[DAS2] Notes from the weekly DAS/2 teleconference, 9 Oct 2006

Lincoln Stein lstein at cshl.edu
Mon Oct 23 14:01:01 UTC 2006

Hi Folks,

I'm going to miss today's conference call again. I've been scheduled to
interview a job candidate and I can't change it.


On 10/9/06, Steve Chervitz <Steve_Chervitz at affymetrix.com> wrote:
> Notes from the weekly DAS/2 teleconference, 9 Oct 2006
> $Id: das2-teleconf-2006-10-09.txt,v 1.1 2006/10/09 17:24:14 sac Exp $
> Note taker: Steve Chervitz
> Attendees:
>   Affy: Steve Chervitz, Ed Erwin, Gregg Helt
>   UCLA: Allen Day, Brian O'connor
> Action items are flagged with '[A]'.
> These notes are checked into the biodas.org CVS repository at
> das/das2/notes/2006. Instructions on how to access this
> repository are at http://biodas.org
> 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
> -------
> * Status reports
> Topic: Status reports
> ---------------------
> gh: Funding thru end of may. shifting times around a bit here at
> affy. gh going up to a greater percentage during this period.
> going down to half time for next month due to house-related work.
> Focusing now on cleaning up impl of writeback on igb client. clean
> impl based on ideas sketched out at code sprint in Aug.
> Spec issue:
> -----------
> gh: was there a resolution to the feature group assembly conversation
> on email thread.
> aday: died out. so the assumption is: no change.
> [A] Ask andrew about feature group assembly resolution, if any.
> ee: new release of IGB. bug fix then patch release. rapid turn
> around. Exposed need for more throurough testing.
> Specifying multiple urls for get more info links. sources for urls:
> track lines in psl/bed files. Also supporting das files (1 and
> probably 2)
> noticed: feature tag can give feat label and ID. IGB ignores these
> labels, because they seem to be attached to wrong thing. feat in das/1
> is like 'exon' group is 'mrna'. it's the mrna we want the label on,
> not exon where the labels are on.
> gh: if people just label parent. names don't have to be unique. id is
> unique uri, name is displayed name. parser isn't looking into that now.
> [A] Ed will look into using feature name as label in IGB client
> sc: Installed updated das2_server code on affy the das/2 server
> (netaffxdas.affymetrix.com). Installed new, efficient version of exon
> array data for hg18 (Mar 2006) assembly on this server. (igb's 'Bprobe1'
> parser, generates new bp2 format files). Probe and probeset data
> loaded fine, but exon/transcript cluster data failed with exception
> about 'Probe_count is zero for <probesetID>'.
> gh: problem: the bp2 data format isn't designed for representing
> transcripts/exon just probe. problem in the part that generates the
> bp2 files. can take a look at that.
> [A] Gregg will look into steve's Bprobe1 parser error. Needs source gff.
> ee: Can you verify that the gff data you are loading doesn't have
> unmapped probes, probe sets? Some are not mapped after lifting from
> previous genome assembly.
> [A] Steve will remove unmapped objects in the source gff used for bp2
> aday: working on UML for integrating the writeback and the read
> features. Also retrieval of dynamic features as well. Sent out example
> query. working on getting them all into a single model, determines
> what do do based on input query.
> will impl own block caching rather than apache caching.
> If I see a writeback coming in , can see which types have been
> modified, within each region. can fork off process to re-generate them
> after doing the writeback. will be a lot faster.
> Have a flowchart. partway through creating UML classes, functions,
> return types. Using poseidon.
> [A] Allen will distribute uml diagrams for das/2 modeling when ready
> gh: will locking be a part of that?
> aday: can make sure it's compatible. don't know how much of that to
> impl now.
> gh: useful to think about how to model that too.
> [A] Allen will include locking in his UML modelling.
> aday: flowchart is pretty generic. can be used by other servers.
> bo: no das work because of work on manuscript.
> started sourceforge project for das/2 assay "gyrax" (nee hyrax --
> already taken at sf).
> The motivation for this project is to take the das/2 objects in igb
> and make them more generic. This project can host these objects. They
> could then be used for other apps (igb, gyrax, others). Mark
> Carlson in lab is working on the gyrax client.  Could be a nice
> library for use by other apps, gui or not, that are built on top of a
> das server.
> gh: parts of the igb objects are tied into genometry model, a separate
> package also. but both of these could be separated from igb.
> ee: There was some email on genoviz forum where someone is writing an
> app based on old NGSDK objects, on the help forum on
> sourceforge. problems with >30,000 glyphs. advice: switch to efficient
> glyph versions (special drawing alg if children are too small to see).
> gh: Lots of caveats...There is code that hasn't been touched in a
> while.
> gh: question about hardware quote for UCLA
> [A] Allen will send gregg hardware quote for UCLA (<$5k)
> sc: status of hardware for affy das server upgrade?
> gh: plan to order end of oct, should have in place in first two weeks
> of nov.
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Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
(516) 367-8380 (voice)
(516) 367-8389 (fax)
SANDRA MICHELSEN, AT michelse at cshl.edu

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