From Steve_Chervitz at affymetrix.com Mon Jul 9 14:16:04 2007 From: Steve_Chervitz at affymetrix.com (Steve Chervitz) Date: Mon, 09 Jul 2007 11:16:04 -0700 Subject: [DAS2] Notes from the biweekly DAS/2 teleconference, 9 Jul 2007 Message-ID: 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 Attendees: 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: 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 ------- * 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 genome. 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 From Steve_Chervitz at affymetrix.com Wed Jul 25 13:57:58 2007 From: Steve_Chervitz at affymetrix.com (Steve Chervitz) Date: Wed, 25 Jul 2007 10:57:58 -0700 Subject: [DAS2] OmicBrowse from RIKEN Message-ID: I just noticed this blurb in the latest BioInform, 20 July 07: > Japan?s RIKEN has released an update for the OmicBrowse genome browser, which > displays an integrated view of multiple omics annotations filtered with > ontologies. New functions include access controls over secure datasets, the > ability to change the browser's window size, and genome annotations for human, > mouse, rat, C. elegans, Arabidopsis, and rice. http://omicspace.riken.jp/omicBrowse/OmicBrowseRegister.html They provide a Flash-based client, Java servlet-based server, and a DAS/1 adapter. Their publication mentions DAS but their system is based on a new protocol called "Semantic-Space-based Distributed Annotation System (SDAS)". They don't cite any spec or other document describing this protocol: http://bioinformatics.oxfordjournals.org/cgi/content/full/23/4/524 It has some interesting comparative genomics capabilities: http://omicspace.riken.jp/HelpOmicBrowse/2D.html Anyone have experience with it or understand exactly how SDAS works relative to DAS/1 or DAS/2? Steve From lstein at cshl.edu Wed Jul 25 15:22:51 2007 From: lstein at cshl.edu (Lincoln Stein) Date: Wed, 25 Jul 2007 15:22:51 -0400 Subject: [DAS2] OmicBrowse from RIKEN In-Reply-To: References: Message-ID: <6dce9a0b0707251222w3a983265qef56193a744163c0@mail.gmail.com> It looks very interesting, but this is the first I've heard of SDAS. Lincoln On 7/25/07, Steve Chervitz wrote: > > I just noticed this blurb in the latest BioInform, 20 July 07: > > > Japan?s RIKEN has released an update for the OmicBrowse genome browser, > which > > displays an integrated view of multiple omics annotations filtered with > > ontologies. New functions include access controls over secure datasets, > the > > ability to change the browser's window size, and genome annotations for > human, > > mouse, rat, C. elegans, Arabidopsis, and rice. > > http://omicspace.riken.jp/omicBrowse/OmicBrowseRegister.html > > They provide a Flash-based client, Java servlet-based server, and a DAS/1 > adapter. Their publication mentions DAS but their system is based on a new > protocol called "Semantic-Space-based Distributed Annotation System > (SDAS)". > They don't cite any spec or other document describing this protocol: > > http://bioinformatics.oxfordjournals.org/cgi/content/full/23/4/524 > > It has some interesting comparative genomics capabilities: > http://omicspace.riken.jp/HelpOmicBrowse/2D.html > > Anyone have experience with it or understand exactly how SDAS works > relative > to DAS/1 or DAS/2? > > Steve > > > _______________________________________________ > DAS2 mailing list > DAS2 at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/das2 > -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) FOR URGENT MESSAGES & SCHEDULING, PLEASE CONTACT MY ASSISTANT, SANDRA MICHELSEN, AT michelse at cshl.edu From Steve_Chervitz at affymetrix.com Mon Jul 9 18:16:04 2007 From: Steve_Chervitz at affymetrix.com (Steve Chervitz) Date: Mon, 09 Jul 2007 11:16:04 -0700 Subject: [DAS2] Notes from the biweekly DAS/2 teleconference, 9 Jul 2007 Message-ID: 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 Attendees: 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: 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 ------- * 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 genome. 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 From Steve_Chervitz at affymetrix.com Wed Jul 25 17:57:58 2007 From: Steve_Chervitz at affymetrix.com (Steve Chervitz) Date: Wed, 25 Jul 2007 10:57:58 -0700 Subject: [DAS2] OmicBrowse from RIKEN Message-ID: I just noticed this blurb in the latest BioInform, 20 July 07: > Japan?s RIKEN has released an update for the OmicBrowse genome browser, which > displays an integrated view of multiple omics annotations filtered with > ontologies. New functions include access controls over secure datasets, the > ability to change the browser's window size, and genome annotations for human, > mouse, rat, C. elegans, Arabidopsis, and rice. http://omicspace.riken.jp/omicBrowse/OmicBrowseRegister.html They provide a Flash-based client, Java servlet-based server, and a DAS/1 adapter. Their publication mentions DAS but their system is based on a new protocol called "Semantic-Space-based Distributed Annotation System (SDAS)". They don't cite any spec or other document describing this protocol: http://bioinformatics.oxfordjournals.org/cgi/content/full/23/4/524 It has some interesting comparative genomics capabilities: http://omicspace.riken.jp/HelpOmicBrowse/2D.html Anyone have experience with it or understand exactly how SDAS works relative to DAS/1 or DAS/2? Steve From lstein at cshl.edu Wed Jul 25 19:22:51 2007 From: lstein at cshl.edu (Lincoln Stein) Date: Wed, 25 Jul 2007 15:22:51 -0400 Subject: [DAS2] OmicBrowse from RIKEN In-Reply-To: References: Message-ID: <6dce9a0b0707251222w3a983265qef56193a744163c0@mail.gmail.com> It looks very interesting, but this is the first I've heard of SDAS. Lincoln On 7/25/07, Steve Chervitz wrote: > > I just noticed this blurb in the latest BioInform, 20 July 07: > > > Japan?s RIKEN has released an update for the OmicBrowse genome browser, > which > > displays an integrated view of multiple omics annotations filtered with > > ontologies. New functions include access controls over secure datasets, > the > > ability to change the browser's window size, and genome annotations for > human, > > mouse, rat, C. elegans, Arabidopsis, and rice. > > http://omicspace.riken.jp/omicBrowse/OmicBrowseRegister.html > > They provide a Flash-based client, Java servlet-based server, and a DAS/1 > adapter. Their publication mentions DAS but their system is based on a new > protocol called "Semantic-Space-based Distributed Annotation System > (SDAS)". > They don't cite any spec or other document describing this protocol: > > http://bioinformatics.oxfordjournals.org/cgi/content/full/23/4/524 > > It has some interesting comparative genomics capabilities: > http://omicspace.riken.jp/HelpOmicBrowse/2D.html > > Anyone have experience with it or understand exactly how SDAS works > relative > to DAS/1 or DAS/2? > > Steve > > > _______________________________________________ > DAS2 mailing list > DAS2 at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/das2 > -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) FOR URGENT MESSAGES & SCHEDULING, PLEASE CONTACT MY ASSISTANT, SANDRA MICHELSEN, AT michelse at cshl.edu