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Author Notes:

A vision for Galaxy was originally articulated by Ross Hardison, who is also the major source of support and critical feedback.

The authors would like to thank Jim Kent and David Haussler for their continuing support and making UCSC Genome Browser uplink and connection possible.

Istvan Albert pioneered initial aspects of Galaxy design; Efforts of the Galaxy Team (Enis Afgan, Guru Ananda, Dannon Baker, Nate Coraor, Jeremy Goecks, Greg Von Kuster, Ross Lazarus) were instrumental for making this work happen.

The following individuals also contributed to the Galaxy project at different stages: Richard Burhans; Ramkrishna Chakrabarty; Laura Elnitski; Belinda Giardiane; Bob Harris; Jianbin He; Kanwei Li; Webb Miller; Cathy Riemer; Kelly Vincent; and Yi Zhang.

Robert Castelo, France Denoeud, Roderic Guigo, Erika Kvikstad, Julien Lagarde, and Kateryna Makova provided critical comments during software testing.

Ramana Davuluri gave permission to use the MPromDB data in these protocols.

Subject:

Research Funding:

This work was funded by an NIH grant GM07226405S2 to KDM; a Beckman Foundation Young Investigator Award to AN; NSF grant DBI 0543285 and NIH grant HG004909 to AN and JT; NIH grants HG005133 and HG005542 to JT and AN; as well as funds from Penn State University and the Huck Institutes for the Life Sciences to AN and from Emory University to JT.

Additional funding is provided, in part, under a grant with the Pennsylvania Department of Health using Tobacco Settlement Funds.

Keywords:

  • biology
  • genomic data
  • data analysis
  • unified portals
  • Web application
  • on-the-fly analyses
  • UCSC Genome Browser
  • relevant data
  • Galaxy
  • interface

Using Galaxy to Perform Large‐Scale Interactive Data Analyses

Tools:

Journal Title:

Current Protocols in Bioinformatics

Volume:

Volume 19, Number 1

Publisher:

Type of Work:

Article | Post-print: After Peer Review

Abstract:

While most experimental biologists know where to download genomic data, few have a concrete plan on how to analyze it. This situation can be corrected by: (1) providing unified portals serving genomic data and (2) building Web applications to allow flexible retrieval and on‐the‐fly analyses of the data. Powerful resources, such as the UCSC Genome Browser already address the first issue. The second issue, however, remains open. For example, how to find human protein‐coding exons with the highest density of single nucleotide polymorphisms (SNPs) and extract orthologous sequences from all sequenced mammals? Indeed, one can access all relevant data from the UCSC Genome Browser. But once the data is downloaded how would one deal with millions of SNPs and gigabytes of alignments? Galaxy (http://g2.bx.psu.edu) is designed specifically for that purpose. It amplifies the strengths of existing resources (such as UCSC Genome Browser) by allowing the user to access and, most importantly, analyze data within a single interface in an unprecedented number of ways.

Copyright information:

Copyright © 2007 John Wiley & Sons, Inc.

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