Galaxy Publication Library
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. |
| +Education | Publications using / referencing / discussing Galaxy in an education/training 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 platform 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 Platform tags (”>”)
Publications that mention or use a public Galaxy platform are tagged with the platform’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
- 1000th Galaxy CiteULike Paper, June 6, 2013
- 2500 Galaxy Papers & Counting, August 12, 2015
- Galaxy: the first 5,000 pubs, October 16, 2017
- 7,500 pubs in library, April 23, 2019
- Galaxy: the first 10,000 pubs, August 26, 2020
CiteULike & Mendeley
The Galaxy publication library resided in CiteULike from 2011-2017. In that time the library went from 0 to over 4800 publications. In 2017 we started looking for a replacement and settled on Zotero, which has a desktop client and great collaborative features. We made the switch from CiteULike to Zotero in September 2017.
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.