[Gmod-ajax] JBrowse 1.5.0 released, includes direct BigWig access!

[Robert B. <rb...@gm...>]

Hello all,

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 theDalliance Genome 
Explorer <http://www.biodalliance.org/>that can read wiggle data 
directly from compressedBigWig files 
<http://genome.ucsc.edu/goldenPath/help/bigWig.html>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 seenhere 
<http://jbrowse.org/code/JBrowse-1.5.0-full/index.html?loc=ctgA%3A6481..27220&tracks=DNA%2Cvolvox_microarray.bw%2Cvolvox_microarray.wig&data=sample_data%2Fjson%2Fvolvox>.

As usual, this release comes in two flavors: the “minimal” release 
(JBrowse-1.5.0-min.zip 
<http://jbrowse.org/wordpress/wp-content/plugins/download-monitor/download.php?id=12>– 
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 
<http://jbrowse.org/wordpress/wp-content/plugins/download-monitor/download.php?id=11>– 
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).

    *

      Added a|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|wiggle_xyplot|glyph type
      (i.e.|Bio::Graphics::Glyph::wiggle_xyplot|).

    *

      Added highly configurable behavior for left-clicking and
      right-clicking features in HTML-based feature tracks. If a
      |menuTemplate|option 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
      context menus.

    *

      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,|add-track-json.pl|that developers
      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
      default.

-- 

Robert Buels
Lead Developer
JBrowse - http://jbrowse.org