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

Fri Feb 4 22:14:35 UTC 2011

On Fri, Feb 4, 2011 at 1:29 PM, Suzanna Lewis <suzi at berkeleybop.org> wrote:

> Gregg? Maybe you and I should talk about this. And perhaps you could get an
> idea when you are in Hinxton of what it takes to organize one of these.
>
> Not a promise, but it might be possible for us to host this in Berkeley/Bay
> Area. We'll explore feasibility a bit more first. Be good to how many people
> might be interested.
>

Count me in!

Steve

> -S
>
> On Feb 4, 2011, at 12:57 PM, Andy Jenkinson wrote:
>
> > Hi David,
> >
> > I guess one of the big reasons to want a proxy is it allows you to use
> DAS sources you don't control, which is obviously potentially a really big
> benefit with so many DAS/1 sources around. I don't know if this is what Jim
> is trying to achieve though. In truth this has always been the difficulty
> with the das/das2 tech divide really, with such a huge existing
> implementation base there's a very high "activation energy" in switching!
> >
> > What was the issue with the ensembl servers?
> >
> > Jon and I have talked a few times about organising a DAS workshop in
> North America, we just need someone to host (and to an extent fund) it. Do
> you have any suggestions? Almost all of the attendees for our workshops are
> from Europe, in fact lots are from Hinxton. So what sort of demand do you
> think there would be stateside for such an event? Enough for a standalone
> workshop, or more conducive to an add-on to or collaboration with another
> event?
> >
> > Maybe we can look into webcasting the talks? No idea how to go about this
> though!
> >
> > On 4 Feb 2011, at 19:13, David Nix wrote:
> >
> >> 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.
> >>>
> >>> _______________________________________________
> >>> DAS mailing list
> >>> DAS at lists.open-bio.org
> >>> http://lists.open-bio.org/mailman/listinfo/das
> >>>
> >>
> >> _______________________________________________
> >> DAS mailing list
> >> DAS at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/das
> >>
> >>
> >> _______________________________________________
> >> DAS mailing list
> >> DAS at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/das
> >
> >
> > _______________________________________________
> > DAS mailing list
> > DAS at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/das
>
>
> _______________________________________________
> DAS mailing list
> DAS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/das
>