Using galaxy to perform large-scale interactive data analyses

Jennifer Hillman-Jackson, Dave Clements, Daniel Blankenberg, James Taylor, Anton Nekrutenko, Galaxy Team

Research output: Contribution to journalArticle

83 Citations (Scopus)

Abstract

Innovations in biomedical research technologies continue to provide experimental biologists with novel and increasingly large genomic and high-throughput data resources to be analyzed. As creating and obtaining data has become easier, the key decision faced by many researchers is a practical one: where and how should an analysis be performed? Datasets are large and analysis tool set-up and use is riddled with complexities outside of the scope of core research activities. The authors believe that Galaxy provides a powerful solution that simplifies data acquisition and analysis in an intuitive Web application, granting all researchers access to key informatics tools previously only available to computational specialists working in Unix-based environments.We will demonstrate through a series of biomedically relevant protocols how Galaxy specifically brings together (1) data retrieval from public and private sources, for example, UCSC's Eukaryote and Microbial Genome Browsers, (2) custom tools (wrapped Unix functions, format standardization/conversions, interval operations), and 3rd-party analysis tools.

Original languageEnglish (US)
Article number10.5
JournalCurrent Protocols in Bioinformatics
Issue numberSUPPL.38
DOIs
StatePublished - Jun 1 2012

Fingerprint

Galaxies
Microbial Genome
Research Personnel
Biomedical Technology
Informatics
Information Storage and Retrieval
Eukaryota
Biomedical Research
Research
Standardization
Data acquisition
Genes
Innovation
Throughput

All Science Journal Classification (ASJC) codes

  • Structural Biology
  • Biochemistry

Cite this

Hillman-Jackson, Jennifer ; Clements, Dave ; Blankenberg, Daniel ; Taylor, James ; Nekrutenko, Anton ; Team, Galaxy. / Using galaxy to perform large-scale interactive data analyses. In: Current Protocols in Bioinformatics. 2012 ; No. SUPPL.38.
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Using galaxy to perform large-scale interactive data analyses. / Hillman-Jackson, Jennifer; Clements, Dave; Blankenberg, Daniel; Taylor, James; Nekrutenko, Anton; Team, Galaxy.

In: Current Protocols in Bioinformatics, No. SUPPL.38, 10.5, 01.06.2012.

Research output: Contribution to journalArticle

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