Citing Galaxy
Please do not forget to cite Galaxy in any research that uses or extends Galaxy.
Primary Publication
When you use Galaxy and want to publish your work, please cite this paper:
- The Galaxy Community. The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update, Nucleic Acids Research, 2024;, gkae410, https://doi.org/10.1093/nar/gkae410
This and other references are also available in GitHub as a CITATION file.
Depending on the additional Galaxy services you used please refer to the following:
| Service | Reference |
|---|---|
| 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. If you are unsure how to cite your local Galaxy, contact your cloud provider or systems administrator. (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 |
| Refencing the Galaxy Training Network and online educational services | Cite Training & Education if you have used the GTN and online educational services. Individual GTN tutorials also provide a citation block at the end that should be cited when applicable. |
| 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.
If you are unsure how to cite Galaxy please check out some of the examples.
Citing Specific Galaxy Components / Features
Cite these papers if you want to cite a particular aspect of Galaxy.
ToolShed
Please cite the following Galaxy Toolshed paper when you have ran tools inside Galaxy:
- 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
In addition to that, please do not forget to give credit to the individual tools you used in your analysis! References for individual tools are provided at the end of the tool page inside Galaxy. If you are unsure where to find this information, please refer to this example
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
DataSource Tools
- Daniel Blankenberg, Nate Coraor, Gregory Von Kuster, James Taylor, Anton Nekrutenko, and The Galaxy Team. Integrating diverse databases into an unified analysis framework: a Galaxy approach. Database (Oxford). 2011 Apr 29;2011:bar011. doi:10.1093/database/bar011.
External Display Applications
- Daniel Blankenberg, John Chilton, and Nate Coraor. Galaxy External Display Applications: Closing a dataflow interoperability loop. Nat Methods (2020). doi:10.1038/s41592-019-0727-x
Interactive Environments
- Björn Grüning, Helena Rasche, Boris Rebolledo-Jaramillo, Carl Eberhard, Torsten Houwaart, John Chilton, Nate Coraor, Rolf Backofen, James Taylor, Anton Nekrutenko. Jupyter and Galaxy: Easing entry barriers into complex data analyses for biomedical researchers, PLOS Computational Biology, doi:10.1371/journal.pcbi.1005425
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.
Training and 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.
Citation examples
Examples of papers mentioning Galaxy
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 quantification25, 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]."
Finding tool references
When you search for a tool inside Galaxy, navigate to the bottom of the page. There you will see a reference box that can be copied and used directly.
Visual example: