- mature release
- active development
- active support
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.
Visit the JBrowse website.
Download JBrowse from http://jbrowse.org/install/
The Getting Started with JBrowse Tutorial provides a basic step-by-step recipe for quickly getting up and running with JBrowse.
0. Install libpng, Zlib, and GD development libraries, plus make and a C compiler. On Ubuntu, you could do this with:
sudo apt-get install libpng-dev libgd2-noxpm-dev build-essential
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
cd /var/www unzip JBrowse-*.zip
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 in the
jbrowse/ directory itself. Note that
setup.sh does not need to be run as root or with
4. Visit http://your.machine.address/jbrowse/index.html?data=sample_data/json/volvox. If you can see the included Volvox example data, you are ready to configure JBrowse to show your own data!
See the JBrowse Configuration Guide for information on:
- Formatting reference sequences (e.g. from FASTA files, or a Chado database)
- Feature Tracks (e.g. from BED or GFF files, a Chado database, or the UCSC genome browser)
- Image Tracks (e.g. from WIG files)
- Wiggle/BigWig Tracks
- Name Search and Autocompletion
- Removing tracks
- Compressing data stored on the server
- URL control
- Faceted track selection
- Anonymous usage statistics
To upgrade an existing JBrowse (1.3.0 or later) to the latest version, simply move its data directory (and
jbrowse_conf.json if you are using it) into the directory of a newer JBrowse, and the new JBrowse will display that data.
To upgrade a 1.2.x JBrowse, copy its data directory into the new JBrowse directory, and point your browser at compat_121.html in the new JBrowse directory, instead of index.html.
For data format specifications, developer information, and so forth, see JBrowse Advanced Topics.
Publications, Tutorials, and Presentations
- JBrowse Tutorial - from the 2012 GMOD Summer School
- Getting Started with JBrowse Tutorial - part of the JBrowse documentation
- Tutorial from 2010 - from the 2010 GMOD Summer School - Americas
- August 2012 - presentation given as part of the 2012 GMOD Summer School: PDF
- April 2012 - GMOD 2012 Community Meeting, Robert Buels: PDF
- January 2012 - Plant and Animal Genome (PAG) XX: PDF
- April 2010 - UCSC genome browser group ("genecats") meeting: PDF
- August 2009 - GMOD Community Meeting: Talk summary
Contacts and Mailing Lists
Please direct questions and inquiries regarding JBrowse to the mailing lists below.
Requests for help should be directed to firstname.lastname@example.org.
|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+)|
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.
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 anyone and everyone. Please contact Robert Buels if you would like to listen in or participate.
More on JBrowse