Dear Galaxy users,
We are happy to announce the release of version 1.6 of the Genomic HyperBrowser, a analysis web server built on top of Galaxy. This release is a companion to an article recently published in Nucleic Acids Research, to be included with the 2013 Webserver issue:
Sandve, Geir K., et al. "The Genomic HyperBrowser: an analysis web server for genome-scale data." Nucleic acids research (2013) (http://nar.oxfordjournals.org/content/early/2013/04/29/nar.gkt342.full)
To quote the abstract of the article:
"The Genomic HyperBrowser (http://hyperbrowser.uio.no) is an open-ended web server for the analysis of genomic track data. Through the provision of several highly customizable components for processing and statistical analysis of genomic tracks, the HyperBrowser opens for a range of genomic investigations, related to, e.g., gene regulation, disease association or epigenetic modifications of the genome."
In this article, an overview of most of the 42 tools and 83 analyses included with the Genomic HyperBrowser is presented (for the first time) in table form.
The Genomic HyperBrowser will also be presented in the 2013 Galaxy Community Conference (http://wiki.galaxyproject.org/Events/GCC2013), in the Training day workshop titled "Statistical Genome Analysis with Galaxy", and also in a regular talk.
The focus of this release has been on new and revamped tools:
1. A set of new tools has been added:
- Visualize track elements relative to anchor regions - Create high-resolution map of track distribution along genome - Create high-resolution map of multiple track distributions along genome - Extract segments where value is greater/less than threshold
2. A new hypothesis test for 3D-colocalization of genomic elements has been added (along with a tool for easier access to the analysis). This hypothesis tests checks whether the elements of a genomic track is positioned on the DNA (in interphase) closer in 3D than expected by chance. The methodology has been published in a separate article:
Paulsen, Jonas, et al. "Handling realistic assumptions in hypothesis testing of 3D co-localization of genomic elements." Nucleic acids research (2013). (http://nar.oxfordjournals.org/content/early/2013/04/08/nar.gkt227.full)
Included with this analysis are readily preprocessed Hi-C datasets for the cell lines GM06990, GM12878, hESC, K562, and RWPE1 for human (hg19), in addition to cell lines cortex and mEsc for mouse (mm9), all available in several resolutions.
3. The usability of tools has been improved:
- The structure of the HyperBrowser tools has been rearranged, and renamed for easier understanding and use - Help text and usage examples (using Galaxy Pages with embedded histories) has been added to most tools
4. Numerous bug fixes and improvements have been made, including the fixing of several memory leaks.
We hope you will find the Genomic HyperBrowser and new additions useful. Please let us know if you experience any problems, need help with your analysis, or have ideas for new functionality!
For the HyperBrowser team, Sveinung Gundersen
-- Sveinung Gundersen, PhD Student, Bioinformatics, Dept. of Tumor Biology, Inst. for Cancer Research, The Norwegian Radium Hospital, Montebello, 0310 Oslo, Norway