[DAS2] Notes from the biweekly DAS/2 teleconference, 19 Mar 2007

Steve Chervitz Steve_Chervitz at affymetrix.com
Mon Mar 19 17:47:57 UTC 2007

Notes from the biweekly DAS/2 teleconference, 19 Mar 2007

$Id: das2-teleconf-2007-03-19.txt,v 1.2 2007/03/19 17:46:41 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
    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

Instructions on how to access the DAS/2 CVS repository are at

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 issues
 * Status reports, including report from Lincoln on hapmap and das2
 * Gregg's post-grant status
 * 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,

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

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: I am planning to leave Affy at end of the grant. Will focus on
doing hands-on DAS/2 evangelism, ideally work with UCSC. Then will
take some time off.  Affy wasn't interested in supporting das w/o some
outside funding. Therefore, it's a good time to transition.

Regarding UCSC? ready to go down there and write some code. They have
a das/1 server, they just need someone with DAS/2 expertise that I can
provide. biggest prob 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

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

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