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The Stanford Microarray Database accommodates additional microarray platforms and data formats.

Catherine A Ball1, Ihab A B Awad, Janos Demeter

  • 1Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA. ball@genome.stanford.edu

Nucleic Acids Research
|December 21, 2004
PubMed
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The Stanford Microarray Database (SMD) provides broad access to microarray data and analysis tools. It now supports multiple platforms and facilitates data sharing and publication adhering to MIAME standards.

Area of Science:

  • Bioinformatics
  • Genomics
  • Data Management

Background:

  • The Stanford Microarray Database (SMD) is a vital resource for researchers.
  • It supports hundreds of Stanford researchers and their collaborators.
  • SMD serves the broader biological research community.

Purpose of the Study:

  • To enhance the SMD's functionality and data accessibility.
  • To support a wider range of microarray platforms and analysis software.
  • To facilitate data sharing and publication compliance.

Main Methods:

  • Expanded data storage to include Affymetrix GeneChips, Agilent arrays, and SpotReader data.
  • Implemented software for MAGE-ML document acceptance and submission.
  • Developed a new tool for facilitating data sharing among users.

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Main Results:

  • SMD now accepts data from multiple microarray platforms and analysis software.
  • SMD facilitates MIAME-compliant data submission to ArrayExpress and GEO.
  • Enhanced data sharing capabilities are available for users.

Conclusions:

  • SMD has expanded its capabilities to support diverse microarray data.
  • The database promotes data sharing and adherence to publishing standards.
  • SMD's open-source code allows global researchers to deploy their own installations.