The Generic Genome Browser: A Building Block for a Model Organism System Database

  1. Lincoln D. Stein1,5,
  2. Christopher Mungall2,
  3. ShengQiang Shu2,
  4. Michael Caudy3,
  5. Marco Mangone1,
  6. Allen Day1,
  7. Elizabeth Nickerson1,
  8. Jason E. Stajich4,
  9. Todd W. Harris1,
  10. Adrian Arva1, and
  11. Suzanna Lewis2
  1. 1Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11790, USA; 2Department of Molecular and Cell Biology, Berkeley Drosophila Genome Project, University of California, Berkeley, California 94720, USA; 3 Department of Neuroscience, Cornell University Medical College at Burke Medical Research Institute, White Plains, New York 10605, USA; 4 University Program in Genetics, Duke University, Durham, North Carolina 27710, USA

Abstract

The Generic Model Organism System Database Project (GMOD) seeks to develop reusable software components for model organism system databases. In this paper we describe the Generic Genome Browser (GBrowse), a Web-based application for displaying genomic annotations and other features. For the end user, features of the browser include the ability to scroll and zoom through arbitrary regions of a genome, to enter a region of the genome by searching for a landmark or performing a full text search of all features, and the ability to enable and disable tracks and change their relative order and appearance. The user can upload private annotations to view them in the context of the public ones, and publish those annotations to the community. For the data provider, features of the browser software include reliance on readily available open source components, simple installation, flexible configuration, and easy integration with other components of a model organism system Web site. GBrowse is freely available under an open source license. The software, its documentation, and support are available at http://www.gmod.org.

Footnotes

  • 5 Corresponding author.

  • E-MAIL lstein{at}cshl.org; FAX (516) 367-8389.

  • Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.403602.

    • Received May 7, 2002.
    • Accepted August 9, 2002.
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