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
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.
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