From Steve_Chervitz at affymetrix.com Mon Apr 2 13:37:22 2007 From: Steve_Chervitz at affymetrix.com (Steve Chervitz) Date: Mon, 02 Apr 2007 10:37:22 -0700 Subject: [DAS2] Notes from the biweekly DAS/2 teleconference, 2 Apr 2007 Message-ID: Notes from the biweekly DAS/2 teleconference, 2 Apr 2007 $Id: das2-teleconf-2007-04-02.txt,v 1.1 2007/04/02 17:36:32 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 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 stuff * Status reports Topic: General Stuff -------------------- gh: Andrew Dalke and I met a week ago in Bay area, talked about das1->das2 proxy. He'll be in UK in 4 wks to visit with Sanger, and Andreas to get the proxy going at the DAS/2 registry. I also spoke with Andreas over phone. Still wants to do work, but juggling priorities. Status Reports -------------- ee: this is my last week on this call (moving to new project at Affy). Lots of work trying to finish things up for igb and das/2 grant. Developed style sheet system for use in igb, v0.1. It works, not sure if well enough for the das/2 spec, but we might consider using it as a basis for the das/2 spec. it's an xml style sheet, cascading, app-specific, user-specific, doc-specific with rules of precedence. independent of data format, so it will work regardless of where data came from (das2xml or gff3 or else). can specify styles for things that have multiple levels of hierarchy (mrna->exons-> etc.). Not as completely finished as I'd have liked, but a decent start. ee: Other things I did: focused on igb as a client. Users specifying prefs in igb w/o editing files, but via gui now. Future work: will be documenting things i have done, but not much more development of new features. gh: there will be a new igb release in 2-weeks. I will take over release cycle. stylesheet stuff should play nice with the 5-level stuff for affy data that Steve has been working with (exon/gene array). you can say: "these things here, although they are children of this, you display them outside. you can display two different things in the same track. ee: can display children outside of their parent, or have multiple displays for a single thing. gh: I worked on getting better graph support into das2 server and igb to do graphs (plots) in das2. it's there on server side, indexing data and serving it up efficiently. client is working. now just a matter of installing. other stuff: tricks to better organize types, better than a flat list of annotation types, but more as a tree. First set of experiments will have 50 different annotation types (e.g., cell lines). Doing this outside of the das protocol itself, as a convention in type names to be path names. Builds a tree where each node in path E.g.,: geneprediction/genescan geneprediction/geneid ... Will create a node for geneprediction, you can then collapse/expand it in the UI. Trouble: Using tabletree component, and there's no good impl in Java swing for this yet. ee: not based on ontology? gh: no. looking at the SO (sequence ontology), my use case is, how do you split off gene predictions from alignments, etc. It doesn't say "predicted transcript" for example. There's no way in SO to differentiate something based on gene prediction from something that has been experimentally observed. I'm just doing this as a convention for now to see how it works. we can revisit doing it as an ontology. gh: also am working on adding better feat filter support on the affy das/2 server. also am working on draft of das/2 paper to get it out before end of grant. Should be able to extend the grant beyond the end of May and end of june given current burn rate. sc: very busy past few weeks on Affy-related work: Netaffx annotation update and new product support (Human Gene array "HuGene"). Added support to Affy public das servers for the new array, das/1 and das/2. Plan to be working on configuring the new replacement machine for the Affy das public server this week and next. Primary focus is setting up a local mirror for the data that is on the public machine. gh: Space requirements for mirroring the affy public server data must account for adding tiling graph data, (40-60 G). gh: have you looked into the maximum RAM per java thread on the new machine? sc: no. am thinking now that having multiple threads segregated by technology type (ivt, exon, gene, etc.) will be better. This way, we won't have to take down the whole server just to fix or add data for one array. gh: ok, as long as we can make it look like it's all coming from the same server url. sc: shouldn't be a problem with url rewriting. [NOTE: the following was added after teleconference: sc: I did some work on the biodas.org site adding teleconference schedule and links to meeting minutes (see 'Community Portal' page). Also added entry for genome annotation to wikiomics.org site and created reciprocal links to/from biodas.org. See the first sentence of the biodas.org main page for the link. Also added link from wikipedia page to wikiomics.org site, see http://en.wikipedia.org/wiki/Genome_annotation#Genome_annotation ] bo: last week I filed - so am completely done with degree. yay! next two weeks can dedicate to helping Allen Day with revision of das/2 server. He can assign me tasks. Will know more after meeting with him tomorrow. gh: writeback? bo: not sure. he said he made lots of progress on revision of server. He'll assign me things on his todo list, bugracker. getting it packaged up out the door. postdocing in a second lab to finish projects/papers for ~6 mos. next report will have more to say. gh: let me know if things need to happen in igb to set status of writeback, e.g. Wrapup ------- Next meeting: 16 April 2007 From aloraine at gmail.com Mon Apr 2 14:19:27 2007 From: aloraine at gmail.com (Ann Loraine) Date: Mon, 2 Apr 2007 13:19:27 -0500 Subject: [DAS2] paper? was: Re: Notes from the biweekly DAS/2 teleconference, 2 Apr 2007 Message-ID: <83722dde0704021119p36e61e76vae9729315cf0cba@mail.gmail.com> Dear all, Sorry I didn't come to the meeting today! I just wanted to ask about the DAS2 paper. The BioMoby group are working on a draft, and it seems to be near finishing. If you are at the proper stage for it, it would be terrific if the DAS2 project could be published soon, since the two projects have similarities. I expect that if the two papers came out at about the same time, some "buzz" could be generated over bioinformatics Web services, which I expect would be great for both projects. Also, it would be good to explain how the two approaches are complementary, and not competing. If people think the two are doing the same thing, then support would be harder to get. btw, the BioMoby draft is under version control in the BioMoby cvs repository. It might be good to take a look. All the best! Ann On 4/2/07, Steve Chervitz wrote: > Notes from the biweekly DAS/2 teleconference, 2 Apr 2007 > > $Id: das2-teleconf-2007-04-02.txt,v 1.1 2007/04/02 17:36:32 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 > 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 stuff > * Status reports > > Topic: General Stuff > -------------------- > > gh: Andrew Dalke and I met a week ago in Bay area, talked about > das1->das2 proxy. He'll be in UK in 4 wks to visit with Sanger, and > Andreas to get the proxy going at the DAS/2 registry. I also spoke > with Andreas over phone. Still wants to do work, but juggling > priorities. > > Status Reports > -------------- > > ee: this is my last week on this call (moving to new project at > Affy). Lots of work trying to finish things up for igb and das/2 > grant. Developed style sheet system for use in igb, v0.1. It works, > not sure if well enough for the das/2 spec, but we might consider > using it as a basis for the das/2 spec. it's an xml style sheet, > cascading, app-specific, user-specific, doc-specific with rules of > precedence. independent of data format, so it will work regardless of > where data came from (das2xml or gff3 or else). can specify styles for > things that have multiple levels of hierarchy (mrna->exons-> > etc.). Not as completely finished as I'd have liked, but a decent start. > > ee: Other things I did: focused on igb as a client. Users specifying prefs > in igb w/o editing files, but via gui now. Future work: will be > documenting things i have done, but not much more development of new > features. > > gh: there will be a new igb release in 2-weeks. I will take over > release cycle. stylesheet stuff should play nice with the 5-level > stuff for affy data that Steve has been working with (exon/gene array). you > can say: "these things here, although they are children of this, you display > them outside. you can display two different things in the same track. > ee: can display children outside of their parent, or have multiple > displays for a single thing. > > gh: I worked on getting better graph support into das2 server and igb > to do graphs (plots) in das2. it's there on server side, indexing data > and serving it up efficiently. client is working. now just a matter of > installing. other stuff: tricks to better organize types, better than > a flat list of annotation types, but more as a tree. First set of > experiments will have 50 different annotation types (e.g., cell > lines). Doing this outside of the das protocol itself, as a > convention in type names to be path names. Builds a tree where each > node in path > E.g.,: geneprediction/genescan > geneprediction/geneid > ... > Will create a node for geneprediction, you can then collapse/expand it > in the UI. Trouble: Using tabletree component, and there's no good > impl in Java swing for this yet. > > ee: not based on ontology? > > gh: no. looking at the SO (sequence ontology), my use case is, how do > you split off gene predictions from alignments, etc. It doesn't say > "predicted transcript" for example. There's no way in SO to > differentiate something based on gene prediction from something that > has been experimentally observed. I'm just doing this as a convention > for now to see how it works. we can revisit doing it as an ontology. > > gh: also am working on adding better feat filter support on the affy > das/2 server. also am working on draft of das/2 paper to get it out > before end of grant. Should be able to extend the grant beyond the end > of May and end of june given current burn rate. > > sc: very busy past few weeks on Affy-related work: Netaffx annotation > update and new product support (Human Gene array "HuGene"). Added > support to Affy public das servers for the new array, das/1 and > das/2. Plan to be working on configuring the new replacement machine > for the Affy das public server this week and next. Primary focus is > setting up a local mirror for the data that is on the public machine. > > gh: Space requirements for mirroring the affy public server data must > account for adding tiling graph data, (40-60 G). > > gh: have you looked into the maximum RAM per java thread on the new > machine? > sc: no. am thinking now that having multiple threads segregated by > technology type (ivt, exon, gene, etc.) will be better. This way, we > won't have to take down the whole server just to fix or add data for > one array. > gh: ok, as long as we can make it look like it's all coming from the > same server url. > sc: shouldn't be a problem with url rewriting. > > [NOTE: the following was added after teleconference: > > sc: I did some work on the biodas.org site adding teleconference > schedule and links to meeting minutes (see 'Community Portal' > page). Also added entry for genome annotation to wikiomics.org site > and created reciprocal links to/from biodas.org. See > the first sentence of the biodas.org main page for the link. Also > added link from wikipedia page to wikiomics.org site, see > http://en.wikipedia.org/wiki/Genome_annotation#Genome_annotation > ] > > bo: last week I filed - so am completely done with degree. yay! next > two weeks can dedicate to helping Allen Day with revision of das/2 > server. He can assign me tasks. Will know more after meeting with him > tomorrow. > > gh: writeback? > > bo: not sure. he said he made lots of progress on revision of > server. He'll assign me things on his todo list, bugracker. getting it > packaged up out the door. postdocing in a second lab to finish > projects/papers for ~6 mos. next report will have more to say. > gh: let me know if things need to happen in igb to set status of > writeback, e.g. > > Wrapup > ------- > Next meeting: 16 April 2007 > > > > _______________________________________________ > DAS2 mailing list > DAS2 at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/das2 > -- Ann Loraine, Assistant Professor Departments of Genetics, Biostatistics, Computer and Information Sciences Associate Scientist, Comprehensive Cancer Center University of Alabama at Birmingham http://www.transvar.org 205-996-4155 From Steve_Chervitz at affymetrix.com Mon Apr 16 13:54:56 2007 From: Steve_Chervitz at affymetrix.com (Steve Chervitz) Date: Mon, 16 Apr 2007 10:54:56 -0700 Subject: [DAS2] Notes from the biweekly DAS/2 teleconference, 16 Apr 2007 Message-ID: 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 Attendees: 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: 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: 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 document. much cleaner MVC architecture. porting model components over at present. 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 From aloraine at gmail.com Tue Apr 17 02:09:41 2007 From: aloraine at gmail.com (Ann Loraine) Date: Tue, 17 Apr 2007 01:09:41 -0500 Subject: [DAS2] Fwd: [MOBY-l] Differences between BioMoby and DAS In-Reply-To: <4623F260.4010201@nbn.ac.za> References: <4623F260.4010201@nbn.ac.za> Message-ID: <83722dde0704162309m49b24b87w2202205a9c6c5058@mail.gmail.com> ---------- Forwarded message ---------- From: Kieran O'Neill Date: Apr 16, 2007 5:02 PM Subject: [MOBY-l] Differences between BioMoby and DAS To: moby-l at lists.open-bio.org -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi there I was wondering if anyone on this list knows of a paper comparing BioMoby and DAS, highlighting the similarities and differences between the two systems. The two are obviously somewhat similar, being systems with a central registry describing distributed web services, but I think they may have slightly different applications. Also, if I'm not mistaken, BioMoby uses an ontology to describe its services, whereas an ontology has yet to be finalised for DAS. Thank-you in advance Kieran - -- "So, did you bring any of these `protons' with you?" - -US border guard to my aunt, the radiographer, on her way to a conference on proton radiotherapy. -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.6 (GNU/Linux) iD8DBQFGI/Jf0TLED9JKVp0RArHQAJ9cpzcgCaDd0gE/pre+xK56C4XN3QCdHZ40 GLAXhon6Pk2Am5Q4JXZ+8Bs= =f5Om -----END PGP SIGNATURE----- _______________________________________________ moby-l mailing list moby-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-l From Steve_Chervitz at affymetrix.com Mon Apr 2 17:37:22 2007 From: Steve_Chervitz at affymetrix.com (Steve Chervitz) Date: Mon, 02 Apr 2007 10:37:22 -0700 Subject: [DAS2] Notes from the biweekly DAS/2 teleconference, 2 Apr 2007 Message-ID: Notes from the biweekly DAS/2 teleconference, 2 Apr 2007 $Id: das2-teleconf-2007-04-02.txt,v 1.1 2007/04/02 17:36:32 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 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 stuff * Status reports Topic: General Stuff -------------------- gh: Andrew Dalke and I met a week ago in Bay area, talked about das1->das2 proxy. He'll be in UK in 4 wks to visit with Sanger, and Andreas to get the proxy going at the DAS/2 registry. I also spoke with Andreas over phone. Still wants to do work, but juggling priorities. Status Reports -------------- ee: this is my last week on this call (moving to new project at Affy). Lots of work trying to finish things up for igb and das/2 grant. Developed style sheet system for use in igb, v0.1. It works, not sure if well enough for the das/2 spec, but we might consider using it as a basis for the das/2 spec. it's an xml style sheet, cascading, app-specific, user-specific, doc-specific with rules of precedence. independent of data format, so it will work regardless of where data came from (das2xml or gff3 or else). can specify styles for things that have multiple levels of hierarchy (mrna->exons-> etc.). Not as completely finished as I'd have liked, but a decent start. ee: Other things I did: focused on igb as a client. Users specifying prefs in igb w/o editing files, but via gui now. Future work: will be documenting things i have done, but not much more development of new features. gh: there will be a new igb release in 2-weeks. I will take over release cycle. stylesheet stuff should play nice with the 5-level stuff for affy data that Steve has been working with (exon/gene array). you can say: "these things here, although they are children of this, you display them outside. you can display two different things in the same track. ee: can display children outside of their parent, or have multiple displays for a single thing. gh: I worked on getting better graph support into das2 server and igb to do graphs (plots) in das2. it's there on server side, indexing data and serving it up efficiently. client is working. now just a matter of installing. other stuff: tricks to better organize types, better than a flat list of annotation types, but more as a tree. First set of experiments will have 50 different annotation types (e.g., cell lines). Doing this outside of the das protocol itself, as a convention in type names to be path names. Builds a tree where each node in path E.g.,: geneprediction/genescan geneprediction/geneid ... Will create a node for geneprediction, you can then collapse/expand it in the UI. Trouble: Using tabletree component, and there's no good impl in Java swing for this yet. ee: not based on ontology? gh: no. looking at the SO (sequence ontology), my use case is, how do you split off gene predictions from alignments, etc. It doesn't say "predicted transcript" for example. There's no way in SO to differentiate something based on gene prediction from something that has been experimentally observed. I'm just doing this as a convention for now to see how it works. we can revisit doing it as an ontology. gh: also am working on adding better feat filter support on the affy das/2 server. also am working on draft of das/2 paper to get it out before end of grant. Should be able to extend the grant beyond the end of May and end of june given current burn rate. sc: very busy past few weeks on Affy-related work: Netaffx annotation update and new product support (Human Gene array "HuGene"). Added support to Affy public das servers for the new array, das/1 and das/2. Plan to be working on configuring the new replacement machine for the Affy das public server this week and next. Primary focus is setting up a local mirror for the data that is on the public machine. gh: Space requirements for mirroring the affy public server data must account for adding tiling graph data, (40-60 G). gh: have you looked into the maximum RAM per java thread on the new machine? sc: no. am thinking now that having multiple threads segregated by technology type (ivt, exon, gene, etc.) will be better. This way, we won't have to take down the whole server just to fix or add data for one array. gh: ok, as long as we can make it look like it's all coming from the same server url. sc: shouldn't be a problem with url rewriting. [NOTE: the following was added after teleconference: sc: I did some work on the biodas.org site adding teleconference schedule and links to meeting minutes (see 'Community Portal' page). Also added entry for genome annotation to wikiomics.org site and created reciprocal links to/from biodas.org. See the first sentence of the biodas.org main page for the link. Also added link from wikipedia page to wikiomics.org site, see http://en.wikipedia.org/wiki/Genome_annotation#Genome_annotation ] bo: last week I filed - so am completely done with degree. yay! next two weeks can dedicate to helping Allen Day with revision of das/2 server. He can assign me tasks. Will know more after meeting with him tomorrow. gh: writeback? bo: not sure. he said he made lots of progress on revision of server. He'll assign me things on his todo list, bugracker. getting it packaged up out the door. postdocing in a second lab to finish projects/papers for ~6 mos. next report will have more to say. gh: let me know if things need to happen in igb to set status of writeback, e.g. Wrapup ------- Next meeting: 16 April 2007 From aloraine at gmail.com Mon Apr 2 18:19:27 2007 From: aloraine at gmail.com (Ann Loraine) Date: Mon, 2 Apr 2007 13:19:27 -0500 Subject: [DAS2] paper? was: Re: Notes from the biweekly DAS/2 teleconference, 2 Apr 2007 Message-ID: <83722dde0704021119p36e61e76vae9729315cf0cba@mail.gmail.com> Dear all, Sorry I didn't come to the meeting today! I just wanted to ask about the DAS2 paper. The BioMoby group are working on a draft, and it seems to be near finishing. If you are at the proper stage for it, it would be terrific if the DAS2 project could be published soon, since the two projects have similarities. I expect that if the two papers came out at about the same time, some "buzz" could be generated over bioinformatics Web services, which I expect would be great for both projects. Also, it would be good to explain how the two approaches are complementary, and not competing. If people think the two are doing the same thing, then support would be harder to get. btw, the BioMoby draft is under version control in the BioMoby cvs repository. It might be good to take a look. All the best! Ann On 4/2/07, Steve Chervitz wrote: > Notes from the biweekly DAS/2 teleconference, 2 Apr 2007 > > $Id: das2-teleconf-2007-04-02.txt,v 1.1 2007/04/02 17:36:32 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 > 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 stuff > * Status reports > > Topic: General Stuff > -------------------- > > gh: Andrew Dalke and I met a week ago in Bay area, talked about > das1->das2 proxy. He'll be in UK in 4 wks to visit with Sanger, and > Andreas to get the proxy going at the DAS/2 registry. I also spoke > with Andreas over phone. Still wants to do work, but juggling > priorities. > > Status Reports > -------------- > > ee: this is my last week on this call (moving to new project at > Affy). Lots of work trying to finish things up for igb and das/2 > grant. Developed style sheet system for use in igb, v0.1. It works, > not sure if well enough for the das/2 spec, but we might consider > using it as a basis for the das/2 spec. it's an xml style sheet, > cascading, app-specific, user-specific, doc-specific with rules of > precedence. independent of data format, so it will work regardless of > where data came from (das2xml or gff3 or else). can specify styles for > things that have multiple levels of hierarchy (mrna->exons-> > etc.). Not as completely finished as I'd have liked, but a decent start. > > ee: Other things I did: focused on igb as a client. Users specifying prefs > in igb w/o editing files, but via gui now. Future work: will be > documenting things i have done, but not much more development of new > features. > > gh: there will be a new igb release in 2-weeks. I will take over > release cycle. stylesheet stuff should play nice with the 5-level > stuff for affy data that Steve has been working with (exon/gene array). you > can say: "these things here, although they are children of this, you display > them outside. you can display two different things in the same track. > ee: can display children outside of their parent, or have multiple > displays for a single thing. > > gh: I worked on getting better graph support into das2 server and igb > to do graphs (plots) in das2. it's there on server side, indexing data > and serving it up efficiently. client is working. now just a matter of > installing. other stuff: tricks to better organize types, better than > a flat list of annotation types, but more as a tree. First set of > experiments will have 50 different annotation types (e.g., cell > lines). Doing this outside of the das protocol itself, as a > convention in type names to be path names. Builds a tree where each > node in path > E.g.,: geneprediction/genescan > geneprediction/geneid > ... > Will create a node for geneprediction, you can then collapse/expand it > in the UI. Trouble: Using tabletree component, and there's no good > impl in Java swing for this yet. > > ee: not based on ontology? > > gh: no. looking at the SO (sequence ontology), my use case is, how do > you split off gene predictions from alignments, etc. It doesn't say > "predicted transcript" for example. There's no way in SO to > differentiate something based on gene prediction from something that > has been experimentally observed. I'm just doing this as a convention > for now to see how it works. we can revisit doing it as an ontology. > > gh: also am working on adding better feat filter support on the affy > das/2 server. also am working on draft of das/2 paper to get it out > before end of grant. Should be able to extend the grant beyond the end > of May and end of june given current burn rate. > > sc: very busy past few weeks on Affy-related work: Netaffx annotation > update and new product support (Human Gene array "HuGene"). Added > support to Affy public das servers for the new array, das/1 and > das/2. Plan to be working on configuring the new replacement machine > for the Affy das public server this week and next. Primary focus is > setting up a local mirror for the data that is on the public machine. > > gh: Space requirements for mirroring the affy public server data must > account for adding tiling graph data, (40-60 G). > > gh: have you looked into the maximum RAM per java thread on the new > machine? > sc: no. am thinking now that having multiple threads segregated by > technology type (ivt, exon, gene, etc.) will be better. This way, we > won't have to take down the whole server just to fix or add data for > one array. > gh: ok, as long as we can make it look like it's all coming from the > same server url. > sc: shouldn't be a problem with url rewriting. > > [NOTE: the following was added after teleconference: > > sc: I did some work on the biodas.org site adding teleconference > schedule and links to meeting minutes (see 'Community Portal' > page). Also added entry for genome annotation to wikiomics.org site > and created reciprocal links to/from biodas.org. See > the first sentence of the biodas.org main page for the link. Also > added link from wikipedia page to wikiomics.org site, see > http://en.wikipedia.org/wiki/Genome_annotation#Genome_annotation > ] > > bo: last week I filed - so am completely done with degree. yay! next > two weeks can dedicate to helping Allen Day with revision of das/2 > server. He can assign me tasks. Will know more after meeting with him > tomorrow. > > gh: writeback? > > bo: not sure. he said he made lots of progress on revision of > server. He'll assign me things on his todo list, bugracker. getting it > packaged up out the door. postdocing in a second lab to finish > projects/papers for ~6 mos. next report will have more to say. > gh: let me know if things need to happen in igb to set status of > writeback, e.g. > > Wrapup > ------- > Next meeting: 16 April 2007 > > > > _______________________________________________ > DAS2 mailing list > DAS2 at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/das2 > -- Ann Loraine, Assistant Professor Departments of Genetics, Biostatistics, Computer and Information Sciences Associate Scientist, Comprehensive Cancer Center University of Alabama at Birmingham http://www.transvar.org 205-996-4155 From Steve_Chervitz at affymetrix.com Mon Apr 16 17:54:56 2007 From: Steve_Chervitz at affymetrix.com (Steve Chervitz) Date: Mon, 16 Apr 2007 10:54:56 -0700 Subject: [DAS2] Notes from the biweekly DAS/2 teleconference, 16 Apr 2007 Message-ID: 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 Attendees: 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: 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: 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 document. much cleaner MVC architecture. porting model components over at present. 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 From aloraine at gmail.com Tue Apr 17 06:09:41 2007 From: aloraine at gmail.com (Ann Loraine) Date: Tue, 17 Apr 2007 01:09:41 -0500 Subject: [DAS2] Fwd: [MOBY-l] Differences between BioMoby and DAS In-Reply-To: <4623F260.4010201@nbn.ac.za> References: <4623F260.4010201@nbn.ac.za> Message-ID: <83722dde0704162309m49b24b87w2202205a9c6c5058@mail.gmail.com> ---------- Forwarded message ---------- From: Kieran O'Neill Date: Apr 16, 2007 5:02 PM Subject: [MOBY-l] Differences between BioMoby and DAS To: moby-l at lists.open-bio.org -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi there I was wondering if anyone on this list knows of a paper comparing BioMoby and DAS, highlighting the similarities and differences between the two systems. The two are obviously somewhat similar, being systems with a central registry describing distributed web services, but I think they may have slightly different applications. Also, if I'm not mistaken, BioMoby uses an ontology to describe its services, whereas an ontology has yet to be finalised for DAS. Thank-you in advance Kieran - -- "So, did you bring any of these `protons' with you?" - -US border guard to my aunt, the radiographer, on her way to a conference on proton radiotherapy. -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.6 (GNU/Linux) iD8DBQFGI/Jf0TLED9JKVp0RArHQAJ9cpzcgCaDd0gE/pre+xK56C4XN3QCdHZ40 GLAXhon6Pk2Am5Q4JXZ+8Bs= =f5Om -----END PGP SIGNATURE----- _______________________________________________ moby-l mailing list moby-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-l