Citing Galaxy

Please cite Galaxy in any research that uses or extends Galaxy.

So, how can you do that? It depends on your research:

If you are	then please
Referring to the Galaxy Project in general	Cite the primary publication.
Referring to specific public Galaxy platforms or using them in your methods	Cite that platform's primary publication.
Using a local or temporary cloud instance	Cite the primary publication and mention that a local or cloud based Galaxy was used. (Note: We suspect that this is the most under-reported use of Galaxy.)
Referencing a specific aspect of Galaxy	Cite a publication about that specific topic, if one is available. Topics with pubs include: • Galaxy Application Programming Interface (API) • Cloud • Data Managers • DataSource Tools • External Display Applications • Interactive Environments • Reproducibility • ToolShed • Training & Education
Referencing a Galaxy web resource other than those above	See Citing Medicine: NLM Style Guide for Authors, Editors, and Publishers for how to cite web pages, wikis, and just about everything else.

Which Galaxy?

If you used Galaxy in your methods, please specify which instances of Galaxy were used: Was it usegalaxy.org, one of the other public Galaxy servers, cloud sevices, VMs or containers (and see each resource's page for citation info), or a local install?

Some excellent examples (emphasis added):

Used usegalaxy.org: from Hoyt et al.:

"The sequencing data were uploaded to the Galaxy web platform, and we used the public server at usegalaxy.org to analyze the data (Afgan et al. 2016)."
Used a public server: from Bhargava, et al.:

"RAW files generated directly from the mass spectrometer were imported into Galaxy-P platform⁵³ for protein identification and quantification^{25, 51}."

Which publication should you cite when using public accessible Galaxy platform? Most of the platform descriptions include a Citation(s) section.
Used a non-public server, from de Carvalho Augusto et al:

"All analyses were done on the Galaxy instance of the IHPE http://bioinfo.univ-perp.fr) [28]."

Primary Publication

If you use, extend or reference Galaxy in your published work, please cite this publication:

Enis Afgan, Dannon Baker, Bérénice Batut, Marius van den Beek, Dave Bouvier, Martin Čech, John Chilton, Dave Clements, Nate Coraor, Björn Grüning, Aysam Guerler, Jennifer Hillman-Jackson, Vahid Jalili, Helena Rasche, Nicola Soranzo, Jeremy Goecks, James Taylor, Anton Nekrutenko, and Daniel Blankenberg. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update, Nucleic Acids Research, Volume 46, Issue W1, 2 July 2018, Pages W537–W544, doi:10.1093/nar/gky379

This and other references are also available in GitHub as a CITATION file.

Citing Specific Galaxy Components / Features

Cite these papers if you want to cite a particular aspect of Galaxy.

Application Programming Interface (API)

Clare Sloggett, Nuwan Goonasekera and Enis Afgan. BioBlend: automating pipeline analyses within Galaxy and CloudMan. Bioinformatics (2013) 29(13): 1685-1686 doi:10.1093/bioinformatics/btt199

Cloud

Enis Afgan, Andrew Lonie, James Taylor, Nuwan Goonasekera. CloudLaunch: Discover and deploy cloud applications, Future Generation Computer Systems, 2018, doi:10.1016/j.future.2018.04.037

Data Managers

Daniel Blankenberg, James E. Johnson, The Galaxy Team, James Taylor and Anton Nekrutenko. Wrangling Galaxy's Reference Data. Bioinformatics (2014) 30(13): 1917-1919 doi:10.1093/bioinformatics/btu119

Reproducibility

Björn Grüning, John Chilton, Johannes Köster, Ryan Dale, Nicola Soranzo, Marius van den Beek, Jeremy Goecks, Rolf Backofen, Anton Nekrutenko, James Taylor. Practical Computational Reproducibility in the Life Sciences, Cell Systems, Volume 6, Issue 6, 2018, Pages 631-635, ISSN 2405-4712, doi:10.1016/j.cels.2018.03.014.

ToolShed

Daniel Blankenberg, Gregory Von Kuster, Emil Bouvier, Dannon Baker, Enis Afgan, Nicholas Stoler, the Galaxy Team, James Taylor and Anton Nekrutenko. Dissemination of scientific software with Galaxy ToolShed. Genome Biology (2014) 15:403 doi:10.1186/gb4161

Training & Education

Bérénice Batut, Saskia Hiltemann, Andrea Bagnacani, Dannon Baker, Vivek Bhardwaj, Clemens Blank, Anthony Bretaudeau, Loraine Brillet-Guéguen, Martin Čech, John Chilton, Dave Clements, Olivia Doppelt-Azeroual, Anika Erxleben, Mallory Ann Freeberg, Simon Gladman, Youri Hoogstrate, Hans-Rudolf Hotz, Torsten Houwaart, Pratik Jagtap, Delphine Lariviere, Gildas Le Corguillé, Thomas Manke, Fabien Mareuil, Fidel Ramírez, Devon, Ryan, Florian Christoph Sigloch, Nicola Soranzo, Joachim Wolff, Pavankumar Videm, Markus Wolfien, Aisanjiang Wubuli, Dilmurat Yusuf, Galaxy Training Network, James Taylor, Rolf Backofen, Anton Nekrutenko, Björn Grüning. Community-Driven Data Analysis Training for Biology, Cell Systems, Volume 6, Issue 6, 27 June 2018, Pages 752-758.e1

Online Education

Serrano-Solano, B., Föll, M. C., Gallardo-Alba, C., Erxleben, A., Rasche, H., Hiltemann, S., Fahrner, M., Dunning, M. J., Schulz, M. H., Scholtz, B., Clements, D., Nekrutenko, A., Batut, B., & Grüning, B. A. (2021). Fostering accessible online education using Galaxy as an e-learning platform. PLOS Computational Biology, 17(5), e1008923. doi: 10.1371/journal.pcbi.1008923

Galaxy Publication Library

This page highlights only a few Galaxy related publications. However, the set of relevant publications is orders of magnitude larger. The Galaxy Group on Zotero lists published articles, conference proceedings, theses, book chapters and books that use, extend, reference or implement Galaxy in any way. The library contains thousands of publications all classified with ~19 Galaxy specific tags. See the Galaxy Publication Library page for more.

See the Citations section of the project statistics page for a summary of citations of project papers.