Galaxy Publication Library

Galaxy Publication Library at Zotero

The Galaxy Project uses the Zotero social bookmarking service to organize publications that reference Galaxy. The Galaxy Group lists published articles, conference proceedings, theses, book chapters and books that use, extend, reference or implement Galaxy. You can search the library at Zotero, or through the unified Galaxy search.

(Need to cite Galaxy in a publication? See Citing Galaxy.)

Tags

The library makes extensive use of tags to categorize publications and enable smarter searching. Tags come from two sources:

1. Galaxy Specific Tags

These tags specify how each publication relates to the Galaxy Project. They are manually added to papers when they are added to the group. Every publication should have at least one Galaxy specific tag, and publications can have more than one tag.

Galaxy specific tags all start with "+":

Tag Explanation
+Galactic Publication is about Galaxy.
+Stellar Publication features Galaxy prominently.
+Cloud Publications referencing / extending / discussing Galaxy in a cloud context.
+HowTo Papers about how to use Galaxy for specific analyses. These are tutorials.
+IsGalaxy Publications about Galaxy itself or installations of Galaxy.
+Methods Uses Galaxy in their methods. If it's clear from the paper, which instance was used, then methods papers will also include one or more of these tags:
  +UseCloud   Uses a custom built cloud based instance of Galaxy in its methods.
  +UseLocal   Uses a local installation of Galaxy in its methods.
  +UseMain   Uses the project's public server, usegalaxy.org (a.k.a. Main, in its methods.
  +UsePublic   Uses a publicly accessible Galaxy instance or a Galaxy service in its methods.
+Other Publications that don't fit well under any other tag.
+Project Publications with a Galaxy team member as an author.
+RefPublic References a publicly accessible Galaxy instance or a Galaxy service. This is distinct from the +UsePublic tag.
+Reproducibility Reproducibility and persistence in science.
+Shared Publications that have published workflows, histories, datasets, pages, or visualizations in a Galaxy instance.
+Tools Tools that run in, have been ported to, or interact with Galaxy
+Unknown Publications that we know refer to Galaxy, but we aren't sure how because they are behind a paywall we don't have access to. These are revisited periodically.
+Visualization Publications referencing Galaxy in a visualization and/or visual analytics context.
+Workbench Publication mentions Galaxy as a platform.

Public server and services tags (">")

Publications that mention or use a public Galaxy server or service are tagged with the server's name, preceded by a ">". For example, the >RepeatExplorer tag lists all papers that use or reference the RepeatExplorer public server.

Note: We only started using ">" tags after the move to Zotero in September 2017. Publications before that might have these tags, but most won't.

2. Automatically Added Tags

Zotero is configured to also add any keywords it can detect automatically when the paper is added. These tags are listed after Galaxy Specific tags, and there is no particular rhyme or reason to them. These tend to describe the research topic or domain. Prosapip1 and Genome evolution are examples.

Note: only papers added after the library was moved to Zotero in September 2017 have automatically added tags.

Want to Help?

Please see the instructions for contributing. We'd love to have your help.

Some History

Milestones

CiteULike

citeulike

The Galaxy publication library resided in CiteULike from 2011-2017. In that time the library went from 0 to over 4800 publications. (That library is still available on CiteULike, by the way.) In 2017 we started looking for a replacement and settled on Zotero, which has a desktop client and great collaborative features, and was already in use by the Galaxy Training Network. We made the switch from CiteULike to Zotero in September 2017.

Mendeley

Mendeley

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