I’m very pleased to announce the release of JBrowse 1.5.0! There are three headline features in this release. First, we’ve integrated a direct-access BigWig data backend, adapted from the Dalliance Genome Explorer that can read wiggle data directly from compressed BigWig files stored on your web server. Second, there is now a beautiful, full-featured canvas-based
Wiggle track type. Third, we have a very powerful new click system that allows JBrowse administrators complete flexibility in configuring what happens when a user left- or right-clicks a feature in an HTML-based feature track, including right-click context menus.
A demonstration of JBrowse 1.5.0 showing a test BigWig-based wiggle track (alongside an old-style image-based wiggle track for comparison) can be seen here, and a whole-genome RNA-seq profile of tomato, with corresponding gene models, can be seen here.
As usual, this release comes in two flavors: the “minimal” release (JBrowse-1.5.0-min.zip – 2.8M) that includes only the software and documentation necessary to format your own data and run the browser, and the “full” release (JBrowse-1.5.0-min.zip – 27.2M) that includes the developers’ test suite, more sample data files, and developer documentation.
Here is the full list of new improvements in 1.5.0:
Added a direct-access storage driver for BigWig data files, based
on code from the Dalliance Genome Explorer by Thomas Down. BigWig
file access is supported now by the current versions of all major
browsers except Internet Explorer (which is expected to work when
version 10 is released along with Windows 8).
canvas-based wiggle track implementation for quantitative
data that, when used with the new BigWig storage backend, removes
the need to pre-generate rendered images of wiggle data. Its
display is also highly configurable, with configuration options
modeled on the GBrowse
Added highly configurable behavior for left-clicking and
right-clicking features in HTML-based feature tracks. If a
menuTemplateoption is specified in the track configuration,
right-clicking a feature brings up a context menu, the items in
which can be configured to do nearly anything, but that are easy to
configure for the very common use case of wanting to display
content from a certain URL. Feature left-clicks are also
configurable using the same mechanism. Thanks to Alexie
Papanicolaou and Temi Varghese for the initial implementation of
Improved the default HTML feature left-click dialog box. It is now
both prettier, and more comprehensive, displaying all available
data for the feature.
Added a small helper script,
and advanced users can use to programmatically add a block of track
configuration JSON to an existing JBrowse configuration file.
Improved / fixed vertical alignment of sub-elements of HTML
features, including subfeatures and the arrowheads that show
strand. All elements in a feature are now vertically centered by