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

TLDR

The Generic Model Organism System Database Project aims to create reusable software components for model organism databases, exemplified by GBrowse, a web‑based tool for visualizing genomic annotations. GBrowse implements a web‑based interface that lets users scroll, zoom, search, toggle and reorder tracks, upload and publish private annotations, while for developers it relies on open‑source components, offers simple installation, flexible configuration, and easy integration with other model organism web sites. GBrowse is freely available under an open source license.

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.