TY - GEN
T1 - Lessons learned from Galaxy, a web-based platform for high-throughput genomic analyses
AU - Goecks, Jeremy
AU - Afgan, Enis
AU - Baker, Dannon
AU - Blankenberg, Dan
AU - Coraor, Nate
AU - Eberhard, Carl
AU - Von Kuster, Greg
AU - Lazarus, Ross
AU - Li, Kanwei
AU - McManus, Scott
AU - Nekrutenko, Anton
AU - Taylor, James
PY - 2012
Y1 - 2012
N2 - 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.
AB - 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.
KW - Galaxy
KW - Genomics
KW - High-performance computing
KW - Reproducibility
KW - Transparency
KW - Usability
KW - Web portal
UR - http://www.scopus.com/inward/record.url?scp=84873649400&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84873649400&partnerID=8YFLogxK
U2 - 10.1109/eScience.2012.6404442
DO - 10.1109/eScience.2012.6404442
M3 - Conference contribution
AN - SCOPUS:84873649400
SN - 9781467344678
T3 - 2012 IEEE 8th International Conference on E-Science, e-Science 2012
BT - 2012 IEEE 8th International Conference on E-Science, e-Science 2012
T2 - 2012 IEEE 8th International Conference on E-Science, e-Science 2012
Y2 - 8 October 2012 through 12 October 2012
ER -