Nucleic Acids Research Advance Access published online on December 20, 2006
Nucleic Acids Research, doi:10.1093/nar/gkl1019
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Database Issue |
The Stanford Microarray Database: implementation of new analysis tools and open source release of software
1 Department of Biochemistry, Stanford University School of Medicine Stanford, CA, USA 2 Department of Genetics, Stanford University School of Medicine Stanford, CA, USA 3 Iconix Biosciences Mountain View, CA 94043, USA 4 Lewis-Sigler Institute for Integrative Genomics, Princeton University Princeton, NJ, USA 5 Howard Hughes Medical Institute Stanford, CA, 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, 2006. Revised October 27, 2006. Accepted October 30, 2006.
The Stanford Microarray Database (SMD; http://smd.stanford.edu/) is a research tool and archive that allows hundreds of researchers worldwide to store, annotate, analyze and share data generated by microarray technology. SMD supports most major microarray platforms, and is MIAME-supportive and can export or import MAGE-ML. The primary mission of SMD is to be a research tool that supports researchers from the point of data generation to data publication and dissemination, but it also provides unrestricted access to analysis tools and public data from 300 publications. In addition to supporting ongoing research, SMD makes its source code fully and freely available to others under an Open Source license, enabling other groups to create a local installation of SMD. In this article, we describe several data analysis tools implemented in SMD and we discuss features of our software release.
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