The Generic Genome Browser: A building block for a model organism system database

Stein, L. D., Mungall, C., Shu, S. Q., Caudy, M., Mangone, M., Day, A., Nickerson, E., Stajich, J. E., Harris, T. W., Arva, A., Lewis, S. (October 2002) The Generic Genome Browser: A building block for a model organism system database. Genome Research, 12 (10). pp. 1599-1610. ISSN 1088-9051

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URL: http://www.ncbi.nlm.nih.gov/pubmed/12368253
DOI: 10.1101/gr.403602

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.

Item Type: Paper
Uncontrolled Keywords: Animals Computer Graphics Database Management Systems/*trends *Databases, Genetic Diptera/genetics Drosophila Proteins/genetics Drosophila melanogaster/genetics *Genome Transcription Factors/genetics
Subjects: bioinformatics
bioinformatics > genomics and proteomics > databases
bioinformatics > genomics and proteomics
bioinformatics > genomics and proteomics > computers > computer software
CSHL Authors:
Communities: CSHL labs > Stein lab
Dolan DNA Learning Center
Watson School > Publications
Depositing User: Matt Covey
Date: October 2002
Date Deposited: 30 Oct 2013 19:43
Last Modified: 19 Sep 2014 14:15
PMCID: PMC187535
Related URLs:
URI: http://repository.cshl.edu/id/eprint/28793

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