From Steve_Chervitz at affymetrix.com Fri Aug 10 19:53:14 2007 From: Steve_Chervitz at affymetrix.com (Steve Chervitz) Date: Fri, 10 Aug 2007 16:53:14 -0700 Subject: [DAS2] Notes from the biweekly DAS/2 teleconference, 6 Aug 2007 Message-ID: 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 From Steve_Chervitz at affymetrix.com Fri Aug 10 23:53:14 2007 From: Steve_Chervitz at affymetrix.com (Steve Chervitz) Date: Fri, 10 Aug 2007 16:53:14 -0700 Subject: [DAS2] Notes from the biweekly DAS/2 teleconference, 6 Aug 2007 Message-ID: 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