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
trackSelectorTypeconfig 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.