Lessons learned from Galaxy, a web-based platform for high-throughput genomic analyses

Jeremy Goecks, Enis Afgan, Dannon Baker, Dan Blankenberg, Nate Coraor, Carl Eberhard, Greg Von Kuster, Ross Lazarus, Kanwei Li, Scott McManus, Anton Nekrutenko, James Taylor

Research output: Chapter in Book/Report/Conference proceedingConference contribution

4 Citations (Scopus)

Abstract

High throughput sequencing assays have given rise to the field of genomics and transformed biomedical research into a computational science. Due to the large size of genomics datasets, high-performance computing is essential for analysis. Galaxy (http://galaxyproject.org) is a popular Web-based platform that can be used for all facets of genomic analyses, including data retrieval and integration, multi-step analysis, repeated analyses via workflows, visualization, collaboration, and publication. This paper describes Galaxy and discusses four lessons learned from the development of Galaxy. First, Galaxy uses open, extensible frameworks so that it can be adapted to new technologies as they become available. Second, by leveraging Web technologies, Galaxy makes genomics tools accessible to everyone and provides a common platform for collaboration. Third, Galaxy fosters community amongst both developers and users and encourages each community to adapt and extend Galaxy to meet their needs. Finally, Galaxy software development and genomic research are closely coupled, and challenges encountered during genomic research drive Galaxy development.

Original languageEnglish (US)
Title of host publication2012 IEEE 8th International Conference on E-Science, e-Science 2012
DOIs
StatePublished - Dec 1 2012
Externally publishedYes
Event2012 IEEE 8th International Conference on E-Science, e-Science 2012 - Chicago, IL, United States
Duration: Oct 8 2012Oct 12 2012

Other

Other2012 IEEE 8th International Conference on E-Science, e-Science 2012
CountryUnited States
CityChicago, IL
Period10/8/1210/12/12

Fingerprint

Throughput
Software engineering
Assays
Visualization
Genomics

Keywords

  • Galaxy
  • Genomics
  • High-performance computing
  • Reproducibility
  • Transparency
  • Usability
  • Web portal

ASJC Scopus subject areas

  • Computer Science (miscellaneous)

Cite this

Goecks, J., Afgan, E., Baker, D., Blankenberg, D., Coraor, N., Eberhard, C., ... Taylor, J. (2012). Lessons learned from Galaxy, a web-based platform for high-throughput genomic analyses. In 2012 IEEE 8th International Conference on E-Science, e-Science 2012 [6404442] https://doi.org/10.1109/eScience.2012.6404442

Lessons learned from Galaxy, a web-based platform for high-throughput genomic analyses. / Goecks, Jeremy; Afgan, Enis; Baker, Dannon; Blankenberg, Dan; Coraor, Nate; Eberhard, Carl; Von Kuster, Greg; Lazarus, Ross; Li, Kanwei; McManus, Scott; Nekrutenko, Anton; Taylor, James.

2012 IEEE 8th International Conference on E-Science, e-Science 2012. 2012. 6404442.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Goecks, J, Afgan, E, Baker, D, Blankenberg, D, Coraor, N, Eberhard, C, Von Kuster, G, Lazarus, R, Li, K, McManus, S, Nekrutenko, A & Taylor, J 2012, Lessons learned from Galaxy, a web-based platform for high-throughput genomic analyses. in 2012 IEEE 8th International Conference on E-Science, e-Science 2012., 6404442, 2012 IEEE 8th International Conference on E-Science, e-Science 2012, Chicago, IL, United States, 10/8/12. https://doi.org/10.1109/eScience.2012.6404442
Goecks J, Afgan E, Baker D, Blankenberg D, Coraor N, Eberhard C et al. Lessons learned from Galaxy, a web-based platform for high-throughput genomic analyses. In 2012 IEEE 8th International Conference on E-Science, e-Science 2012. 2012. 6404442 https://doi.org/10.1109/eScience.2012.6404442
Goecks, Jeremy ; Afgan, Enis ; Baker, Dannon ; Blankenberg, Dan ; Coraor, Nate ; Eberhard, Carl ; Von Kuster, Greg ; Lazarus, Ross ; Li, Kanwei ; McManus, Scott ; Nekrutenko, Anton ; Taylor, James. / Lessons learned from Galaxy, a web-based platform for high-throughput genomic analyses. 2012 IEEE 8th International Conference on E-Science, e-Science 2012. 2012.
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