Revision as of 14:35, 16 February 2012

JBrowse is a genome browser with a fully dynamic AJAX interface. JBrowse renders most tracks using client-side JavaScript, with JSON as its data transfer format. JBrowse is being developed as the official successor to GBrowse.

Demo

D. melanogaster

Quick Start: Tutorial

The Getting Started with JBrowse Tutorial provides a basic step-by-step recipe for quickly getting up and running with JBrowse.

Installation

See Installing JBrowse on Mac OS X and Linux for step-by-step installation instructions.

Download JBrowse

Prerequisites

• Perl modules from CPAN:
  • BioPerl 1.6
  • JSON
  • JSON::XS (optional, for speed)
  • Heap::Simple
  • Heap::Simple::XS
  • PerlIO::gzip
  • Devel::Size
• libpng

Usage

• General Usage, including information about:
  • The JBrowse user interface
  • Creating sequence tracks (e.g. from FASTA files, or a Chado database)
  • Creating feature tracks (e.g. from BED or GFF files, a Chado database, or the UCSC genome browser)
  • Creating image tracks (e.g. from WIG files)
  • Making features searchable by name
  • Removing tracks

• Additional topics:
  • Using Configuration Files
  • Using a Database

JBrowse Development

JBrowse is an open-source project. Contributions are encouraged and welcomed. There is a developer mailing list and teleconferences on the 3rd Monday of the month at 2pm Pacific US time. Please contact Ian Holmes if you want to participate in the call.

The JBrowse source code is kept on GitHub

Contact

Please direct questions and inquiries regarding JBrowse to the mailing lists below.

Presentations

• Talk at the April 21, 2010 UCSC genome browser group ("genecats") meeting.
• JBrowse: A next-generation genome browser - Presentation by Ian Holmes at the August 2009 GMOD Meeting. See the talk's summary for more.
• JBrowse - Presentation by Mitch Skinner at the January 2009 GMOD Meeting. See the talk's summary for more.
• Presentation by Ian Holmes at July 2008 GMOD Meeting. See the talk's summary for more.

See also

• JBrowse Home Page
• JBrowse Quick Tutorial - JBrowse administration.
• JBrowseDev/Upcoming Future JBrowse features