[DAS] GenoPub GenoViz DAS/2 Server

[David Nix]

Hello Folks,

I wanted to point folks to our recently published DAS/2 paper, http://www.biomedcentral.com/1471-2105/11/455 .

It details three software applications developed for our Microarray/ Next Generation Sequencing and Bioinformatics Core facilities.  One of which is a web app DAS/2 server that provides, among other things, a user friendly interface to the Genoviz DAS/2 server and the ability to distribute both public and private datasets.  This is a light weight application that we hope people will install in their labs and at their institutions and use to distribute massive genomic datasets.  The use of alternative formats, including several binary file types, accelerates the delivery of genomic data more than 100x relative to DAS XML.

Currently, 25 laboratories at the University of Utah are using GenoPub and the Integrated Genome Browser to distribute and visualize ~1100 genomic datasets.  We are also publically hosting ~600 chIP-chip, chIP-seq, and transcriptome datasets from a variety of sources including signal and chIP-seq peak calls from the UCSC ENCODE project and several large chIP-seq mapping projects (Barski et al. Mikkelsen et al.).

Here are some relevant links:


 *   Our production server: http://bioserver.hci.utah.edu:8080/DAS2DB/genopub (guest login: as "guest", pw: "guest")
 *   A demo server you can modify: http://diserafed.hci.utah.edu:8080/das2genopub/genopub (login: "test.user", pw: "test"
 *   Our wiki describing how to upload annotations into GenoPub as well as install your own server: http://bioserver.hci.utah.edu/BioInfo/index.php/Software:DAS2
 *   This software is part of the open source GenoViz project: http://sourceforge.net/projects/genoviz/ .

I can also provide folks with temporary user accounts on our production server if they would rather hold off on instantiating their own DAS/2 server.

-cheers, D


--
David Austin Nix, PhD | Bioinformatics Shared Resource | Huntsman Cancer Institute | 2000 Circle of Hope | SLC, UT 84112 | Rm: 3165 | Vc: 801.587.4611 | Fx: 801.585.6458 | david.nix at hci.utah.edu | Skype/iChat: LiveNix | WebSite: http://bioserver.hci.utah.edu | DAS/2: http://bioserver.hci.utah.edu:8080/DAS2DB/genome