Notes from the weekly DAS/2 teleconference, 5 Dec 2005. $Id: das2-teleconf-2005-12-05.txt,v 1.2 2005/12/05 19:55:54 sac Exp $ Note taker: Steve Chervitz Attendees: Affy: Steve Chervitz, Ed E., Gregg Helt CSHL: Lincoln Stein UC Berkeley: Suzi Lewis Sanger: Andreas Prlic U Alabama: Ann Loraine Action items are flagged with '[A]'. These notes are checked into the biodas.org CVS repository at das/das2/notes/2005. Instructions on how to access this repository are at http://biodas.org DISCLAIMER: The note taker aims for completeness and accuracy, but these goals are not always achievable, given the desire to get the notes out with a rapid turnaround. So don't consider these notes as complete minutes from the meeting, but rather abbreviated, summarized versions of what was discussed. There may be errors of commission and omission. Participants are welcome to post comments and/or corrections to these as they see fit. Today's topic: Implementation status reports --------------------------------------------- Gregg ------ * Planning new IGB release in 2-3 weeks * Revised IGB docs * Updating the IGB DAS client - Want to make the DAS/1 iface more like DAS/2. Currently, they are isolated in the code and the interface. Maybe done w/in next 2 weeks. Question: Has anyone use the agile 2D java stuff? ( http://www.cs.umd.edu/hcil/agile2d/ ) AL: Hasn't used it but used jazz (piccolo). Couldn't figure how to get it to zoom in only 1D. they do 2D. GH: Looking to speed up rendering in IGB. The Affy transcriptarium loses hardware acceleration when using normal java 2d/swing stuff (one cpu controling 8 monitors). agile 2d background: Billed as a drop in replacement for java 2d that runs on top of open GL. Significant speed ups on solaris, other platforms. But Gregg finds it is slower on windows. Requies open GL for java that does lots of native stuff underneath. May work on mac OS X. The focus on windows b/c in order to use spotfire and other windows-only apps. AP: Does it use double buffering? GH: Yes. Swing does this. Builds volatile image. Hooks into hardware acceleration graphics card. If you can construct a volatile img, rendering goes through graphics hardware, which is a big speed up. But swing can't deal w/ multiple graphics cards (Direct X limitation?). Open gl may deal with things better in this regard. AL: Maybe get a consultant. This is very specialized stuff. GH: Getting some time from sun java graphics engineers could help. Ed E ---- * Debugging for DAS/1 in IGB client - Fixed bug in the Affy DAS/1 server. - Also fixed a few bugs in parser (concerned note, length tags -- not heavily used). Steve ------ * Working on hooking up tomcat to apache to enable apache to handle requests that are fed to an underlying servlet engine. - Have made progress but need to do more testing before installing on netaffxdas server machine. GH: Ultimate goal is to release the Affy DAS/2 server as a servlet using standard configuration. Isn't this sevlet-under-apache configuration fairly standard? AP: We provide a war file. users can plug this into their app server. SC: The apache-tomcat config is quite common for ISPs or other situations where you need to redirect apache to different servlets depending on different companies, products, etc. SC: Assuming the apache configuration is ready, is the DAS/2 server code ready to go? GH: depends on how much of the spec we want to support. Estimates 6mos to 1yr before releasing our server. Also probably just release DAS/2. DAS/1 is also just partial and does some custom things. Better to focus on fleshing out DAS/2 server. SC: Possible complexities for apache/tomcat due to our port forwarding schemes (DAS/1 and DAS/2 servers running on different ports). GH: There's no reason we can't run these servers on different machines. GH: Steve's time for DAS work? SC: Have to transition back to NetAffx now, but can still proceed with DAS work, just less cpu cycles. Can still take and post notes. Ann ---- * Working on new arabidopsis 2010 proposal from last year. - Main aim of grant: setting up data archive for arab, and for people to add to it. Currently scattered. people put data on their website and move on. No easy way to collect it in one place. - Setting up a web service at UAB, give it an ID, info about id (e.g., whose affy, tair, agi). The server will return synonyms for that ID. Goal is to be a backend for IGB to do searches for an ID. Will talk to the UAB server via some data format. - Grant will include funding for uab and Affy (usability enhancements for IGB as front end for data repository, figuring out protocol for talking to id server) GH: Will you run DAS/2 servers at UAB? AL: Yes, we'll set up the servers, but not do server development itself. Can test and offer feedback from installation issues, etc. GH: Will data repository be in Alabama? AL: Yes. We have good sysadmin support. Originally TAIR would do it, but we've built things up since then. Grant will be more smaller scale than last year. No comparative genomics viewers. Sticking to core expertise. Focus on getting one genome right. Also funding for genoviz sdk. library upkeep. tutorials. GH: Reimplement IGB on top of picolo! AL: Looking to Affy on fancy graphics stuff since they know the libraries better than anyone else. GH: Regarding your synonym resolver - have you talked to suzi about what they're doing? AL: No. Looked at the flynome link steve mentioned (http://flynome.com). If there's a standard out there we'd love to use it. LS: There is Gene Seer developed here - a synonlym database for gene IDs. Supports many to may associations between synonly and the canonical forms. No interface besides a web-form. May make sense to provide access to it via DAS/2. GH: layering a DAS/2 interface on top of the synomym service might be nice. [A] Ann will help develop gene synonym server on top of DAS/2 EE: In IGB we have a need for synomym service for genome builds (e.g. hg16 = build34). Currently a hack in IGB, would be nice to do via DAS. AL: Plan to start with arab first. GH: Using Gene Seer scheme for your storage you will get a lot of other genomes for free. AL: Is it open source? LS: Yes, but it's not my code (ravi@cshl.edu) heavily used in cshl. Loaded with all model orgs. This is now public: http://geneseer.cshl.edu - published in bioinformatics. - no arabidopsis (rat, mouse, human, celegans, yeast). [A] Ann will contact Ravi re: Gene Seer & get letter to submit w/ her proposal. SC: Does Gene Seer contain LSIDs? LS: No, but could be added as a synonym. Every name has a species, and unique type (embl, ncbi). E.g., you can search for rad5 - in all species, or in yeast, or as a locus name in yeast. Used for the RNAi libraries here. AL: Is anyone else building such a resource? LS: Google maybe.... Andreas ------- * Not much coding for DAS/2. Waiting for issues with spec to be discussed. (next week). DAS/2 interface should be easy to add. GH: Spec is changing, so impl is hard to do. AP: Database and java server-side code has been running a while. A new interface should be easy to do. Andrew (via Gregg) ------------------ * Planning to get the registry-related stuff formalized in the spec soon. * Working on setting up web service for validation on open-bio server with Chris D. * Updating spec but is slow going. Will join the call next week. LS: Whose in charge of updating the spec now -- me, Steve, Andrew? [A] Andrew is now responsible for updating the spec. Lincoln -------- * Update on the NCI DAS/2 project: - Awarded grant for (funded by NCI) after 1 year negotiating. - caBIG grid depends on caBIO java lib/API from NCI. They had dropped all DAS support when going from caCORE v2 -> v3. - Brian Gilman proposes to add DAS/2 support to caCORE v3. o First, create plugin API for caCORE. Will allow you to add in class libs without recompiling java code. Permits caCORE to speak arbitrary protocols (~3 mos work). o Then implement DAS/2 plugin (~3 mos work). o Starting on 12/17. o Will use Alan Day's biopackages DAS/2 server (gmod), serving hap map through that. Client will be caBIO. ---- [A] Discuss spec issues for next weeks teleconf: regions, seq, registry, etc.