JBrowse 1

JBrowse 1.3.0, a major release!

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!

  • Added support for** "rubberband" dynamic zooming**, in which users can click and drag to select a region to zoom to. Dragging on any scale bar, or shift-dragging on the main track pane, triggers a dynamic zoom.
  • Correcting a long-standing oversight, wiggle data tracks and feature histograms now have numerical y-axis scales that show the numerical values of the data.
  • Server-side data-formatting scripts now support a** --compress option** to compress (gzip) feature and sequence data to conserve server ** disk space**. Using this option requires some web server configuration. Under Apache, AllowOverride FileInfo (or AllowOverride All) must be set for the JBrowse data directories in order to use the included .htaccess files, and mod_headers and mod_setenvif must be installed and enabled. Under nginx a configuration snippet like the following should be included in the configuration:
      location ~* "\.(json'txt)z$" {
               add_header Content-Encoding  gzip;
               gzip off;
               types { application/json jsonz; }
      }
  • flatfile-to-json.pl: now much faster and more memory-efficient, especially for GFF3 files. Remember that '###' directives are very important to have in large GFF3 files! Also removed nonfunctional --extraData switch.
  • Added ability to turn off some JBrowse UI panels via URL arguments to the default index.html, or via arguments to the Browser constructor itself. Can dynamically turn off the navigation box, the overview panel, and the track list, respectively. When all of these are off, and if run in an iframe, JBrowse is running in an "embedded mode" that looks similar to the output of GBrowse's gbrowse_img script, with the exception that the view in this case is a fully functioning, scrollable and zoomable JBrowse. See the GMOD wiki (https://gmod.org/wiki/JBrowse) for more on how to set up embedded mode. Thanks to Julie Moon, a co-op student working at OICR, for this work!
  • Improved graphical look and feel.
  • Browser support for this release:
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
  • Added an automated-setup script, setup.sh, that tries to install Perl prerequisites, format Volvox example data, and install Wiggle and BAM support (fetching samtools from SVN if necessary) automatically.
  • Navigating to JBrowse with missing or malformed configuration or data will now bring up an error page with useful messages and links to help documentation, instead of a blank white page.
  • JBrowse data directories now include an Apache .htaccess in their root directory that, if mod_headers is installed and AllowOverride FileInfo or AllowOverride All is enabled, will emit the proper HTTP ** headers to allow cross-origin XHR requests** for the data.
  • A new "Help" link in the upper right, or pressing "?" on the keyboard, brings up a "JBrowse Help" dialog box with basic usage information and links to more help information.
  • Arrowheads indicating strandedness are now drawn inside feature boundaries.
  • Clicking on the overview bar or the main scale bar now centers the view at the clicked position. In addition, while holding down shift, clicking in the main track panel will also center the view at that position.
  • Added bin/remove-track.pl,** a script to remove a track** from a JBrowse data directory. Run bin/remove-track.pl -? to see its documentation.
  • Added build instrumentation to support a JSDoc-based system of developer API documentation. This documentation is still far from complete.
  • Ian Davis contributed code to add a view of the reverse strand of ** the sequence in the DNA track**. Thanks Ian!
  • Fixed bug in which, for some sequence chunk sizes, the DNA bases would display incorrectly.
  • Added minor gridlines to the main track view.
  • Fixed a long-standing off-by-one bug where the window could not be scrolled to view the last base in the reference sequence.
  • Coordinates displayed in the user interface are now 1-based closed ** coordinates**, which are more familiar to most users. Previously, the labels displayed interbase (i.e. 0-based half-open) coordinates.
  • NON-BACKWARDS-COMPATIBLE improvements to the JSON format used for track configuration, feature data, and image data
  • initial support for a new hook system for greater administrator-configurability of feature display
  • support for more than one level of subfeatures
  • Miscellaneous improvements and refactoring of data-formatting Perl code.
  • More detailed POD-based help documentation on all scripts
  • --tracklabel options to all scripts replaced with --trackLabel.
  • New suite of integration tests, and some unit tests, for server-side Perl code.
  • Beginnings of a suite of Selenium-based integration tests for the front-end JavaScript code.
  • Support for Apple touch-based devices merged into normal index.html, so that the same link can be used regardless of the browsing platform.
  • Bug fixed in which non-stranded features do not display properly (a problem with the CSS styles).
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