JBrowse

Status

• Mature release
• Active development
• Active support

Resources

• Home Page
• Quickstart
• Blog
• Configuration
• Demo
• Mailing Lists

JBrowse is a genome browser with an AJAX-based interface. JBrowse renders most tracks using client side JavaScript and JSON as its data transfer format. JBrowse is the official successor to GBrowse.

Demo

D. melanogaster

Installation

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

Prerequisites

• From CPAN:
  • BioPerl 1.6
  • JSON
  • JSON::XS (optional, for speed)
• libpng

Usage Notes

• 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

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

Downloads

From GitHub.

Screenshots

Demo screenshot from 2009/03/24, showing region of Drosophila melanogaster 2R.

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.

Contact

Mailing lists

	Mailing List Link	Description	Archive(s)
JBrowse	gmod-ajax	JBrowse help and general questions.	Nabble (2010/05+), Sourceforge
	jbrowse-dev	JBrowse development discussions.	Nabble (2011/08+)

Original author

Mitch Skinner