[DAS2] Notes from the biweekly DAS/2 teleconference, 16 Apr 2007

Steve Chervitz Steve_Chervitz at affymetrix.com
Mon Apr 16 17:54:56 UTC 2007

Notes from the biweekly DAS/2 teleconference, 16 Apr 2007

$Id: das2-teleconf-2007-04-16.txt,v 1.1 2007/04/16 17:50:47 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
    CSHL: Lincoln Stein
    UAB: Ann Loraine
    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: General discussion
gh: talking to jim kent/UCSC about adding support for das/2 at ucsc.

al: what about igb?
gh: support is an issue now (since Ed E. has been switched to another
project at Affy).  
al: if we get funding, I can pay for support for genoviz and igb. part
of my grant goal was to build other apps as demonstrations for the
toolkit. we have funds for gregg to visit birmingham 1/year. Since it's
open source, shouldn't be a problem. Would like Ed E. to continue
acting as liason between affy and other open source developers working
on the software. the biggest blindspot for me is interactivity between
igb and other affy software packages. need to make sure that my plant
igb installation can play nicely with arabidopsis tiling array data.
gh: that's right up my alley so we should talk.

[A] Ann talk with gregg about tiling support in igb for arabidopsis

gh: may need to reinstate support for igb pending user feedback.
al: what about having ed as a liason between affy and other oss devs?
he's good to advise on how various proposed changes to code base will
affect the system in general.

[A] Ann talk to Ed, Gregg, and manager about being an igb liason

sc: speaking a bit for Ed, I know he's interested in igb so he might
be interested in continuing in his spare time, especially if you get
funded and can support him.

gh: regarding the das/2 grant: talked with Peter Good, no problem with
no-cost extension. should extend out till end of july (rather than May).

Topic: Status
bo: got up to speed on allen's revised server. new server is using
catalyst as the MVC architecture rather than our own impl. Working on
getting up to speed with the new framework and importing model
objects. dynamic feature type server, writeback server integrated with das/2
dynamic means: run blat dynamically, get results back as a das/2
much cleaner MVC architecture. porting model components over at
Allen is doing the blat server and writeback server.
another week or two to port all model objects over. we have more time
to spend on this than originally thought. Probably stretching over the
next month.

[A] Gregg will get back to UCLA folks on funding

gh: impl-wise, working on affy server. need to get to a stable point
to hand over to steve on affy colo. largely doing work to more fully
implement feature filters (at present it's restricted). also work on
igb client. new release of igb is needed. Due in next two weeks.
Ed's been doing more igb client work than I. he got some nice
stylesheet work integrated before
he left. It's not the same stylesheet spec as on the das/2 spec right
now. He changed some things, fine since nobody has impl'd it. Does
some nice things like cascading from parent to child.

[A] Ed will present the changes he made to stylesheet spec (in a future mtg)

ls: moved hapmap and vert promoter db's to cshl to maintain long-term
(from boston in brian gilmans' shop). will be stable das/2 servers for
the community. url: http://das2.hapmap.org

gh: das/2 support in gbrowse?
ls: that's on the todo list, need to finish client library. missing
part that parses features. then gbrowse will act as as das/2 client
gh: gbrowse ajax stuff looks interesting.

sc: working on new affy das server machine set up. Got all the data on
the existing public machine mirrored locally and on the new
box. Should be easier to keep that data up to date now (rsync).
Todo: test the max memory per java process. Also planning to rig the
servers to divvy up data for different arrays between different java
processes. This will make maintenance easier since we won't need to
bring down support for all arrays to add/modify one. Plan to use
apache rewrite rules to make it appear to be a single server

gh: there has been some trouble with URL rewriting in the past.

[A] Steve to test affy das rewrite rules on new machine

sc: also I'll be attending BioIT world meeting in boston at end of
april/early may. Talking with the semantic web folks. Can spread the
word about das as well.

[A] Steve will give summary of BioIT-world meeting

al: getting grant application ready. Set up plant igb. talks to das/1
server hosted at plant-gdb (Iowa).  had trouble with bad xml breaking
the xml parser in igb. to my knowledge it's the only plant das server
out there. lincoln will register the gramene server.

[A] Ann will test igb with gramene das data

changes to bed parser in igb. have been communicating with ed about
that. one change has been committed to codebase.
focusing on parsers now, setting up quickload site. Will proably need
to setup my own resource.

want to do an initial release of plant igb at end of april. announce
on arabidopsis list, look at feedback. may advertise on google.

sc: also can put it on the biodas.org site, listing of servers. it's a
wiki now, so you can add it yourself.

al: want to have igb launch buttons on tair website.
gh: serving arabidopsis tiling array graphs?
al: via download and then load into igb. looking at harvesting other
data sources from other groups (joe ecker, tair). how to best
distribute them is an issue.
gh: via das/2 would be the way to go.

[A] Ann talk to gregg about distributing arabidopsis graphs via das/2

[A] Ann to make sure plant igb can work with affy servers

ls: clarification: there's no das server for gramene. we can do it but
it will be das/1 initially.
al: should be fine, since igb can talk with das/1
gh: igb impl doesn't caputure all ambiguity of the spec. it also needs
a little quickload for gramene as well. a lift and an assembly file to
be able to load from those servers. Adding a few new orgs would be
easy to do, rather than fix the das/1 client impl. (the das/2 client
does not have this problem).

Wrap up
[A] Next meeting in two weeks: 30 Apr 2007

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