[DAS2] Notes from the biweekly DAS/2 teleconference, 9 Jul 2007

Steve Chervitz Steve_Chervitz at affymetrix.com
Mon Jul 9 18:16:04 UTC 2007

Notes from the biweekly DAS/2 teleconference, 9 Jul 2007

$Id: das2-teleconf-2007-07-09.txt,v 1.2 2007/07/09 18:11:53 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, 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 discussion
 * Status updates

Topic: Status updates

gh: (status) making igb more das2 centric, replacing the quickload
system (an integral part of igb) and instead relying on das2
stuff. going well. has given more capabilities and faster loading
(using optimized content formats for acccessing data from affy
server). overhauled gui for accessing das/2 genomes and which
annotation types to load from das2 servers. background threading - so
one server can't hold everything up. UI is smarter - split into
two. switch genomes pick genome from das2 servers, then show what
types are available, restricting to annotation types for the selected

revising the affy das2 server to inject properties into types response
to give hints about how you should load the annotations, to replicate
the usability features of quick load. Automatically load a skeleton of
annotations. E.g., load all annots of this type for the whole seq
rather than just what you are currently using. The properties are
usefule. XSLT transform transforming output of server and into format
for IGB display. Handy to not have to modify server.

Fixing issues arising from replacing quickload (bookmark, search by
name/id). Also working to get das server to serve up cytological
bands, needed to replace quickload.

sc: do the feat filter limitations still exist?
gh: managed to fix some of those, but there are still some
restrictions. the feat query filter is almost fully compliant, uses
error codes if it doesn't like what you're asking it. Returns response
to large, because it only wants one type in the query.

[A] Gregg will get folks involved in the weekly meetings

gh: work on writeback should pick up now. andreas (prlic) has an
intern working on rewrite server for sanger. Just getting started.
suzi (lewis) is interested, now that apollo project has funding.
Would like to get allen (day) back in as well.

bo: will let Alan know.

igb/das2 release timeframe: in 2-3 weeks. want to get a pre-release
out sooner for das folks to look at, likely next week.

sc: (status) looked into error on the biodas.org wiki site. Noticed
content of all pages was blank last night. Sent in request to open-bio
helpdesk and it has been fixed by open-bio.org admins. Cause: there
was an incompatibility between wikimedia and an updated extension.

Other das work: Planning to migrate the quickload
data over to das2 on the public affy server when gregg decommissions
the quickload with the next release.

Noticed a transient 502 bad gateway error on an NCBI apache server
(same as what we get when the public affy das server throws error
codes - due to our use of rewrite rules probably). I asked NCBI for
advice on this, but got no reply (yet).  We sill have this problem
since we are using apache rewrite rules to hide the different port
numbers for our das/1 vs das/2 servers.

gh: can we stop doing this?
sc: when we only have one server (das2). it can just be on port 80.
gh: or use rewriting for the quickload server.
sc: would require apache to be on a different port.
gh: may be best to wait till we remove quickload and das/1 servers.

bo: (status) no das work in progress now. Plan to work on getting our server
caching stuff packaged up. The original caching was under development,
not in CVS or documented. Will work on getting that in with readme.

[A] Gregg will start working on das/2 paper

bo: can help out on this. allen is also interested.
sc: me too.

Next Meeting:
23 July 2007

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