Notes from the biweekly DAS/2 teleconference, 19 Mar 2007 $Id: das2-teleconf-2007-03-19.txt,v 1.3 2007/03/19 19:06:02 sac Exp $ Teleconference Info: * Schedule: Biweekly on Monday * Time of Day: 9:30 AM PST, 17:30 GMT * Dialin (US): 800-531-3250 * Dialin (Intl): 303-928-2693 * Toll-free UK: 08 00 40 49 467 * Toll-free France: 08 00 907 839 * Conference ID: 2879055 * Passcode: 1365 Attendees: Affy: Steve Chervitz, Ed Erwin, Gregg Helt CSHL: Lincoln Stein Note taker: Steve Chervitz Action items are flagged with '[A]'. These notes are checked into the biodas.org CVS repository at das/das2/notes/ and are viewable on-line at http://biodas.org/documents/das2/notes/ Instructions on how to access the DAS/2 CVS repository are at http://www.biodas.org/wiki/DAS/2#CVS_Access 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. Agenda ------- * General issues * Status reports, including report from Lincoln on hapmap and das2 * Other items * Gregg's agenda * IGB support post-March Topic: General Issues ---------------------- ls: Regarding the coordinate stuff for global seq ids, need clarification (see me message on list). gh: for each release we should have the xml snippet for the coordinates, four attribs for authority, etc. so people can see directly what they need to provide in their DAS/2 request. [A] gregg will send global seq ID coordinate XML example to Lincoln Topic: Status reports ---------------------- gh: working on getting good reporesentations of graphs for Affy das/2 server serving up tiling array data. Serving up slices of graphs. Working well on my test server, better than expected. Slow thing is the indexing the first time it sees a file. Chrm1 at 5bp resolution tiling array data, 120M data points, slicing indexing takes a couple of seconds the first time, other times there's no delay. this is serving up in an optimized format. Need to serve in std das/2 format with a feature per data point. Not too hard. Planning to deploy in April when Steve gets new server running. Drosophila time-course public data. 8-9 time points RNA expression tiling arrays. When phase 3 ENCODE paper comes out, we'll have a pointer to our server for viewing that data. Also need to beef up feat filter queries to support full spec on the Affy das/2 server. transition IGB from using quickload and replace all quickload stuff with das/2, so we don't need to maintain two code bases and data respositories. ls: hapmap das/2 server is up and running. temporarily at Brian Gilman's consultancy business. He's coming here to CSHL to get a permanent version running on hapmap.org by next week. There's a whole API for accessing that data in the form that's required by NCI's caBIO project (caCORE). After server goes up, I'll point coordinates that location, documentation. It works with other das/2 sources as well, (Affy, biopackages). gh: So it will put any of that DAS-available data into caCORE object model? ls: yes. It also can give data as DOM models, might be easier for some users/apps. gh: Rolling this into the next caBIO release? ls: yes. ls: Will provide snp's and haplotype blocks as features. one track per population. we can put as many tracks in as you need. Just one set now. There are 4 populations grouped into three panels, since two pop's don't have enough diffs to break them out. [A] lincoln send gregg pointer to current hapmap server for testing sc: Working on configuring the new affy das/2 public server, a replacement machine with a lot more RAM than current box. Have been busy with other Affy work (new Netaffx release, new product support, etc.) but should be mostly done with this by end of March. Should be able to devote some solid blocks to DAS work (target: 3wks). Plan is to support as many Affy products as we can. Less focus on supporting UCSC-provided annotations (since they're the best source for them). sc: Gregg, have you considered using the same approach for serving annotations by your das/2 server as you are doing to support graphs? Could ease memory requirements. gh: possible, but not practical, since it would require a new format for every feature type. Graphs are relatively straightforward to serve up via an indexing strategy. Doing something similar for features would mean essentially writing a database app. Other Items: ------------- gh: grant admin says our burn rate is lower than anticipated. we can apply for a no-cost extension. should last at least till the end of June as for funding. We'll apply for that. Not sure what it means for CSHL. last time it took 3-4 mos to sort it out. ls: start working on it now. there were communication problems in the past. would be great if Allen could extend another month or two. gh: Andrew will come visit me in the next day or two. Will get the latest from him. He's been working on the transformational das1-> das2 proxy. Want to get the Ensembl people to use it ASAP. [A] get a usable das1->das2 proxy server, deploy at Ensembl gh: Need to look at how to support scores in das/2. we dropped score element. You can add arbitrary elements to das/2. You can put in multiple diff scores that way, or use XML namespaces to bring in a das/2 score element. Want to have a recommended way of doing this. Need more input from others. In Europe they're using score a lot more than here in the States. [A] come up with recommended way to support scores in DAS/2 Topic: Gregg's agenda ---------------------- gh: After the grant, I will focus on doing hands-on DAS/2 evangelism, focussing on UCSC given their proximity. They have a das/1 server, they just need help from someone with DAS/2 expertise. biggest problem with das/2 is adoption outside of the grant people. sc: considered using Andrew's proxy? gh: might be OK for a temporary solution, but it wouldn't be as efficient as directly supporting das/2, and I know Jim et al are interested in efficiency. Since I'm in the area, I can help them get into DAS/2 directly, which would help with DAS/2 acceptance by the community. gh: Another goal was to have a DAS/2 paper ready and submitted before I leave, want to have a rough draft in april. Plan to submit to an open source journal: Biomedcentral, PLoS, or other. [A] Gregg will circulate draft of DAS/2 paper, draft in April. Topic: IGB Support ------------------- ee: Regarding IGB support, Affy is not supporting IGB after March, they are moving me to a different project. Support for IGB could return if there's enough interest. sc: how self-supporting is the igb community? ee: not much. gh: Ann Loraine has interest as do internal Affy users. sc: Sourceforge has a new wiki project that's in beta now, for adding a wiki to your project's web page. Could help make the IGB community self-supporting, on-line docs, FAQ, etc. I volunteered to participate, but haven't done anything with it yet. gh: IGB has a good user's guide now, thanks to Ed's recent update. ee: I'm also working on plugin interface and documenting the http API protocol, things that will make it easier for others to use IGB with other programs.