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 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]."

Primary Publication

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

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)

Cloud

Data Managers

DataSource Tools

External Display Applications

Interactive Environments

Reproducibility

ToolShed

Training & Education

Online Education

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.