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: http://jbrowse.org/install/
The source code for JBrowse can be downloaded from http://github.com/GMOD/jbrowse.
The Getting Started with JBrowse Tutorial provides a basic step-by-step recipe for quickly getting up and running with JBrowse.
For a full JBrowse installation, 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++
svnSubversion client (for fetching the
samtoolscode, needed for BAM support)
- development libraries and header files (not just compiled shared objects) for:
For tips on installing these baseline libraries, see JBrowse Troubleshooting.
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 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 in the
jbrowse/ directory itself.
setup.sh does not need to be run as root or with
4. When 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
For data format specifications, developer information, and so forth, see JBrowse Advanced Topics.
Publications, Tutorials, and Presentations
- 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.
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