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

[PubMed] - [Nucleic Acids Research]

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.

Most creative visualization award @ Illumina iDEA challenge

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:

• Automagic index creation: If you try loading a file that is not yet indexed, GenomeView will now ask to do it for you.
• Speed and memory improvements: We have significantly optimized the way annotation feature and sequences are handled so it is easier to load monstrous draft genomes with 65,000 contigs and 500,000 annotation items without needing a gigantic computer.

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.

Selected changes
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.

In this release of GenomeView the visualization of individual short reads, as well as coverage plots has been significantly improved.

With directional RNA-seq the read sense is now visually indicated, even for paired-end data. Hovering over individual reads will show detailed information about each read. When reads of a pair overlap, this is visually indicated.

The main new feature we want to highlight in this release is the ability to control the GenomeView applet from the webpage in which it is embedded using JavaScript. The details are laid out in the integration manual. In short you can use JavaScript to load data and move around in GenomeView. In this context we have also made available a minimal applet that has no menu or side bar.

Furthermore, several options to alter the appearance of GenomeView on start-up have been added.

Release 1370 focuses on making the first-time-user experience a lot more agreeable by providing the Genome Explorer.

Genome Explorer is a portal to a set of instances of GenomeView with preloaded data. When you start GenomeView you will now be presented with the Genome Explorer which allows you to load data from a number of genomes. For now, we provide a number of tutorial genomes which illustrate a number of features of GenomeView.

Release 1320 fixes a number of bugs that prevented pile up tracks from showing up when loading them from a URL. Under the hood, we are also working on getting the indexing done on multiple alignment files, so expect more on that in the next release.