Difference between revisions of "JBrowse"
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= Presentations = | = Presentations = | ||
| − | + | {| class="wikitable" | |
| − | + | |- | |
| − | + | |April 2010 | |
| − | + | |Mitch Skinner | |
| + | | UCSC genome browser group ("genecats") meeting | ||
| + | | [[Media:JBrowse-UCSC-4-21-10.pdf|PDF]] | ||
| + | |- | ||
| + | |August 2009 | ||
| + | |Ian Holmes | ||
| + | |[[August 2009 GMOD Meeting|GMOD Community Meeting]] | ||
| + | |[[ August 2009 GMOD Meeting#JBrowse | Talk summary ]] | [[Media:Aug2009JBrowse.pdf|PDF]] | ||
| + | |- | ||
| + | |January 2009 | ||
| + | |Mitch Skinner | ||
| + | |[[January 2009 GMOD Meeting|GMOD Community Meeting]] | ||
| + | |[[ January 2009 GMOD Meeting#JBrowse | Talk summary ]] | [[:Image:Jan2009JBrowse.pdf|PDF]] | ||
| + | |- | ||
| + | |July 2008 | ||
| + | |Ian Holmes | ||
| + | |[[July 2008 GMOD Meeting|GMOD Community Meeting]] | ||
| + | |[[ July 2008 GMOD Meeting#GBrowse 3.0 | Talk summary ]] | [[:Image:GBrowse3GMOD2008.pdf|PDF]] | ||
| + | |- | ||
| + | |} | ||
= See also = | = See also = | ||
Revision as of 01:07, 4 April 2012
- Mature release
- Active development
- Active support
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.
Contents
Demo
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.
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:
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.
The lead developer of JBrowse is Robert Buels. Much of the code was originally written by Mitch Skinner.
Developer Communication
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 Ian Holmes if you want to participate in the call.
Presentations
| April 2010 | Mitch Skinner | UCSC genome browser group ("genecats") meeting | |
| 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 |
See also
- JBrowse Home Page
- JBrowse Quick Tutorial - JBrowse administration.
- JBrowseDev/Upcoming Future JBrowse features
