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Galaxy: a Comprehensive Approach for Supporting Accessible, Reproducible, and Transparent Computational Research in the Life Sciences

Overview
Journal Genome Biol
Specialties Biology
Genetics
Date 2010 Aug 27
PMID 20738864
Citations 1645
Authors
Affiliations
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Abstract

Increased reliance on computational approaches in the life sciences has revealed grave concerns about how accessible and reproducible computation-reliant results truly are. Galaxy http://usegalaxy.org, an open web-based platform for genomic research, addresses these problems. Galaxy automatically tracks and manages data provenance and provides support for capturing the context and intent of computational methods. Galaxy Pages are interactive, web-based documents that provide users with a medium to communicate a complete computational analysis.

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References
1.
Reich M, Liefeld T, Gould J, Lerner J, Tamayo P, Mesirov J . GenePattern 2.0. Nat Genet. 2006; 38(5):500-1. DOI: 10.1038/ng0506-500. View

2.
Rice P, Longden I, Bleasby A . EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000; 16(6):276-7. DOI: 10.1016/s0168-9525(00)02024-2. View

3.
Stajich J, Block D, Boulez K, Brenner S, Chervitz S, Dagdigian C . The Bioperl toolkit: Perl modules for the life sciences. Genome Res. 2002; 12(10):1611-8. PMC: 187536. DOI: 10.1101/gr.361602. View

4.
Mesirov J . Computer science. Accessible reproducible research. Science. 2010; 327(5964):415-6. PMC: 3878063. DOI: 10.1126/science.1179653. View

5.
Oinn T, Addis M, Ferris J, Marvin D, Senger M, Greenwood M . Taverna: a tool for the composition and enactment of bioinformatics workflows. Bioinformatics. 2004; 20(17):3045-54. DOI: 10.1093/bioinformatics/bth361. View