On Fri, Feb 4, 2011 at 1:29 PM, Suzanna Lewis <[email protected]> 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" <[email protected]> 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 > >> <[email protected]> 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 > >>> [email protected] > >>> http://lists.open-bio.org/mailman/listinfo/das > >>> > >> > >> _______________________________________________ > >> DAS mailing list > >> [email protected] > >> http://lists.open-bio.org/mailman/listinfo/das > >> > >> > >> _______________________________________________ > >> DAS mailing list > >> [email protected] > >> http://lists.open-bio.org/mailman/listinfo/das > > > > > > _______________________________________________ > > DAS mailing list > > [email protected] > > http://lists.open-bio.org/mailman/listinfo/das > > > _______________________________________________ > DAS mailing list > [email protected] > http://lists.open-bio.org/mailman/listinfo/das > _______________________________________________ DAS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/das
