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Nucleic Acids Research 2005 33(Database Issue):D580-D582; doi:10.1093/nar/gki006
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Nucleic Acids Research, 2005, Vol. 33, Database issue D580-D582
© 2005, the authors
Nucleic Acids Research, Vol. 33, Database issue © Oxford University Press 2005; all rights reserved

The Stanford Microarray Database accommodates additional microarray platforms and data formats

Catherine A. Ball1,*, Ihab A. B. Awad2, Janos Demeter1, Jeremy Gollub1, Joan M. Hebert3, Tina Hernandez-Boussard1, Heng Jin1, John C. Matese4, Michael Nitzberg1, Farrell Wymore1, Zachariah K. Zachariah1, Patrick O. Brown1,5 and Gavin Sherlock2

1 Department of Biochemistry and 2 Department of Genetics, 3 Stanford University School of Medicine, Stanford, CA, USA, 4 Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA and 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 3, 2004; Accepted September 13, 2004

The Stanford Microarray Database (SMD) (http://smd.stanford.edu) is a research tool for hundreds of Stanford researchers and their collaborators. In addition, SMD functions as a resource for the entire biological research community by providing unrestricted access to microarray data published by SMD users and by disseminating its source code. In addition to storing GenePix (Axon Instruments) and ScanAlyze output from spotted microarrays, SMD has recently added the ability to store, retrieve, display and analyze the complete raw data produced by several additional microarray platforms and image analysis software packages, so that we can also now accept data from Affymetrix GeneChips (MAS5/GCOS or dChip), Agilent Catalog or Custom arrays (using Agilent's Feature Extraction software) or data created by SpotReader (Niles Scientific). We have implemented software that allows us to accept MAGE-ML documents from array manufacturers and to submit MIAME-compliant data in MAGE-ML format directly to ArrayExpress and GEO, greatly increasing the ease with which data from SMD can be published adhering to accepted standards and also increasing the accessibility of published microarray data to the general public. We have introduced a new tool to facilitate data sharing among our users, so that datasets can be shared during, before or after the completion of data analysis. The latest version of the source code for the complete database package was released in November 2004 (http://smd.stanford.edu/download/), allowing researchers around the world to deploy their own installations of SMD.

The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use permissions, please contact journals.permissions{at}oupjournals.org.


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