; Roosens, Nancy H. C.; Winand, Raf; Vanneste, Kevin (2025-01-08). "Galaxy @Sciensano: a comprehensive bioinformatics portal for genomics-based microbial typing, characterization, and outbreak detection". BMC Genomics. 26 (1): 20. doi:10.1186/s12864-024-11182-5. ISSN 1471-2164. PMC 11715294. PMID 39780046.
^ Gangiredla, Jayanthi; Rand, Hugh; Benisatto, Daniel; Payne, Justin; Strittmatter, Charles; Sanders, Jimmy; Wolfgang, William J.; Libuit, Kevin; Herrick, James B.; Prarat, Melanie; Toro, Magaly; Farrell, Thomas; Strain, Errol (2021-02-10). "GalaxyTrakr: a distributed analysis tool for public health whole genome sequence data accessible to non-bioinformaticians". BMC Genomics. 22 (1): 114. doi:10.1186/s12864-021-07405-8. ISSN 1471-2164. PMC 7877046. PMID 33568057.
^ Yin, Xiaole; Zheng, Xiawan; Li, Liguan; Zhang, An-Ni; Jiang, Xiao-Tao; Zhang, Tong (2023-08-01). "ARGs-OAP v3.0: Antibiotic-Resistance Gene Database Curation and Analysis Pipeline Optimization". Engineering. 27: 234–241. Bibcode:2023Engin..27..234Y. doi:10.1016/j.eng.2022.10.011. ISSN 2095-8099.
^ de Koning, Willem; Miladi, Milad; Hiltemann, Saskia; Heikema, Astrid; Hays, John P; Flemming, Stephan; van den Beek, Marius; Mustafa, Dana A; Backofen, Rolf; Grüning, Björn; Stubbs, Andrew P (2020-10-20). "NanoGalaxy: Nanopore long-read sequencing data analysis in Galaxy". GigaScience. 9 (10): giaa105. doi:10.1093/gigascience/giaa105. ISSN 2047-217X. PMC 7568507. PMID 33068114.
^ Thiel, William H (2016). "Galaxy Workflows for Web-based Bioinformatics Analysis of Aptamer High-throughput Sequencing Data". Molecular Therapy - Nucleic Acids. 5 (8): e345. doi:10.1038/mtna.2016.54. PMC 5023399. PMID 28131286.
^ Thiel, William H.; Giangrande, Paloma H. (2016-03-15). "Analyzing HT-SELEX data with the Galaxy Project tools – A web based bioinformatics platform for biomedical research". Methods. Nucleic Acid Aptamers. 97: 3–10. doi:10.1016/j.ymeth.2015.10.008. ISSN 1046-2023. PMC 4792767. PMID 26481156.

[1] "Project Licenses". GitHub.

[2] The Galaxy Community (20 May 2024). "The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update". Nucleic Acids Research. 52 (Web Server Issue): W83 – W94. doi:10.1093/nar/gkae410. PMC 11223835. PMID 38769056.

[3] Pireddu, Luca; Leo, Simone; Soranzo, Nicola; Zanetti, Gianluigi (2014-09-20). "A Hadoop-Galaxy adapter for user-friendly and scalable data-intensive bioinformatics in Galaxy". Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics. BCB '14. New York, NY, USA: Association for Computing Machinery. pp. 184–191. doi:10.1145/2649387.2649429. ISBN 978-1-4503-2894-4.

[4] Nasr, Engy; Amato, Pierre; Bhardwaj, Anshu; Blankenberg, Daniel; Brites, Daniela; Cumbo, Fabio; Do, Katherine; Ferrari, Emanuele; Griffin, Timothy J. (2024-12-27). "microGalaxy: A gateway to tools, workflows, and training for reproducible and FAIR analysis of microbial data". bioRxiv 10.1101/2024.12.23.629682.

[5] Foschini, Maria P.; Morandi, Luca; Sanchez, Alejandro M.; Santoro, Angela; Mulè, Antonino; Zannoni, Gian Franco; Varga, Zsuzsanna; Moskovszky, Linda; Cucchi, Maria C.; Moelans, Cathy B.; Giove, Gianluca; van Diest, Paul J.; Masetti, Riccardo (2020-06-17). "Methylation Profile of X-Chromosome–Related Genes in Male Breast Cancer". Frontiers in Oncology. 10: 784. doi:10.3389/fonc.2020.00784. ISSN 2234-943X. PMC 7313421. PMID 32626651.

[6] Mitolo, Micaela; Zoli, Matteo; Testa, Claudia; Morandi, Luca; Rochat, Magali Jane; Zaccagna, Fulvio; Martinoni, Matteo; Santoro, Francesca; Asioli, Sofia; Badaloni, Filippo; Conti, Alfredo; Sturiale, Carmelo; Lodi, Raffaele; Mazzatenta, Diego; Tonon, Caterina (2022-06-03). "Neuroplasticity Mechanisms in Frontal Brain Gliomas: A Preliminary Study". Frontiers in Neurology. 13. doi:10.3389/fneur.2022.867048. ISSN 1664-2295. PMC 9204970. PMID 35720068.

[7] Lo, Chien-Chi; Shakya, Migun; Connor, Ryan; Davenport, Karen; Flynn, Mark; Gutiérrez, Adán Myers y; Hu, Bin; Li, Po-E; Jackson, Elais Player; Xu, Yan; Chain, Patrick S G (2022-05-13). "EDGE COVID-19: a web platform to generate submission-ready genomes from SARS-CoV-2 sequencing efforts". Bioinformatics. 38 (10): 2700–2704. doi:10.1093/bioinformatics/btac176. ISSN 1367-4803. PMC 9113274. PMID 35561186.

[8] Bogaerts, Bert; Van Braekel, Julien; Van Uffelen, Alexander; D’aes, Jolien; Godfroid, Maxime; Delcourt, Thomas; Kelchtermans, Michael; Milis, Kato; Goeders, Nathalie; De Keersmaecker, Sigrid C. J.; Roosens, Nancy H. C.; Winand, Raf; Vanneste, Kevin (2025-01-08). "Galaxy @Sciensano: a comprehensive bioinformatics portal for genomics-based microbial typing, characterization, and outbreak detection". BMC Genomics. 26 (1): 20. doi:10.1186/s12864-024-11182-5. ISSN 1471-2164. PMC 11715294. PMID 39780046.

[9] Gangiredla, Jayanthi; Rand, Hugh; Benisatto, Daniel; Payne, Justin; Strittmatter, Charles; Sanders, Jimmy; Wolfgang, William J.; Libuit, Kevin; Herrick, James B.; Prarat, Melanie; Toro, Magaly; Farrell, Thomas; Strain, Errol (2021-02-10). "GalaxyTrakr: a distributed analysis tool for public health whole genome sequence data accessible to non-bioinformaticians". BMC Genomics. 22 (1): 114. doi:10.1186/s12864-021-07405-8. ISSN 1471-2164. PMC 7877046. PMID 33568057.

[10] Yin, Xiaole; Zheng, Xiawan; Li, Liguan; Zhang, An-Ni; Jiang, Xiao-Tao; Zhang, Tong (2023-08-01). "ARGs-OAP v3.0: Antibiotic-Resistance Gene Database Curation and Analysis Pipeline Optimization". Engineering. 27: 234–241. Bibcode:2023Engin..27..234Y. doi:10.1016/j.eng.2022.10.011. ISSN 2095-8099.

[11] Koning, Willem; Miladi, Milad; Hiltemann, Saskia; Heikema, Astrid; Hays, John P; Flemming, Stephan; van den Beek, Marius; Mustafa, Dana A; Backofen, Rolf; Grüning, Björn; Stubbs, Andrew P (2020-10-20). "NanoGalaxy: Nanopore long-read sequencing data analysis in Galaxy". GigaScience. 9 (10): giaa105. doi:10.1093/gigascience/giaa105. ISSN 2047-217X. PMC 7568507. PMID 33068114.

[12] Thiel, William H (2016). "Galaxy Workflows for Web-based Bioinformatics Analysis of Aptamer High-throughput Sequencing Data". Molecular Therapy - Nucleic Acids. 5 (8): e345. doi:10.1038/mtna.2016.54. PMC 5023399. PMID 28131286.

[13] Thiel, William H.; Giangrande, Paloma H. (2016-03-15). "Analyzing HT-SELEX data with the Galaxy Project tools – A web based bioinformatics platform for biomedical research". Methods. Nucleic Acid Aptamers. 97: 3–10. doi:10.1016/j.ymeth.2015.10.008. ISSN 1046-2023. PMC 4792767. PMID 26481156.

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