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. -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
