JBrowse 1.4.0 has been released! There are two headline features in this release: a new, extremely powerful faceted track selector that makes it easy for users to search through hundreds or thousands of tracks based on their metadata, and much better support for large numbers of reference sequences, enabled by retiring the old reference sequence dropdown selector in favor of adding a new find-as-you-type feature to the location box.
A demonstration of the faceted track selector can be seen here. This contains a snapshot of the modENCODE track metadata taken from http://data.modencode.org. Note that the track data and reference sequences in this track selection demo are not real: the reference sequences and wiggle data are all just copies of the volvox wiggle test track from the JBrowse test suite.
As is becoming the norm, this release comes in two flavors: the “minimal” release (JBrowse-1.4.0-min.zip – 2.6M) that includes only the software and documentation necessary to format your own data and run the browser, and the “full” release (JBrowse-1.4.0-full.zip – 5.5M) that includes the developers’ test suite, more sample data files, and developer documentation.
There have been lots of improvements over the 1.3 series:
- Added a full-featured faceted track selector for users that have
many (hundreds or thousands) of tracks. This can be turned on by
trackSelectorType config variable to “Faceted”. See
the JBrowse wiki for more documentation on how to use faceted track
selection. (issue #95)
- Removed the dropdown selector for reference sequences in favor of
making the location box auto-complete reference sequence and
feature names. This makes JBrowse much more scalable to large
numbers of reference sequences. (fixes issues #3, #60, and #101)
- Added a vertical-scrolling marker on the right side of the track
pane, making it much easier to discern the vertical position of the
track display. (issue #93).
- biodb-to-json.pl and flatfile-to-json.pl now load all available
feature data: all attributes of features are now encoded in the
JSON and are available for use by feature callbacks. (issue #72)
- Feature labels now do not scroll off screen if any part of the
feature is still visible (fixes issue #62).
- Added jbrowse_conf.json, a default JSON-format configuration file,
to the JBrowse root directory. Makes it easier to get started
with more advanced JBrowse configuration.
- JBrowse instances now report anonymous usage statistics to the JBrowse developers. This data is very important to the JBrowse project,
since it is used to make the case to grant agencies for continuing
to fund JBrowse development. No research data is transmitted, the
data collected is limited to standard Google Analytics, along with
a count of how many tracks the JBrowse instance has, how many
reference sequences are present, their average length, and what
types of tracks (wiggle, feature, etc) are present. Users can
disable usage statistics by setting “suppressUsageStatistics: true”
in the JBrowse configuration.
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.
Download .zip (35M)
JBrowse 1.3.1 has been released, this is a minor release with fixes for some bugs found in 1.3.0.
- JBrowse-1.3.1-min.zip – 2.0MB
- Includes all that is needed for running JBrowse and formatting your own data.
- JBrowse-1.3.1-full.zip – 4.7MB
- Includes developer API documentation, developer test suites, additional sample data
Changes in this release
* 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
* 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
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!
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 http://jbrowse.org/releases/jbrowse-1.2.2.zip
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: http://jbrowse.org/releases/jbrowse-1.2.1-hg19mini.tar.gz
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.
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.
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.
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:
- Introductions; quick survey of projects built on, or with, JBrowse
- JBrowse funding situation
- JBrowse software developments
- JBrowse and Web-Apollo
- Any other business
Please email Ian if there is anything you’d like to have on the agenda.
- Dial Toll-Free Number: 866-740-1260 (U.S. & Canada)
- Enter access code 4867508#