Nucleic Acids Research Advance Access originally published online on October 25, 2008
Nucleic Acids Research 2009 37(Database issue):D898-D901; doi:10.1093/nar/gkn786
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Nucleic Acids Research, 2009, Vol. 37, Database issue D898-D901
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
This article appears in the following Nucleic Acids Research issue: Database issue [View the issue table of contents]
Articles |
Implementation of GenePattern within the Stanford Microarray Database
1Departments of Genetics, Stanford University School of Medicine, CA 94305, USA and 2Departments of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
*To whom correspondence should be addressed. Tel: +1 650 724 3028; Fax: +1 650 724 3701; Email: ball{at}genome.stanford.edu
Received September 15, 2008. Accepted October 9, 2008.
Hundreds of researchers across the world use the Stanford Microarray Database (SMD; http://smd.stanford.edu/) to store, annotate, view, analyze and share microarray data. In addition to providing registered users at Stanford access to their own data, SMD also provides access to public data, and tools with which to analyze those data, to any public user anywhere in the world. Previously, the addition of new microarray data analysis tools to SMD has been limited by available engineering resources, and in addition, the existing suite of tools did not provide a simple way to design, execute and share analysis pipelines, or to document such pipelines for the purposes of publication. To address this, we have incorporated the GenePattern software package directly into SMD, providing access to many new analysis tools, as well as a plug-in architecture that allows users to directly integrate and share additional tools through SMD. In this article, we describe our implementation of the GenePattern microarray analysis software package into the SMD code base. This extension is available with the SMD source code that is fully and freely available to others under an Open Source license, enabling other groups to create a local installation of SMD with an enriched data analysis capability.