[DAS2] DAS/2 weekly meeting notes

[Chervitz, Steve]

Notes from the weekly DAS/2 teleconference, 3 Nov 2005.

$Id: das2-teleconf-2005-11-03.txt,v 1.2 2005/11/04 00:23:27 sac Exp $

Attendees: 
  Affy: Steve Chervitz, Ed Erwin, Gregg Helt
  UCLA: Brian O'connor, Mark Carlson
        
These notes are checked into the biodas.org CVS repository at
das/das2/notes/2005. Instructions on how to access this
repository are at http://biodas.org

Status Reports
--------------

Gregg:

* A lot happened last week:
  - Major IGB public release (4.02) last Friday (10/28)
  - Attended and presented IGB demo at CSHL Genome Informatics meeting
    on Sunday (10/30)
  - Finished and submitted DAS/2 continuation grant on Tue (11/1).

* Held a DAS/2 BOF (birds of a feather meeting) at CSHL. Good
  discussion and turnout (15). Collected feedback from EBI/Sanger
  folks. Asked people to download the client (IGB) and hit the servers
  (Affy, UCLA), so be looking for more traffic soon.

* TODO: Monitor DAS/2 traffic, collect usage stats for both servers:
    http://netaffxdas.affymetrix.com
    http://biopackages.net.
  Especially check for performance degradation under load.
  Need to parse apache and server logs for things like: # users,
  typical query times, etc.

* IGB demo went well. People were impressed with speed. Requests for
  Gregg's in-memory java DAS/2 server, but code is not yet ready for
  public consumption.

Ed:

* Reviewing various technologies of possible interest:
  - HTTP communication protocol, necessary commands.
  - Using a bean-based property editor for IGB

* Spent time answering user questions on IGB forum (only 1 person posted
  trouble with installing data for use with new IGB release -- not
  bad). Gregg adds: Also no negative feedback from internal release.

Steve:

* Spec work: Posted message about types and features issues in the
  retrieval spec last Thurs (10/26). Mentioned Lincoln's response
  (doing away with xml:base and going with his namespace scheme).
  Gregg talked with Lincoln about this at CSHL and clarified that
  xml:base is for resolving relative URLs in attributes or CDATA
  elements, whereas xmlns is for resolving names of attributes and
  elements. Steve will post response to DAS/2 discussion list about
  this. 

* Tested the IGB release on OS X last week prior to release. Noted the
  display bug that Gregg knows about (disappearing view when you
  select a new DAS/2 annotation source). Found trouble with quick load
  synonym on the Affy internal server synonym. Ed fixed.

* Installed new assembly (Human Nov 2002) available via quickload and
  DAS/2. Gregg says: Use DAS/1 for new genomes at this stage.

* DAS/2 discussion list troubleshooting. Problem with open-bio
  sendmail, DNS.

Brian, Mark:

* Using the DAS/2 layer from the IGB code base and extending it for
  their assay and ontology namespaces. Want to put this new code in
  separate packages to avoid stepping on other IGB functionality.
  DAS/2 layer is currently in com.affymetrix.igb.das2.

 Options
 1. Add subpackages to com.affymetrix.igb.das2.
 2. Move das2 out from under igb to com.affymetrix.das2.
 3. Move das2 out of com.affymetrix to be totally separate. Then
    com.affymetrix.igb.das2 and the assay/ontology code would depend
    on it. 

 Brian is fine with #2. Gregg will check and remove any dependencies
 with the das2 package on IGB code.

* Plan to release their code internally in December. Code is in their
  own CVS repository now. Genoviz/IGB code has not been committed to
  SF yet.

---------------------------
TODO

* Summarize CSHL genome informatics meeting happenings relevant to
  DAS/2 when others who were there are dialed in.

* Move teleconf meeting to a more UK-friendly time. US is now on
  standard time. 9am PST = 12pm EST = 17:00 GMT.
  How does this work for folks?