JBrowse 1

JBrowse 1.6.4 bugfix release

October 16, 2012

JBrowse 1.6.4 has been released, containing fixes for some small issues in the 1.6.3 release.

Files for download:

  • JBrowse-1.6.4-min.zip - 2.8M

  • JBrowse-1.6.4-full.zip - 27.3M Changes in this release:

  • Improvements to the scalability of generate-names.pl. Many thanks to Steffi Geisen for her ongoing help with this.

    *   Users can now manually specify which tracks will be indexed to

    enable autocompletion and searching for their feature names in the JBrowse location box. * The lazy-trie name indexing structure now correctly handles the case of large numbers of features that may share the same name. Before, it was generating files that were too large for the client to handle.

  • Fixed off-by-one error in Wiggle track display code: wiggle data was incorrectly displayed shifted one base to the left of its proper position. Thanks to Steffi Geisen for noticing this.

  • Fixed bug in which the reference-sequence selection box did not automatically update in all situations to reflect the current reference sequence.

JBrowse 1.6.3 bugfix release

September 28, 2012

JBrowse 1.6.3 has been released, containing fixes for some small issues in the 1.6.2 release.

Files for download:

  • JBrowse-1.6.3-min.zip - 2.8M

  • JBrowse-1.6.3-full.zip - 27.3M Changes in this release:

  • Fixed bug with shift-rubberband-zooming not working on Windows (issue #150) (Erik Derohanian).

  • Fixed "Can't locate JSON.pm" errors with add-track-json.pl.

  • Added a reference-sequence-selection dropdown box, similar to the old one, that is shown by default if fewer than 30 reference sequences, otherwise it's off unless refSeqDropdown: true is set in the configuration (issue #138).

  • Fixed bug in which popup dialog boxes showing other websites showed the website in only the top portion of the dialog box. Only present in some browsers (issue #149).

  • Fix coordinate display bug in feature detail popups. The feature's position was being displayed in interbase coordinates, but should be displayed in 1-based coordinates. Thanks to Steffi Geisen for pointing this out.

  • Added a style.height option to Wiggle tracks to control the track's height in pixels (issue #131) (Erik Derohanian).

  • Added support for a style.trackLabelCss configuration variable to allow customizing the appearance of the label for a particular track (issue #4) (Erik Derohanian).

JBrowse 1.6.2 bugfix release

September 10, 2012

JBrowse 1.6.2 has been released, containing fixes for some small issues in the 1.6.1 release.

Files for download:

  • JBrowse-1.6.2-min.zip - 2.8M

  • JBrowse-1.6.2-full.zip - 27.3M Changes in this release:

  • Fixed feature-layout performance problem when zoomed very far in on features that are much larger than the viewing window.

  • Added a default menuTemplate to all HTML-based features, so that all HTML features now have a right-click menu by default.

  • Add css configuration variable that allows users to specify either strings or URLs containing CSS to add.

  • improved bin/ucsc-to-json.pl error messages

  • bin/add-track-json.pl now replaces tracks in the target configuration if they have the same label.

@rbuels and JBrowse at the Semantic Web BioHackathon 2012

September 7, 2012

I had the great honor of being invited to the [BioHackathon 2012](BioHackathon 2012), held this past week in Toyama, Japan and funded by Japan's National Bioscience Database Center (NBDC) and Database Center for Life Science (DBCLS). It's been an exhausting week of immersing myself in Semantic Web technologies: RDF, SPARQL, SADI, and lots and lots of ontologies. A lot of work still needs to be done, but there really are revolutionary capabilities coming to bioinformatics from this direction.

At the hackathon, I worked on a SPARQL-based data backend for JBrowse, which will be released as part of the upcoming JBrowse 1.7.0. It is shaping up to be surprisingly fluid, especially given the less-than-speedy reputation of today's triple stores.

Until it is merged into master, work on the JBrowse triple store can be seen at https://github.com/GMOD/jbrowse/compare/master...triplestore

JBrowse 1.6.1 bugfix release

August 28, 2012

JBrowse 1.6.1 has been released, containing fixes for some small issues in the 1.6.0 release.

Files for download:

  • JBrowse-1.6.1-min.zip - 2.8M

  • JBrowse-1.6.1-full.zip - 27.3M Changes in this release:

  • JBrowse now attempts to prevent feature labels being obscured by track labels by keeping the feature labels a bit further away from the left side of the view, if possible.

  • Fixed bug in which welcome page was not shown when JBrowse has not been configured yet (issue #130).

  • Fixed bug in which passing tracklist=0 (as when running the browser in embedded mode) caused JBrowse to crash (issue #132).

  • Added dependency on Bio::GFF3::LowLevel::Parser 1.4, which has an important bugfix related to multi-location features (issue #109).

JBrowse 1.6.0 released, includes feature descriptions and more!

August 25, 2012

I'm very pleased to announce the release of JBrowse 1.6.0! This release is not quite as major as the previous two releases, but there are still some nice things added.

As usual, this release comes in two flavors: the "minimal" release (JBrowse-1.6.0-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-1.6.0-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 1.6.0:

  • Added description capabilities to HTML-based features, similar to GBrowse's descriptions. If zoomed in far enough (as defined by style.descriptionScale), adds a second line of text below the feature's label that shows the content's of the featur's Note or description attribute (issue #67).

  • Give prepare-refseqs.pl the capability to load reference sequences from embedded FASTA sections in GFF3 files (issue #128).

  • Configuration files can now recursively include eachother, and tracks sections are merged intelligently.

  • Made sequence tracks not disappear when zoomed out too far to see base pairs. Instead, sequence tracks simply display lines suggesting that DNA would be visible at higher magnification. (issue #124).

  • Double-clicking track labels in the simple track selector now turns the track on (issue #123).

  • Fixed bug in BigWig tracks that use the "scale": "log" option: did not render properly when the wiggle data included 0's. This was due to the fact that the origin was being mapped to Infinity. Thanks to the Mockler Lab for the fix! (issue #127).

  • Fixed bug in NCList binary search code in which zero-length features at node boundaries would not be found (fix by Ed Lee).

  • Fixed bug in which dragging the scroll bar on the simple track selector can sometimes cause a drag-and-drop to erroneously begin (issue #89).

  • Fixed some bugs in the layout of HTML-based features in which features in different blocks would overlap in some circumstances. Under the hood, replaced the contour-based layout engine with a simpler, not-much-slower implementation that is more correct in the general case (issue #122).

  • Fixed a bug with vertical centering of strand arrows and other sub-elements of HTML-based features.

JBrowse 1.5.0 released, includes direct BigWig access!

August 13, 2012

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).

  • 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.

JBrowse 1.4.2 released

July 12, 2012

JBrowse 1.4.2 has been released, containing some small fixes for issues in the 1.4.1 release.

  • JBrowse-1.4.2-min.zip - 2.6M

  • JBrowse-1.4.2-full.zip - 5.5M Changes in this release:

  • Restore support for histScale, subfeatureScale, and labelScale in --clientConfig command-line options and track configuration JSON. Thanks to Hernán Bondino for pointing this out.

JBrowse 1.4.1 released

July 10, 2012

JBrowse 1.4.1 has been released, containing some small fixes for issues in the 1.4.0 release.

  • JBrowse-1.4.1-min.zip - 2.6M

  • JBrowse-1.4.1-full.zip - 5.5M Changes in this release:

  • Made displayColumns option for the faceted track selector case-insensitive, and interpret a column name of "Name" as meaning the track's key.

  • bam-to-json.pl now filters out alignments that are not at least two nucleotides in length. Thanks to Tristan Lubinski for assistance.

  • Introduced limits on the sizes of cookies that can be set, preventing '400 bad request' errors (issue #113).

JBrowse 1.4.0 released, includes faceted track selection!

June 14, 2012

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 https://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 setting the 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.
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