May 7, 2012
Oscar Westesson has contributed a nice demonstration of using JBrowse 1.2.1 to display and compare performance of four different XRate grammars on the poliovirus genome.
View demo Download .zip (35M)
Thanks Oscar!
April 19, 2012
JBrowse 1.3.1 has been released, this is a minor release with fixes for some bugs found in 1.3.0.
Fixed memory-management bug that caused way too much RAM to be used by FeatureTrack loading (flatfile, bam, and biodb-to-json.pl) when loading with very large numbers of reference sequences. Big thanks to Tristan Lubinski for help in isolating this.
Fixed some bugs in BAM support section of setup.sh autosetup script, thanks to Tristan Lubinski for help in isolating this as well.
Added an example document with an iframe running JBrowse in embedded mode in docs/examples/embedded_mode.html
flatfile-to-json.pl now loads the 'score' attribute of features in the JSON.
April 13, 2012
JBrowse version 1.3.0 has arrived!
We have a long list of improvements in this release, some of which have been a long time coming. It's full speed ahead from here: more major new features are just around the corner!
This release comes in two flavors: the "minimal" release (JBrowse-1.3.0-min.zip - 2.0M) that includes only the software and documentation necessary to format your own data and run the browser, and the "full" release (JBrowse-1.3.0-full.zip - 4.7M) that includes the developers' test suite, more sample data files, and developer documentation.
One important note about browser support: as of this 1.3.0 release, JBrowse no longer supports Microsoft Internet Explorer 6.
And now, the Big List of New Features!
location ~* "\.(json'txt)z$" {
add_header Content-Encoding gzip;
gzip off;
types { application/json jsonz; }
}
| Google Chrome 18 | perfect |
| Google Chrome 17 | perfect |
| Mozilla Firefox 11.0 | perfect |
| Mozilla Firefox 10.1 | perfect |
| Mozilla Firefox 10.0.2 | perfect |
| Mozilla Firefox 3.6.28 | nonfunctional |
| Apple Safari 5.1.5 (Lion) | perfect |
| Microsoft Internet Explorer 9 | good |
| Microsoft Internet Explorer 8 | good |
| Microsoft Internet Explorer 7 | minor problems |
| Microsoft Internet Explorer 6 | not tested |
| KDE Konqueror 4.7.4 | nonfunctional |
| KDE Konqueror 4.5.5 | nonfunctional |
| Opera (all versions) | not tested |
March 25, 2012
This is a minor bugfix release, containing fixes for display of unstranded features and a correction to the tutorial HTML file that incorrectly suggested using flatfile-to-json.pl to format feature data from a BAM file.
JBrowse 1.2.2 can be downloaded from https://jbrowse.org/releases/jbrowse-1.2.2.zip
March 22, 2012
A new tar.gz file is available, containing a copy of JBrowse 1.2.1 with Human hg19 data. Being based on a more recent version of JBrowse, it should work much better than the previous hg19 tarball releases. Enjoy!
The new file is here: https://jbrowse.org/releases/jbrowse-1.2.1-hg19mini.tar.gz
March 16, 2012
Great news! JBrowse has been accepted to Google Summer of Code 2012 under the Genome Informatics umbrella organization. Many thanks to Reactome's Robin Haw for shepherding the Genome Informatics organization through the application process!
Are you a college undergraduate interested in working on JBrowse this summer? You should consider applying to Google Summer of Code to fund you for the summer! The student application deadline is April 6, 2012.
January 13, 2012
We're excited to report that Robert Buels has joined the JBrowse team as lead developer, effective January 10, 2012. He succeeds Mitch Skinner, who created JBrowse in its modern form and more recently been working with the JBrowse "sister project", WebApollo.
Rob has been active in open-source bioinformatics for many years, contributing to a long list of projects such as GBrowse, BioPerl, Chado, Bio::Chado::Schema, Catalyst, and DBIx::Class. Before joining JBrowse, Rob was employed as Engineering Lead at the Sol Genomics Network, a clade-oriented database for plants centered on the Solanaceae family.
As JBrowse lead developer, Rob is responsible for the project's technical strategy, architecture, planning, and coordination, as well as a large part of the implementation. In the coming months, he intends to focus on helping JBrowse mature as a project: solidifying its development infrastructure and incorporating new features and contributions from developers around the world.
September 16, 2011
Courtesy of Dave Clements: JBrowse appears (and gets a laugh, for some reason) at 8:41 in this TED talk ("Welcome to the genomic revolution" by Richard Resnick).
In other news, we are happy to report that JBrowse has had its R01 funding support from NHGRI renewed for three years. This enables a whole lot of exciting stuff. We will post further developments here in the coming weeks.
September 15, 2011
The first JBrowse developers' conference call will be held on Monday Sept 19 at 2pm Pacific time. We intend for this to be a monthly event. Call details are below; we hope you will join in.
The main agenda topics for this first call will be:
Please email Ian if there is anything you'd like to have on the agenda.
Call details:
August 3, 2011
Over the summer the JBrowse project has been very capably assisted by two student interns. In Toronto, Natalie Fox has been working on extending the JBrowse user interface and feature set, while in Berkeley, Stephen Cummings has been documenting the existing server-side API. You can track their efforts via the links above, which lead to the GMOD wiki (the new home of JBrowse documentation).
The debt ceiling and budget kerfuffles seem to have delayed things in Bethesda somewhat, with the ripple effect of delaying our process of hiring someone to fill the JBrowse lead developer position, but we hope that will all be resolved soon (watch this space). In the meantime, check out the progress that Natalie has made with faceted browsing and hierarchical track organization -- it is really exciting, and in fact seems quite obviously crucial, as genome databases naturally progress to having hundreds and even thousands of experimental annotation tracks.