JBrowse

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Status
  • Mature release
  • Active development
  • Active support
Resources

JBrowse is a genome browser with a fully dynamic AJAX interface, being developed as the eventual successor to GBrowse. It is very fast and scales well to large datasets. JBrowse does almost all of its work directly in the user's web browser, with minimal requirements for the server.

Demo

D. melanogaster

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

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

1. Download JBrowse onto your web server.

2. Unpack JBrowse into a directory that is served by your web browser. On many systems, this defaults to /var/www.

   cd /var/www
   tar -xzf jbrowse-*.tar.gz

Make sure you have permissions to write to the contents of the jbrowse/ directory you have just created.

3. Run the automated-setup script, ./setup.sh, which will attempt to install all of JBrowse's (modest) prerequisites for you. For the installation to completely succeed, including support for WIG and BAM data, your system must have:

  • a working internet connection for downloading Perl modules from CPAN
  • compilers for C and C++
  • make
  • the svn Subversion client (for fetching the samtools code, needed for BAM support)
  • development libraries and header files (not just compiled shared objects) for:
    • libpng
    • Zlib
    • GD

For tips on installing these baseline libraries, see JBrowse Troubleshooting.

4. When you can see the included Volvox example data, you are ready to configure JBrowse to show your own data! Proceed to the JBrowse Configuration Guide.

JBrowse Configuration Guide

JBrowse Advanced Topics

For data format specifications, developer information, and so forth, see JBrowse Advanced Topics.

Contact

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

In particular, requests for help should be directed to gmod-ajax@lists.sourceforge.net.

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+)

JBrowse Development

JBrowse is an open-source project, started and managed by the laboratory of Ian Holmes at the University of California, Berkeley.

The JBrowse source code repository is kept on GitHub. Please feel very free to fork the code on GitHub and make modifications and improvements, submitting pull requests. GitHub has a very nice tutorial on how to get started with this style of development.

As of January 2012, the lead developer of JBrowse is Robert Buels. Most of JBrowse was originally written by Mitch Skinner.

There is a mailing list for developers, and there is usually a teleconference on the 3rd Monday of the month at 2pm Pacific US time. We welcome participation from Please contact Robert Buels if you would like to listen in or participate.

Presentations

Date Presenter Venue Links
April 2012 Robert Buels GMOD 2012 Community Meeting PDF
January 2012 Robert Buels Plant and Animal Genome (PAG) XX PDF
April 2010 Mitch Skinner UCSC genome browser group ("genecats") meeting PDF
August 2009 Ian Holmes GMOD Community Meeting Talk summary | PDF
January 2009 Mitch Skinner GMOD Community Meeting Talk summary | PDF
July 2008 Ian Holmes GMOD Community Meeting Talk summary | PDF