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Related Concept Videos

DNA Microarrays02:34

DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...

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Microarray Analysis for Saccharomyces cerevisiae
13:17

Microarray Analysis for Saccharomyces cerevisiae

Published on: April 7, 2011

The Stanford Microarray Database: implementation of new analysis tools and open source release of software.

Janos Demeter1, Catherine Beauheim, Jeremy Gollub

  • 1Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA.

Nucleic Acids Research
|December 22, 2006
PubMed
Summary

The Stanford Microarray Database (SMD) archives and analyzes microarray data, offering tools for researchers globally. Its open-source code enables local installations, promoting data sharing and publication.

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Area of Science:

  • Bioinformatics
  • Genomics
  • Data Archiving

Background:

  • Microarray technology generates large datasets requiring robust management.
  • Standardized data formats and analysis tools are crucial for reproducibility.

Purpose of the Study:

  • To introduce the Stanford Microarray Database (SMD) as a comprehensive resource for microarray data.
  • To highlight SMD's functionalities for data storage, annotation, analysis, and sharing.
  • To detail the features of the SMD software release and its open-source availability.

Main Methods:

  • SMD supports major microarray platforms and adheres to MIAME standards.
  • Data import/export capabilities include MAGE-ML.
  • The database provides unrestricted access to analysis tools and public data.

Main Results:

  • SMD serves as a vital research tool for hundreds of researchers worldwide.
  • It facilitates data management from generation to publication.
  • Publicly accessible data from 300 publications is available.

Conclusions:

  • SMD is a valuable, freely available resource for the scientific community.
  • Its open-source nature encourages wider adoption and local installations.
  • The database enhances microarray data analysis, sharing, and dissemination.