Citing Galaxy

Genome Biology Current Protocols in Molecular Biology Genome Research Nature Biotechnology Bioinformatics Current Protocols in Bioinformatics Journal of the American Medical Informatics Association (JAMIA) Cancer Medicine Nature Biotechnology

Please cite Galaxy in any research that uses or extends Galaxy. Please cite the primary publication for project wide citations. There are also several publications on more specific topics that should be referenced when appropriate. Finally, there is a list of Galaxy Project publications by year.

Which Galaxy?

If you used Galaxy in your methods, we also request that you specify which instance(s) of Galaxy were used: Was it usegalaxy.org, one of other public Galaxy servers, a local install, or on a cloud install?

Primary Publication

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

Enis Afgan, Dannon Baker, Marius van den Beek, Daniel Blankenberg, Dave Bouvier, Martin Čech, John Chilton, Dave Clements, Nate Coraor, Carl Eberhard, Björn Grüning, Aysam Guerler, Jennifer Hillman-Jackson, Greg Von Kuster, Eric Rasche, Nicola Soranzo, Nitesh Turaga, James Taylor, Anton Nekrutenko, and Jeremy Goecks. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update. Nucleic Acids Research (2016) 44(W1): W3-W10 doi:10.1093/nar/gkw343

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)

Clare Sloggett, Nuwan Goonasekera and Enis Afgan. BioBlend: automating pipeline analyses within Galaxy and CloudMan. Bioinformatics (2013) 29(13): 1685-1686 doi:10.1093/bioinformatics/btt199

Cloud

Enis Afgan, Brad Chapman and James Taylor. CloudMan as a platform for tool, data, and analysis distribution. BMC Bioinformatics (2012) 13:315 doi:10.1186/1471-2105-13-315

Data Managers

Daniel Blankenberg, James E. Johnson, The Galaxy Team, James Taylor and Anton Nekrutenko. Wrangling Galaxy's Reference Data. Bioinformatics (2014) 30(13): 1917-1919 doi:10.1093/bioinformatics/btu119

Interactive Environments

Björn Grüning, Eric Rasche, Boris Rebolledo-Jaramillo, Carl Eberhard, Torsten Houwaart, John Chilton, Nate Coroar, Rolf Backofen, James Taylor, Anton Nekrutenko. Jupyter and Galaxy: Easing entry barriers into complex data analyses for biomedical researchers, PLOS Computational Biology, doi:10.1371/journal.pcbi.1005425

Reproducibility

Geir Kjetil Sandve, Anton Nekrutenko, James Taylor, Eivind Hovig. Ten Simple Rules for Reproducible Computational Research. PLoS Computational Biology (2013) 9(10): e1003285 doi:10.1371/journal.pcbi.1003285

ToolShed

Daniel Blankenberg, Gregory Von Kuster, Emil Bouvier, Dannon Baker, Enis Afgan, Nicholas Stoler, the Galaxy Team, James Taylor and Anton Nekrutenko. Dissemination of scientific software with Galaxy ToolShed. Genome Biology (2014) 15:403 doi:10.1186/gb4161

Visualization

Jeremy Goecks, Carl Eberhard, Tomithy Too, The Galaxy Team, Anton Nekrutenko and James Taylor. Web-based visual analysis for high-throughput genomics. BMC Genomics (2013) 14:397 doi:10.1186/1471-2164-14-397

Galaxy Project Publications by Year

Papers about or using Galaxy with core team members as authors.

Enhancing pre-defined workflows with ad hoc analytics using Galaxy, Docker and Jupyter. bioRxiv, (2016) doi:10.1101/075457

2017

  1. Björn Grüning, Eric Rasche, Boris Rebolledo-Jaramillo, Carl Eberhard, Torsten Houwaart, John Chilton, Nate Coroar, Rolf Backofen, James Taylor, Anton Nekrutenko. Jupyter and Galaxy: Easing entry barriers into complex data analyses for biomedical researchers, PLOS Computational Biology, doi:10.1371/journal.pcbi.1005425

2016

  1. Nitesh Turaga, Mallory A. Freeberg, Dannon Baker, John Chilton, Galaxy Team, Anton Nekrutenko, James Taylor. A guide and best practices for R/Bioconductor tool integration in Galaxy. F1000Research (2016) 5:2757 doi:10.12688/f1000research.9821.1

  2. Björn Grüning, Eric Rasche, Boris Rebolledo-Jaramillo, Carl Eberhard, Torsten Houwaart, John Chilton, Nate Coroar, Rolf Backofen, James Taylor, Anton Nekrutenko. Enhancing pre-defined workflows with ad hoc analytics using Galaxy, Docker and Jupyter. bioRxiv (2016) doi:10.1101/075457

  3. Nicholas Stoler, Barbara Arbeithuber, Wilfried Guiblet, Kateryna D. Makova, Anton Nekrutenko. Streamlined analysis of duplex sequencing data with Du Novo. Genome Biology (2016) 17:180 doi:10.1186/s13059-016-1039-4

  4. Enis Afgan, Andrew Lonie, JamesTaylor, Karolj Skala, Nuwan Goonasekera. Architectural Models for Deploying and Running Virtual Laboratories in the Cloud MIPRO 2016 Proceedings (2016), Petar Biljanović editor, 298-302, ISSN 1847-3938, ISBN 978-953-233-087-8

  5. Enis Afgan, Dannon Baker, Marius van den Beek, Daniel Blankenberg, Dave Bouvier, Martin Čech, John Chilton, Dave Clements, Nate Coraor, Carl Eberhard, Björn Grüning, Aysam Guerler, Jennifer Hillman-Jackson, Greg Von Kuster, Eric Rasche, Nicola Soranzo, Nitesh Turaga, James Taylor, Anton Nekrutenko, and Jeremy Goecks. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update. Nucleic Acids Research (2016) 44(W1): W3-W10 doi:10.1093/nar/gkw343

  6. Kun Qu, Sara Garamszegi, Felix Wu, Helga Thorvaldsdottir, Ted Liefeld, Marco Ocana, Borges-Rivera, Diego Borges-Rivera, Pochet, Nathalie Pochet, James T. Robinson, Barry Demchak, Tim Hull, Gil Ben-Artzi, Daniel Blankenberg, Galt P. Barber, Brian T. Lee, Robert M. Kuhn, Anton Nekrutenko, Eran Segal, Trey Ideker, Michael Reich, Aviv Regev, Howard Y. Chang, Jill P. Mesirov. Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace. Nature Methods (2016) 13(3): 245-247 doi:10.1038/nmeth.3732

  7. Claus Børnich, Ivar Grytten, Eivind Hovig, Jonas Paulsen, Martin Čech, and Geir Kjetil Sandve. Galaxy Portal: Interacting with the Galaxy platform through mobile devices. Bioinformatics (2016) 32(11): 1743-1745 doi:10.1093/bioinformatics/btw042

2015

  1. Lukas Forer, Enis Afgan, Hansi Weissensteiner, Davor Davidovic, Gunther Specht, Florian Kronenberg, Sebastian Schonherr. Cloudflow - A framework for MapReduce pipeline development in Biomedical Research, Information and Communication Technology, Electronics and Microelectronics (MIPRO), 2015 38th International Convention on, ISBN: 978-953-233-085-4

  2. Enis Afgan, Clare Sloggett, Nuwan Goonasekera, Igor Makunin, Derek Benson, Mark Crowe, Simon Gladman, Yousef Kowsar, Michael Pheasant, Ron Horst, Andrew Lonie, "Genomics Virtual Laboratory: A Practical Bioinformatics Workbench for the Cloud," PLoS ONE 10(10): e0140829. doi:10.1371/journal.pone.0140829

  3. Peter J. A. Cock, John M. Chilton, Björn Grüning, James E. Johnson, and Nicola Soranzo, "NCBI BLAST+ integrated into Galaxy," GigaScience 2015, 4:39 doi:10.1186/s13742-015-0080-7

  4. Craig A. Stewart, Timothy M. Cockerill, Ian Foster, David Hancock, Nirav Merchant, Edwin Skidmore, Daniel Stanzione, James Taylor, Steven Tuecke, George Turner, Matthew Vaughn, Niall I. Gaffney, "Jetstream: a self-provisioned, scalable science and engineering cloud environment," in XSEDE '15 Proceedings of the 2015 XSEDE Conference: Scientific Advancements Enabled by Enhanced Cyberinfrastructure, Article No. 29

  5. Anto P. Rajkumar, Per Qvist, Ross Lazarus, Francesco Lescai, Jia Ju, Mette Nyegaard, Ole Mors, Anders D. Børglum, Qibin Li and Jane H. Christensen, "Experimental validation of methods for differential gene expression analysis and sample pooling in RNA-seq," BMC Genomics 2015, 16:548 doi:10.1186/s12864-015-1767-y

  6. Enis Afgan, Nate Coraor, John Chilton, Dannon Baker, James Taylor, The Galaxy Team, "Enabling cloud bursting for life sciences within Galaxy," in Concurrency and Computation: Practice and Experience (1 June 2015), doi:10.1002/cpe.3536

  7. Enis Afgan, Konstantinos Krampis, Nuwan Goonasekera, Karolj Skala, James Taylor, "Building and Provisioning Bioinformatics Environments on Public and Private Clouds," in Information and Communication Technology, Electronics and Microelectronics (MIPRO), 2015 38th International Convention on

  8. Yin Tang, Emil Bouvier, Chun Kit Kwok, Yiliang Ding, Anton Nekrutenko, Philip C. Bevilacqua and Sarah M. Assmann, "StructureFold: Genome-wide RNA secondary structure mapping and reconstruction in vivo," Bioinformatics (2015) doi:10.1093/bioinformatics/btv213

  9. Blankenberg, James Taylor and Anton Nekrutenko, "Online Resources for Genomic Analysis Using High-Throughput Sequencing, Cold Spring Harbor Protocols doi:10.1101/pdb.top083667

  10. Jorrit Boekel, John M Chilton, Ira R Cooke, Peter L Horvatovich, Pratik D Jagtap, Lukas Käll, Janne Lehtiö, Pieter Lukasse, Perry D Moerland & Timothy J Griffin, "Multi-omic data analysis using Galaxy," Nature Biotechnology 33, 137–139 (2015) doi:10.1038/nbt.3134

  11. Aidan Budd, Manuel Corpas, Michelle D. Brazas, Jonathan C. Fuller, Jeremy Goecks, Nicola J. Mulder, Magali Michaut, B. F. Francis Ouellette, Aleksandra Pawlik, Niklas Blomberg, "A Quick Guide for Building a Successful Bioinformatics Community," PLOS Computational Biology, doi:10.1371/journal.pcbi.1003972

  12. Jeremy Goecks, Bassel F. El-Rayes, Shishir K. Maithel, H. Jean Khoury, James Taylor and Michael R. Rossi, "Open pipelines for integrated tumor genome profiles reveal differences between pancreatic cancer tumors and cell lines," Cancer Medicine, doi:10.1002/cam4.360

2014

  1. Enis Afgan, Dannon Baker, John Chilton, Nate Coraor, The Galaxy Team, James Taylor, "Galaxy Cluster to Cloud - Genomics at Scale," in Proceedings of the 9th Gateway Computing Environments Workshop (2014), pp. 47-50, doi:10.1109/gce.2014.13

  2. S. Leo, L. Pireddu, G. Cuccuru, L. Lianas, N. Soranzo, E. Afgan and G. Zanetti, BioBlend.objects: metacomputing with Galaxy. Bioinformatics (2014) 30(19): 2816-2817 doi:10.1093/bioinformatics/btu386

  3. Daniel Blankenberg and Jennifer Hillman-Jackson, "Analysis of Next-Generation Sequencing Data Using Galaxy," in Methods in Molecular Biology 2014;1150:21-43. doi:10.1007/978-1-4939-0512-6_2

  4. Benjamin Dickins, Boris Rebolledo-Jaramillo, Marcia Shu-Wei Su, Ian M. Paul, Daniel Blankenberg, Nicholas Stoler, Kateryna D. Makova, and Anton Nekrutenko, "Controlling for contamination in re-sequencing studies with a reproducible web-based phylogenetic approach," in BioTechniques Vol. 56, No. 3, March 2014

  5. Daniel Blankenberg, James E. Johnson, The Galaxy Team, James Taylor and Anton Nekrutenko, "Wrangling Galaxy's Reference Data," in Bioinformatics (2014) doi:10.1093/bioinformatics/btu119

  6. Daniel Blankenberg, Gregory Von Kuster, Emil Bouvier, Dannon Baker, Enis Afgan, Nicholas Stoler, the Galaxy Team, James Taylor and Anton Nekrutenko, "Dissemination of scientific software with Galaxy ToolShed," in Genome Biology 2014, 15:403, doi:10.1186/gb4161

  7. B Rebolledo-Jaramillo, MSW Su, N Stoler, J McElhoe, B Dickins, D Blankenberg, TS Korneliussen, F Chiaromonte, R Nielsen, MM Hollandc, IM Paul, A Nekrutenko, KD Makova, "Maternal age effect and severe germ-line bottleneck in the inheritance of human mitochondrial DNA", PNAS 2014; doi:10.1073/pnas.1409328111

2013

  1. Geir Kjetil Sandve, Anton Nekrutenko, James Taylor, Eivind Hovig. Ten Simple Rules for Reproducible Computational Research. PLoS Computational Biology (2013) 9(10): e1003285 doi:10.1371/journal.pcbi.1003285

  2. Richard LeDuc, Matthew Vaughn, John M. Fonner, Michael Sullivan, James G. Williams, Philip D. Blood, James Taylor, William Barnett. Leveraging the national cyberinfrastructure for biomedical research. Journal of the American Medical Informatics Association (JAMIA) (2013) 21(2): 195-199 doi:10.1136/amiajnl-2013-002059

  3. James Taylor, Anton Nekrutenko, Nate Coraor, et al. "A sustainable national gateway for biological computation," Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery (2013)

  4. Yousef Kowsar and Enis Afgan, "Support for data-intensive computing with CloudMan," Information & Communication Technology Electronics & Microelectronics (MIPRO), 2013 36th International Convention on, 243-248; 2013

  5. Jeremy Goecks, Carl Eberhard, Tomithy Too, The Galaxy Team, Anton Nekrutenko and James Taylor. Web-based visual analysis for high-throughput genomics. BMC Genomics (2013) 14:397 doi:10.1186/1471-2164-14-397

  6. Clare Sloggett, Nuwan Goonasekera and Enis Afgan. BioBlend: automating pipeline analyses within Galaxy and CloudMan. Bioinformatics (2013) 29(13): 1685-1686 doi:10.1093/bioinformatics/btt199

2012

  1. Enis Afgan, Brad Chapman and James Taylor, "CloudMan as a platform for tool, data, and analysis distribution", BMC Bioinformatics 2012, 13:315

  2. Jeremy Goecks, Nate Coraor, The Galaxy Team, Anton Nekrutenko & James Taylor, "NGS analyses by visualization with Trackster." Nature Biotechnology 30, 1036–1039 (2012)

  3. Gregory Minevich, Danny S. Park, Daniel Blankenberg, Richard J. Poole and Oliver Hobert, "CloudMap: A Cloud-based Pipeline for Analysis of Mutant Genome Sequences." Genetics. 2012 Oct 11

  4. Ross Lazarus, Antony Kaspi, Mark Ziemann and The Galaxy Team, "Creating re-usable tools from scripts: The Galaxy Tool Factory." Bioinformatics (2012) doi:10.1093/bioinformatics/bts573.

  5. Peter Li, Jeremy Goecks, Tin L. Lee, "Turning pipe dreams into reality." Genome Biology, Vol. 13, No. 8. (2012), 318.

  6. Anton Nekrutenko & James Taylor, "Next-generation sequencing data interpretation: enhancing reproducibility and accessibility." Nature Reviews Genetics. 13, 667-672 (September 2012).

  7. Enis Afgan, Brad Chapman, Margita Jadan, Vedran Franke, James Taylor, "Using Cloud Computing Infrastructure with CloudBioLinux, CloudMan, and Galaxy." Current Protocols in Bioinformatics. 2012 June: Unit 11.9.

  8. Jennifer Hillman-Jackson, Dave Clements, Daniel Blankenberg, James Taylor, Anton Nekrutenko, Galaxy Team, "Using Galaxy to Perform Large-Scale Interactive Data Analyses." Current Protocols in Bioinformatics. 2012 June: Unit 10.5.

2011

  1. Hiroki Goto, Benjamin Dickins, Enis Afgan, Ian M Paul, James Taylor, Kateryna D Makova and Anton Nekrutenko, Dynamics of mitochondrial heteroplasmy in three families investigated via a repeatable re-sequencing study. Genome Biology 2011, 12:R59 doi:10.1186/gb-2011-12-6-r59

  2. Jeremy Goecks, Kanwei Li, Dave Clements, The Galaxy Team, 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.

  3. 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

  4. 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.

  5. 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

  6. 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]

  7. 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. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. Enis Afgan, Dannon Baker, The Galaxy Team, Anton Nekrutenko and James Taylor. "The elastic analysis with galaxy on the cloud." Genome Biology 2010, 11(Suppl 1):P2

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.

2005

  1. 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.

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:

The project as a whole: http://galaxyproject.org/

If you used the public galaxy server ("Main") to do analysis: http://usegalaxy.org/

Direct people here for information on how to download and configure your own local installation: http://getgalaxy.org/

Using or referring to any of the public Galaxy server instances: Please include the name, URL, and primary publication for the server.

Citations

See the Citations section of the project statistics page for a summary of citations of project papers.

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.