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Citing Galaxy

Citing Galaxy

Contents

  1. Primary Publications
  2. Other Publications about Galaxy
    1. 2011
    2. 2010
    3. 2009
    4. 2008
    5. 2007
  3. Citing Galaxy Web Resources
  4. CiteULike
Please cite Galaxy in any research that uses or extends Galaxy. Please use each of the primary publications for project wide citations. There are also several publications on more specific topics that should be referenced, when appropriate.

Primary Publications

If you use or extend Galaxy in your published work, please cite each of the following publications:

  1. Goecks, J, Nekrutenko, A, Taylor, J and The Galaxy Team. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol. 2010 Aug 25;11(8):R86.

  2. Blankenberg D, Von Kuster G, Coraor N, Ananda G, Lazarus R, Mangan M, Nekrutenko A, Taylor J. "Galaxy: a web-based genome analysis tool for experimentalists". Current Protocols in Molecular Biology. 2010 Jan; Chapter 19:Unit 19.10.1-21.

  3. Giardine B, Riemer C, Hardison RC, Burhans R, Elnitski L, Shah P, Zhang Y, Blankenberg D, Albert I, Taylor J, Miller W, Kent WJ, Nekrutenko A. "Galaxy: a platform for interactive large-scale genome analysis." Genome Research. 2005 Oct; 15(10):1451-5.

Other Publications about Galaxy

These papers are either about Galaxy, or prominently feature Galaxy in their analyses. Please cite the appropriate publication if using the specific features of Galaxy described.

2011

  1. Jeremy Goecks, Kanwei Li, Dave Clements, Team, The Galaxy, James Taylor, The Galaxy Track Browser: Transforming the genome browser from visualization tool to analysis tool. Biological Data Visualization (BioVis), 2011 IEEE Symposium on (October 2011), pp. 39-46.

  2. Enis Afgan, Dannon Baker, Nate Coraor, Hiroki Goto, Ian M Paul, Kateryna D Makova, Anton Nekrutenko, James Taylor. Harnessing cloud computing with Galaxy Cloud, Nature Biotechnology 29, 972–974 (2011). doi:10.1038/nbt.2028

  3. Afgan E, Goecks J, Baker D, Coraor N, the Galaxy Team, Nekrutenko A, and Taylor J. "Galaxy - a Gateway to Tools in e-Science". Guide to e-Science: Next Generation Scientific Research and Discovery. K. Yang, Ed., ed: Springer. in press. p. 35.

  4. Afgan E, Baker D, the Galaxy Team, Nekrutenko A, Taylor J. "A reference model for deploying applications in virtualized environments." Concurrency and Computation: Practice & Experience. doi: 10.1002/cpe.1836

  5. Blankenberg D, Taylor J, Nekrutenko A, The Galaxy Team. "Making whole genome multiple alignments usable for biologists." Bioinformatics. 2011 Jul 19. [Epub ahead of print]

  6. Blankenberg D, Coraor N, Von Kuster G, Taylor J, Nekrutenko A, Galaxy Team. "Integrating diverse databases into an unified analysis framework: a Galaxy approach." Database (Oxford). 2011 Apr 29;2011:bar011. Print 2011.

2010

  1. Afgan E, Baker D, Coraor N, Chapman B, Nekrutenko A, Taylor J. "Galaxy CloudMan: Delivering Cloud Compute Clusters". BMC Bioinformatics. 2010 Dec 21. 11(Suppl 12):S4.

  2. Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, Nekrutenko A and The Galaxy Team. "Manipulation of FASTQ data with Galaxy". Bioinformatics. 2010 Jul 15;26(14):1783-5.

  3. Bock C, Von Kuster G, Halachev K, Taylor J, Nekrutenko A, Lengauer T. "Web-based analysis of (epi-) genome data using EpiGRAPH and Galaxy". In "Methods in Molecular Biology: Genetic Variation: Methods And Protocols" (ed. M.R. Barnes and G. Breen). Humana Press, Towata, NJ. 2010 Feb.

  4. Schatz MC. "The missing graphical user interface for genomics." Genome Biol. 2010;11(8):128. Epub 2010 Aug 25.

2009

  1. Koskovsky Pond S, Wadhawan S, Chiaromonte F, Ananda G, Chung W, Taylor J, and Nekrutenko A. "Windshield splatter analysis with the Galaxy metagenomic pipeline". Genome Research. 2009 Nov; 19(11):2144-53.

2008

  1. Lazarus R, Taylor J, Qiu W, Nekrutenko A. "Toward the commoditization of translational genomic research: Design and implementation features of the Galaxy genomic workbench." Summit on Translat Bioinforma. 2008 Mar 1;2008:56-60.

2007

  1. Miller W, Rosenbloom K, Hardison RC, Hou M, Taylor J, Raney B, Burhans R, King DC, Baertsch R, Blankenberg D, et al. "28-Way vertebrate alignment and conservation track in the UCSC Genome Browser". Genome Research. 2007 Dec; 17(12):1797-808.

  2. Taylor J, Schenk I, Blankenberg D, and Nekrutenko, A. "Using Galaxy to Perform Large-Scale Interactive Data Analysis". Current Protocols in Bioinformatics. 2007 Sep; 19:10.5.1-10.5.25.

  3. Blankenberg D, Taylor J, Schenk I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova K, Hardison RC, Nekrutenko A. "A framework for collaborative analysis of ENCODE data: Making large-scale analyses biologist-friendly". Genome Research. 2007 Jun; 17(6):960-4.

Citing Galaxy Web Resources

If you want to cite a particular URL on a Galaxy web site, see the Citing Medicine: NLM Style Guide for Authors, Editors, and Publishers for how to cite web pages, wikis, and just about everything else.

If you want to include a general Galaxy URL, we encourage you to use one of these:

CiteULike

The Galaxy Project uses the CiteULike social bookmarking service to track all of the above papers, plus any paper that references Galaxy. See the CiteULike page for more information.

last edited 2012-01-30 14:45:26 by Dan