[DAS2] Notes from the biweekly DAS/2 teleconference, 2 Apr 2007

Steve Chervitz Steve_Chervitz at affymetrix.com
Mon Apr 2 17:37:22 UTC 2007

Notes from the biweekly DAS/2 teleconference, 2 Apr 2007

$Id: das2-teleconf-2007-04-02.txt,v 1.1 2007/04/02 17:36:32 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

    Affy: Steve Chervitz, Ed Erwin, Gregg Helt
    UCLA: Brian O'connor

Note taker: Steve Chervitz

Action items are flagged with '[A]'.

The teleconference schedule and links to past minutes are now
available from the Community Portal section of the biodas.org site:

Meeting notes are checked into the biodas.org CVS repository at
das/das2/notes/. Instructions on how to access the DAS/2 CVS
repository are at http://www.biodas.org/wiki/DAS/2#CVS_Access

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. 

* General stuff
* Status reports

Topic: General Stuff

gh: Andrew Dalke and I met a week ago in Bay area, talked about
das1->das2 proxy. He'll be in UK in 4 wks to visit with Sanger, and
Andreas to get the proxy going at the DAS/2 registry. I also spoke
with Andreas over phone. Still wants to do work, but juggling

Status Reports

ee: this is my last week on this call (moving to new project at
Affy). Lots of work trying to finish things up for igb and das/2
grant. Developed style sheet system for use in igb, v0.1. It works,
not sure if well enough for the das/2 spec, but we might consider
using it as a basis for the das/2 spec. it's an xml style sheet,
cascading, app-specific, user-specific, doc-specific with rules of
precedence. independent of data format, so it will work regardless of
where data came from (das2xml or gff3 or else). can specify styles for
things that have multiple levels of hierarchy (mrna->exons->
etc.). Not as completely finished as I'd have liked, but a decent start.

ee: Other things I did: focused on igb as a client. Users specifying prefs
in igb w/o editing files, but via gui now. Future work: will be
documenting things i have done, but not much more development of new

gh: there will be a new igb release in 2-weeks. I will take over
release cycle. stylesheet stuff should play nice with the 5-level
stuff for affy data that Steve has been working with (exon/gene array). you
can say: "these things here, although they are children of this, you display
them outside. you can display two different things in the same track.
ee: can display children outside of their parent, or have multiple
displays for a single thing.

gh: I worked on getting better graph support into das2 server and igb
to do graphs (plots) in das2. it's there on server side, indexing data
and serving it up efficiently. client is working. now just a matter of
installing.  other stuff: tricks to better organize types, better than
a flat list of annotation types, but more as a tree. First set of
experiments will have 50 different annotation types (e.g., cell
lines).  Doing this outside of the das protocol itself, as a
convention in type names to be path names. Builds a tree where each
node in path
E.g.,:   geneprediction/genescan
Will create a node for geneprediction, you can then collapse/expand it
in the UI. Trouble: Using tabletree component, and there's no good
impl in Java swing for this yet.

ee: not based on ontology?

gh: no. looking at the SO (sequence ontology), my use case is, how do
you split off gene predictions from alignments, etc. It doesn't say
"predicted transcript" for example. There's no way in SO to
differentiate something based on gene prediction from something that
has been experimentally observed. I'm just doing this as a convention
for now to see how it works. we can revisit doing it as an ontology.

gh: also am working on adding better feat filter support on the affy
das/2 server. also am working on draft of das/2 paper to get it out
before end of grant. Should be able to extend the grant beyond the end
of May and end of june given current burn rate.

sc: very busy past few weeks on Affy-related work: Netaffx annotation
update and new product support (Human Gene array "HuGene"). Added
support to Affy public das servers for the new array, das/1 and
das/2. Plan to be working on configuring the new replacement machine
for the Affy das public server this week and next. Primary focus is
setting up a local mirror for the data that is on the public machine.

gh: Space requirements for mirroring the affy public server data must
account for adding tiling graph data, (40-60 G).

gh: have you looked into the maximum RAM per java thread on the new
sc: no. am thinking now that having multiple threads segregated by
technology type (ivt, exon, gene, etc.) will be better. This way, we
won't have to take down the whole server just to fix or add data for
one array.
gh: ok, as long as we can make it look like it's all coming from the
same server url.
sc: shouldn't be a problem with url rewriting.

[NOTE: the following was added after teleconference:

sc: I did some work on the biodas.org site adding teleconference
schedule and links to meeting minutes (see 'Community Portal'
page). Also added entry for genome annotation to wikiomics.org site
and created reciprocal links to/from biodas.org. See
the first sentence of the biodas.org main page for the link. Also
added link from wikipedia page to wikiomics.org site, see

bo: last week I filed - so am completely done with degree. yay! next
two weeks can dedicate to helping Allen Day with revision of das/2
server. He can assign me tasks. Will know more after meeting with him

gh: writeback?

bo: not sure. he said he made lots of progress on revision of
server. He'll assign me things on his todo list, bugracker. getting it
packaged up out the door. postdocing in a second lab to finish
projects/papers for ~6 mos. next report will have more to say.
gh: let me know if things need to happen in igb to set status of
writeback, e.g.

Next meeting: 16 April 2007

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