[DAS2] Notes from the biweekly DAS/2 teleconference, 6 Aug 2007

[Steve Chervitz]

Notes from the biweekly DAS/2 teleconference, 6 Aug 2007

$Id: das2-teleconf-2007-08-06.txt,v 1.1 2007/08/10 23:52:45 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

Attendees: 
    Affy: Steve Chervitz, Ed Erwin, Gregg Helt

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:
http://www.biodas.org/wiki/BioDAS:Community_Portal

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

DISCLAIMER: 
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. 


Agenda
-------
 * IGB 5.00 alpha pre-release and related discussion


Topic: Status updates
---------------------

NOTE: Since only Affy folks are on this call, we spent most the time
on changes related to the upcoming IGB 5.0 release, which includes
changes to the public Affy DAS/2 server. Here are a few highlights of
general interest.

Main site for IGB: http://genoviz.sourceforge.net

Downloaded and tested Gregg's IGB 5.00 alpha prerelease, looking at
graph support (i.e., displaying a graph of values from a tiling array
experiment over a genomic region).

Some instructions: 
 * Download the 5.00 prerelease jar from
   http://sourceforge.net/project/showfiles.php?group_id=129420
 * The jar is executable, double click it to fire up IGB.
 * In the Data access tab, select NetAffx -> H_Sapiens -> H_sapiens_May_2004
 * Open tiling_array_results, RNA_5bp_resolution and select the
   checkbox for HDF_signal.
 * In the Name Search tab within data access, enter the name of gene
   of interest (e.g., APP). Double click on one of the hits to bring
   it up in the main browser window. Or just zoom into some genomic
   region of interest.
 * Click the Refresh Data button in the upper right corner of the
   main window.
 * A tiling array results track will soon appear. Click on the Sliced
   View tab for a condensed view of exonic regions. Select one of the
   transcripts in the Refseq track to refresh the sliced view, if
   necessary. 
 * It's important that you be zoomed into a not too large genomic region
   before hitting the refresh data button, otherwise IGB will attempt
   to load lots graph data and will probably run out of memory.

We also discussed implications of decommissioning the Affy quickload
server (flat file directory interface to various annotation files
loadable into IGB). The new das/2 server will take the place of
this. Main issue: Folks using old versions of IGB which expects to
have quickload access.

We also talked about running das/2 server on port 80 to get around the
Apache 502 Bad Gateway response that occurs when the das/2 server
throws an HTTP error code. Apache thinks our headers are invalid,
missing a colon somewhere. Steve implemented a partial fix a while
back by putting 'ProxBadHeader Ignore' in httpd.conf, but this is not
ideal since the returned XML is not valid due to the inclusion of part
of the HTTP header in the body. (Anyone with tips on this, chime in!)

This may be due to the use of URL rewrite rules that we use to allow
running the das/2 and das/1 servers to run on different ports yet both
share the same main URL ( http://netaffxdas.affymetrix.com/ ). If we
run the das/2 server on port 80, this may avoid the 502 Bad Gateway
trouble since there would be no need to rewrite URLs. No guarantees
though. It's also possible the errors are originating within the Jetty
code. IGB uses an old version of Jetty (4.x), and upgrading to the
latest 6.x is non-trivial.

Gregg mentioned need to have our das/2 server run using a standard
approach for supporting servlets with Apache (e.g., Tomcat connector)
rather than using Jetty on another port as we have always done. Steve
mentioned that the RIKKEN OmicBrowse does this (see recent email to
this list), they may have some tips. Gregg may gain insight on this
during some collaborative work with UCSC in the coming months.


Next DAS teleconference
-----------------------
Monday, 20 August 2007