[DAS] Status of Trellis/Ivy and DAS1 to DAS2 proxying

[David Nix]

Hello Jim,

If I make a suggestion.  If you're looking to visualize genomic data in IGB, it would be best to use a DAS/2 server such as the Classic (command line) or GenoPub (web app/ relational database) GenoViz DAS/2 server.  DAS/2 is well suited to moving large amounts of sliced graph (gr, sgr, bedgraph, wig, bar, useq...) and alignment data (ie BAM) to client apps.  We're continuing to develop the GenoPub DAS/2 server with 5 year grant support from NHLBI so expect continuing improvements (bulk uploading and file conversion, annotation via ontologies, super group visibility settings, additional file formats, etc.). See http://bioserver.hci.utah.edu/BioInfo/index.php/Software:DAS2  and our paper http://www.biomedcentral.com/1471-2105/11/455

GenoViz folks, correct me if I'm wrong here but I believe the GenoViz DAS/2 server supports  DAS xml datasets so moving data from a DAS/1 server to DAS/2 wouldn't require any data reformatting.  Although for large datasets, it's best to use one of the compressed binary data formats such as bar, bam, or useq.

IGB comes pre configured with the UCSC and Ensembl DAS/1 servers.  This works well for accessing their small annotation datasets (gene models: refseq, knowngenes), but the graph distribution wasn't functional the last I checked.  The problem appeared to be from the server side.

-cheers, David

P.S. I wish I could attend the DAS workshop this year and show you what we've been up to.  Any chance of getting a Skype conference call with posted presentations?  Would be great if someone hosted a DAS Workshop in the US.


On 2/4/11 8:19 AM, "Gregg Helt" <gregghelt at gmail.com> wrote:

The core genomancer code is pretty stable, most of the recent work is
in plugins (and some work in the core to allow more extensive
plugins).

You should be able to get a working DAS1-->DAS2 proxy running from
the current head of the Trellis SVN repository -- you would just need
to add a web.xml config file with servlet parameters to get it going in a
servlet container like Tomcat, or alternatively run the built-in Jetty server
(ExampleJettyDas2Server) and edit servlet parameters directly in code.

But if the intent is to load DAS 1.x data into IGB, I don't think you
need to use Trellis.  Th latest IGB (6.4.1 loaded via WebStart)
already supports DAS 1.5 access.  In the "Data Access" tab, under
"Choose Data Sources and Data Sets" section click the "Configure"
button.  This brings up a window with a "Data Sources" tab, and in
that tab you can click the "Add" button to bring up a dialog that lets
you select "DAS" for the data source type, and enter the URL for a DAS
server.  This worked fine for loading data from the UCSC DAS 1.5
server -- I haven't tried accessing data from any other DAS servers
recently.

I'm forwarding to the genoviz-devel list for IGB developments and
discussion, to see if anyone currently working on IGB can add any more
info.

On Tue, Feb 1, 2011 at 7:51 AM, Jim Procter
<jprocter at compbio.dundee.ac.uk> wrote:
>
> Hi all (but Gregg in particular!)
>
> I was wondering whether the DAS1 to DAS2 proxy component of Trellis/Ivy
> in the Genomancer project (http://code.google.com/p/genomancer/) is
> stable enough to use. We'd like to set up an in house DAS1->2 proxy and
> it looks like there's a moderate amount of commit activity in the
> project at the moment, making me a little nervous about attempting to
> use the code in a production(ish) setting.
>
> many thanks in advance,
> Jim.
>
> --
> -------------------------------------------------------------------
> J. B. Procter  (JALVIEW/ENFIN)  Barton Bioinformatics Research Group
> Phone/Fax:+44(0)1382 388734/345764  http://www.compbio.dundee.ac.uk
> The University of Dundee is a Scottish Registered Charity, No. SC015096.
>
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