There have been a number of changes since the last update that was posted.
First of all, we've switched our versioning system to git, this should make it more straight-forward for more contributors to join.
We've added some extra instructions to be used in session files, this should make session files more versatile.
Redesign rendering of read tracks which should speed up rendering significantly.
Added wild cards to motif searches.
Added code automatic plugin installation option in session files.
Changes in GenomeView
- revamped save dialog to be more comprehensive and intuitive
- ghost outline for total coverage is lighter
- comparative annotations show with intron-exon structure
- use synonym service to find a common name for data entries
- remember last loaded data an location for next start-up
- confirm dialog when closing GV
- location and individual config options can be specified in sessions files
Changes in JAnnot
- fixed issue in EMBL parser for valueless keys
Biggest novelty over the past few months is the ability to create and visualize strand-specific coverage plots.
To create these files, you can use the latest version of tdformat
I've started a twitter account to make smaller announcements as they come online, so feel free to follow @GenomeView to stay up to date on any new developments.
We are pleased and proud to announce that the first GenomeView manuscript has (finally) been published.
GenomeView: a next-generation genome browser
Thomas Abeel; Thomas Van Parys; Yvan Saeys; James Galagan; Yves Van de Peer
Nucleic Acids Research 2011; doi: 10.1093/nar/gkr995
The recent releases between 1682 and 1805 have added a number of new feature to GenomeView, a number of improvements to existing features as well as a whole set of bug fixes.
From now on, the bigWig format, that's been in use over at UCS, is supported by GenomeView. bigWig is used to store large continuous value data files.
The save and export functionality has been expanded to allow more fine grained control of what data has to be saved.
Illumina's technologies have the potential to help us understand diseases and the living world around us at the molecular level. Unlocking that knowledge will enable radical improvements in human health and quality of life over the next decade. A key component to achieving this vision lies in empowering and accelerating the analysis, visualization and interpretation of the data being generated with these technologies. With this in mind, Illumina is announcing the iDEA (Illumina’s Data Excellence Award) Challenge.
GenomeView won the Most Creative Visualization award.
Release 1682 is again a step forward in making GenomeView as user-friendly as possible.
Major new features:
Based on user feedback we have been able to fix another batch of bugs as well as introduce a number of convenient new features. Keep the reports coming, we appreciate all feedback.
GenomeView now remembers in which order tracks are, and will no longer jumble them if you switch chromosomes or when you restart GenomeView. It also remembers which track you made invisible.
The pileup and formats are now also loaded using background threads, which drastically improves the responsiveness of the GUI.
Based on user feedback a number of bugs have been fixed. Furthermore, we have tried to improve usability with a number of small improvements.
Release 4 of the genome of Rattus norvegicus is now included in the Genome Explorer.