User:JimHu/Gbrowse

From GMOD

The GBrowse logo was created by Alex Read, a participant in the Spring 2010 Logo Program, while a design student at Linn-Benton Community College.

GBrowse^[1] is a genome viewer and is GMOD's most popular component. For a list of GBrowse and GMOD installations see the GMOD Users page. For a demo of its features, try the WormBase, FlyBase, or Human Genome Segmental Duplication Database web sites.

Description

GBrowse running on HapMap.org View at full resolution

The Generic Genome Browser (GBrowse) is a combination of database and interactive Web page for manipulating and displaying annotations on genomes. Some of its features:

• Simultaneous bird's eye and detailed views of the genome.
• Scroll, zoom, center.
• Use a variety of premade glyphs or create your own.
• Attach arbitrary URLs to any annotation.
• Order and appearance of tracks are customizable by administrator and end-user.
• Search by annotation ID, name, or comment.
• Supports third party annotation using GFF formats.
• Settings persist across sessions.
• DNA and GFF dumps.
• Connectivity to different databases, including BioSQL and Chado.
• Multi-language support.
• Third-party feature loading.
• Customizable plug-in architecture (e.g. run BLAST, dump & import many formats, find oligonucleotides, design primers, create restriction maps, edit features)

Overview of setting up GBrowse for your website

To set up gbrowse for your own website^[1]

• Choose which version you want to use
• Obtain and install the appropriate software
  • Make sure it works with sample data
• Getting it to work with your favorite data
• Customizing configuration

The sections below are brief descriptions of each of these aspects and link to more detailed descriptions.

GBrowse Versions

GBrowse 1.X (currently 1.70) is the older series that has been in use since 2002. It is recommended for applications which use a single database only and which must support legacy browsers.

GBrowse 2.0 is a rewrite of the original GBrowse to add dynamic updating via AJAX and a smoother user experience. In addition, it provides administrators with the ability to attach a different genome database to each GBrowse track, making it much easier to manage and update tracks. It also provides a distributed backend system of "slave" renderers, allowing each track to be rendered in parallel on a different machine and significantly increasing performance. GBrowse 2.0 is considered stable,but does not have full internationalization support. In addition, there may be issues with older browsers that do not support newer JavaScript features. See the GBrowse 2.0 HOWTO.

Installation

About Databases

Contacts

Please report bugs to the SourceForge Bug Tracker (select 'Category: Gbrowse').

References