Might we add on to the end/beginning of GI instead of running concurrently (assuming CSHL can oblige)? Perhaps we can consider running a workshop at ISMB next year (California?) should interest be sufficient for an event at GI or the like this year?
I just noticed GI is actually in November though, by the way. On 7 Feb 2011, at 16:58, David Nix wrote: > Hmm... > > There's the Genome Informatics meeting in August at CSHL ( > http://meetings.cshl.edu/meetings/info11.shtml). It's not the bay area and > the organizers might already have a set program. There is a "Databases, Data > Mining, Visualization and Curation" session by Alex Bateman and Ting Wang > though. > > -cheers, D > > > > > On 2/7/11 9:25 AM, "Ann Loraine" <[email protected]> wrote: > > Hi, > > Same for us here at UNC Charlotte. > > Meetings I'm attending next include two major plant science meetings > (Arabidopsis and ASPB) and possibly ISMB in Vienna. > > David are there any other meetings you and your group are planning to > attend? > > The ideal setting would be a meeting where we can do outreach and hold > workshop event(s) for users, but also have a developers meeting where we > discuss future directions for the software, DAS spec, etc. > > Are there other meetings that would be a good fit? > > Best, > > Ann > > On 2/7/11 10:58 AM, "David Nix" <[email protected]> wrote: > >> Ah, that makes sense. >> >> As for a US meeting, there are 3 or 4 folks here at the U of Utah that would >> attend an out of state meeting. The bay area would be ideal (thanks Suzi!). >> It might be best to make this part of a larger genomics/ proteomics meeting >> to >> start. This would draw more folks who are interested in distributing their >> own data and working DAS access into their own applications. Are their any >> appropriate upcoming meetings? >> >> -cheers, D >> >> >> On 2/4/11 1:57 PM, "Andy Jenkinson" <[email protected]> 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 >> >> >> >> ------------------------------------------------------------------------------ >> The modern datacenter depends on network connectivity to access resources >> and provide services. The best practices for maximizing a physical server's >> connectivity to a physical network are well understood - see how these >> rules translate into the virtual world? >> http://p.sf.net/sfu/oracle-sfdevnlfb >> _______________________________________________ >> Genoviz-devel mailing list >> [email protected] >> https://lists.sourceforge.net/lists/listinfo/genoviz-devel > > -- > Ann Loraine > Associate Professor > Dept. of Bioinformatics and Genomics, UNCC > North Carolina Research Campus > 600 Laureate Way > Kannapolis, NC 28081 > 704-250-5750 > www.transvar.org > > > _______________________________________________ DAS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/das
