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Galaxy at CiteULike Social Bookmarking Service

Galaxy and CiteULike 101

The Galaxy project uses the CiteULike social bookmarking service to organize papers that are about, use, or reference Galaxy.

CiteULike supports groups. A group is a set of CiteULike users, and the most prominent feature of a group is its library - the set of papers that the group has flagged as relevant to it.

The Galaxy Group is open to any CiteULike user. Once you have joined you can add papers to the group, assign tags, and rate papers.

CiteULike Tags

CiteULike makes extensive use of tags to categorize papers and to help in finding them. The Galaxy group uses this set of tags to categorize papers.




Papers that used Galaxy in their methods. This is the largest category by far.


A methods paper that uses the Main Galaxy server.


A methods paper that uses a local, privae instance of Galaxy


A methods paper that uses a Public Galaxy Server


A methods paper that uses a cloud-based instance of Galaxy


Papers about workflow platforms that include Galaxy, but where Galaxy is not the primary focus of the paper. Includes reviews and papers about other platforms.


Papers that are about other installations of Galaxy. (See also the Public Galaxy Servers list.)


Papers featuring tools that have been ported to Galaxy. This tag was added later, and there are likely papers with the other tag that should be here.


These papers reference Galaxy; we just don't know how because we can't get access to them.


Papers that have published/shared workflows, histories, datasets, pages, visualizations in a Galaxy instance.


Papers that are about the project or Main. Galaxy is the central theme of these papers.


Papers about how to use Galaxy for specific analyses.


Papers with an emphasis on using compute clouds.


Papers about reproducibility and persistence in science.


Paper references a Public Galaxy Server (other than Main).


Papers with an emphasis on visualization and/or visual analytics


Anything that does not fit above.

* Tag was added in 2013.  Older papers won't have these tags.

Every paper should have at least one tag (even if it is just "other"), and papers can have more than one tag.

You can also see papers listed in approximate order of relevance to the Galaxy project. See Citing Galaxy if you want to cite the Galaxy Project itself,

Want to Help?

If you want to help other Galaxy users and sites find papers that are relevant to them, or help the Galaxy Project keep track of what papers (and communities) are using it, then please help by adding relevant papers to the Galaxy Group Library and/or rating the papers that are there.

We particularly need help with papers that were published before 2011.

But not Mendeley, anymore

Mendeley Social Bookmarking Service

The Galaxy CiteULike Group was originally mirrored to a Galaxy Mendeley Group on a weekly basis, complete with the CiteULike tag set.  However, in February 2013, Mendeley stopped supporting their CiteULike to Mendeley bridge, thus greatly increasing the amount of work this mirror took to maintain.  Further complicating things, later that spring Mendeley was purchased by a traditionally closed access publisher.

Note: So, as of February 2013, the Mendeley Galaxy mirror, is no longer being maintained.