From Steve_Chervitz at affymetrix.com Fri Jun 8 13:42:07 2007 From: Steve_Chervitz at affymetrix.com (Steve Chervitz) Date: Fri, 08 Jun 2007 10:42:07 -0700 Subject: [DAS2] Notes from the biweekly DAS/2 teleconference, 14 May 2007 Message-ID: Notes from the biweekly DAS/2 teleconference, 14 May 2007 $Id: das2-teleconf-2007-05-14.txt,v 1.1 2007/06/08 17:41:21 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 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 --------------------- sc: Finished configuring the new machine that will host the Affy public DAS servers. Migrated data from current box, set up local mirrors for affy data and public data on internal machines to enable easy syncing with the box when it moves to the colo. Need to investigate potential issues with the DAS server and affymetrix.com traffic. There has been a spate of dropped downloads lately (e.g., Netaffx annotation files). If DAS traffic has been high, this could be a possible source of trouble. [Note added post facto: DAS traffic was not the issue. It was a client-side problem.] Now that we have memory, we can add support for other arrays and organisms that have UCSC genome assemblies (cow, dog, chicken, rhesus, zebrafish, anopheles). [A] Steve add support on Affy das server for other affy arrays and orgs with UCSC genomes Have also been considering how to support organisms with non-UCSC hosted assembled genomes for which we have arrays (e.g., arabidopsis, rice, poplar) and for other orgs like drosophila where we use an assembly not supported by UCSC (drosophila flybase R5.x, for example). Possible plan: We can we generate psl files for the annotations we have and then convert into a format igb can read (bps). The transcriptome group has interest in this for the mod-encode work, targetting Drosophila release 5. [A] Steve add support on Affy das server for arrays and orgs with non-UCSC genomes gh: das2 code modificatios. have das2 server on internal affy server serving up graph slices for transcriptome tiling array data. practice for public version. Has been up for 1.5 weeks, so far so good. Clever indexing on server to retrieve graph slices out of graph files, mods on igb side to stitch slices together to make them look like one graph in igb. Dynamic type instantiation. request for graph slice, needs to request something that server doesn't yet know about. Names are initially randomly generated -- based on file name. Not meaningful for display. transcriptome db stores where file resides, igb has a plugin tie to transcriptome db, looks up file, tells server where to go to get it. Public server will have structure for where file resides. das2 server will determine typename for each graph based on directory names, will support types query. same idea for dir structure as now for genome annotations. some tricks getting server to view a set of files as one type. don't load into memory, just indexes files. should support many graphs before it impacts memory. Also have worked on overhaul of GUI in igb for selecting/loading type information. planning phase now. previously - panel to navigate genome choice, then switches genome view to that source, then can select the available types based on current view or whole sequence. messy because 1) you always see all possible genomes you can select. - confusing. and 2) types available was only per version, awkward. genome selection is a separate UI, pop up tree you can navigate. tree does not show all servers, sources, versions that igb knows about, it will filter to show only leafs that appropriate to the version you are looking at. So it's a filtered view, any source user could pick is appropriate to the selection. types displayed below, can select checkboxes for what you're interested in. Table view panel will look across all versioned sources for the particular version you are looking at. E.g. versioned source from affy, hapmap, biopackages for may 2004 human, you will see types for all versions. Current way doesn't lend itself to overlay annotations in the same view. Other work: less about UI, working on getting IGB to retain more prefs across sessions. IGB should remember all types you selected in current session, remembers, loads. Now it requires you to select versioned sources individually. One big refresh data button that will trigger loading of all types from every genome based on current view. Universal way to reload data based on current view. Topic: Next meeting ------------------- 28 May 2007 (this is a US holiday, attendance optional) From Steve_Chervitz at affymetrix.com Fri Jun 8 14:26:49 2007 From: Steve_Chervitz at affymetrix.com (Steve Chervitz) Date: Fri, 08 Jun 2007 11:26:49 -0700 Subject: [DAS2] DAS reminders Message-ID: The next DAS/2 teleconference will take place on Monday 11 Jun 2007. Access info is available here: http://www.biodas.org/wiki/BioDAS:Community_Portal#Teleconference_Schedule_a nd_Phone_numbers Tentative agenda: * General discussion * Status updates * DAS/2 publication plans Also, I?d like to remind folks about the BOSC meeting next month in Vienna. It?s too late to submit an abstract, but it would be good to have some DAS representatives there. (I see we do already: Rafael C. Jimenez talking about Dasty2). darin.london at duke.edu wrote: > > The BOSC Organizing Committee are proud to announce BOSC 2007, occurring > in Vienna, Austria on July 19th, 20th. The conference this year > promises to be exciting, as the BOSC developers attempt to define and > solve currently intractable problems in Bioinformatics. Please refer to > the following website for complete information, and requests for > submissions. Thank you, and we hope to see you in Vienna. > > http://open-bio.org/wiki/BOSC_2007 > > > The BOSC organizing Committee > Steve From Steve_Chervitz at affymetrix.com Mon Jun 11 21:28:53 2007 From: Steve_Chervitz at affymetrix.com (Steve Chervitz) Date: Mon, 11 Jun 2007 18:28:53 -0700 Subject: [DAS2] DAS meeting missed Message-ID: Sorry I missed today's DAS teleconf. I was caught up in chaos at home until ~10:30. If folks can sent me a summary of their status updates, I can pull together some meeting notes. As for my status, the new machine for hosting the public Affy DAS servers is now installed and online at http://netaffxdas.affymetrix.com (same address as old server). The number of arrays supported is now significantly larger, thanks to the increased memory on the new box. The array features that we are serving up (probe, probe set locations on various genome builds) are mostly coming from a DAS/1 server, though we hope to move to a single DAS/2 server eventually, once we resolve some data format issues for the 3?-IVT arrays (the DAS/2 server currently only supports the newer exon/gene arrays). There would of course be a generous transition period to allow clients to switch their DAS/1-based code to use DAS/2. Cheers, Steve From Steve_Chervitz at affymetrix.com Mon Jun 25 20:20:39 2007 From: Steve_Chervitz at affymetrix.com (Steve Chervitz) Date: Mon, 25 Jun 2007 17:20:39 -0700 Subject: [DAS2] Accelerating interval queries Message-ID: Of potential interest to genome DAS server implementers: Nested Containment List (NCList): a new algorithm for accelerating interval query of genome alignment and interval databases http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/11/1386 Any comments on this approach or comparison with other methods? Steve From aloraine at gmail.com Mon Jun 25 23:58:13 2007 From: aloraine at gmail.com (Ann Loraine) Date: Mon, 25 Jun 2007 22:58:13 -0500 Subject: [DAS2] Accelerating interval queries In-Reply-To: References: Message-ID: <83722dde0706252058v44900604g263cc7c82ed439d5@mail.gmail.com> Interesting! This is definitely needed. How do we incorporate this into our own schema? On 6/25/07, Steve Chervitz wrote: > Of potential interest to genome DAS server implementers: > > Nested Containment List (NCList): a new algorithm for accelerating interval > query of genome alignment and interval databases > > http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/11/1386 > > Any comments on this approach or comparison with other methods? > > Steve > > _______________________________________________ > DAS2 mailing list > DAS2 at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/das2 > -- Ann Loraine Assistant Professor University of Alabama at Birmingham http://www.transvar.org 205-996-4155 From allenday at ucla.edu Tue Jun 26 02:42:18 2007 From: allenday at ucla.edu (Allen Day) Date: Mon, 25 Jun 2007 23:42:18 -0700 Subject: [DAS2] Fwd: Accelerating interval queries In-Reply-To: <5c24dcc30706252341u7eb58wcc2b12d6a835b1a2@mail.gmail.com> References: <83722dde0706252058v44900604g263cc7c82ed439d5@mail.gmail.com> <5c24dcc30706252341u7eb58wcc2b12d6a835b1a2@mail.gmail.com> Message-ID: <5c24dcc30706252342i2746794eifa651c9d907b8224@mail.gmail.com> And again, from my ucla.edu address :) -Allen ---------- Forwarded message ---------- From: Allen Day Date: Jun 25, 2007 11:41 PM Subject: Re: [DAS2] Accelerating interval queries To: Ann Loraine Cc: Steve Chervitz , DAS/2 Discussion , Scott Cain I see Alex occasionally in my building, I'll ask him next time I see him. Without looking closely at the data structure in the paper, I am thinking we may be able to implement this indexing scheme with the PostgreSQL GiST mechanism for new index strategies. -Allen On 6/25/07, Ann Loraine wrote: > Interesting! > > This is definitely needed. > > How do we incorporate this into our own schema? > > On 6/25/07, Steve Chervitz wrote: > > Of potential interest to genome DAS server implementers: > > > > Nested Containment List (NCList): a new algorithm for accelerating interval > > query of genome alignment and interval databases > > > > http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/11/1386 > > > > Any comments on this approach or comparison with other methods? > > > > Steve > > > > _______________________________________________ > > DAS2 mailing list > > DAS2 at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/das2 > > > > > -- > Ann Loraine > Assistant Professor > University of Alabama at Birmingham > http://www.transvar.org > 205-996-4155 > _______________________________________________ > DAS2 mailing list > DAS2 at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/das2 > -- allenday.skype o: +1 (415) 335-4654 m: +1 (310) 804-5304 -- allenday.skype o: +1 (415) 335-4654 m: +1 (310) 804-5304 From aloraine at gmail.com Tue Jun 26 09:19:00 2007 From: aloraine at gmail.com (Ann Loraine) Date: Tue, 26 Jun 2007 08:19:00 -0500 Subject: [DAS2] Accelerating interval queries In-Reply-To: <5c24dcc30706252341u7eb58wcc2b12d6a835b1a2@mail.gmail.com> References: <83722dde0706252058v44900604g263cc7c82ed439d5@mail.gmail.com> <5c24dcc30706252341u7eb58wcc2b12d6a835b1a2@mail.gmail.com> Message-ID: <83722dde0706260619o7842d2fexdc845adf8d3b0972@mail.gmail.com> Sorry this is so naive... Would implementing this schema require re-building your database, or could you layer it on top an existing schema somehow? -Ann On 6/26/07, Allen Day wrote: > I see Alex occasionally in my building, I'll ask him next time I see > him. Without looking closely at the data structure in the paper, I am > thinking we may be able to implement this indexing scheme with the > PostgreSQL GiST mechanism for new index strategies. > > -Allen > > On 6/25/07, Ann Loraine wrote: > > Interesting! > > > > This is definitely needed. > > > > How do we incorporate this into our own schema? > > > > On 6/25/07, Steve Chervitz wrote: > > > Of potential interest to genome DAS server implementers: > > > > > > Nested Containment List (NCList): a new algorithm for accelerating interval > > > query of genome alignment and interval databases > > > > > > http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/11/1386 > > > > > > Any comments on this approach or comparison with other methods? > > > > > > Steve > > > > > > _______________________________________________ > > > DAS2 mailing list > > > DAS2 at lists.open-bio.org > > > http://lists.open-bio.org/mailman/listinfo/das2 > > > > > > > > > -- > > Ann Loraine > > Assistant Professor > > University of Alabama at Birmingham > > http://www.transvar.org > > 205-996-4155 > > _______________________________________________ > > DAS2 mailing list > > DAS2 at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/das2 > > > > > -- > allenday.skype > o: +1 (415) 335-4654 > m: +1 (310) 804-5304 > -- Ann Loraine Assistant Professor University of Alabama at Birmingham http://www.transvar.org 205-996-4155 From Steve_Chervitz at affymetrix.com Fri Jun 8 17:42:07 2007 From: Steve_Chervitz at affymetrix.com (Steve Chervitz) Date: Fri, 08 Jun 2007 10:42:07 -0700 Subject: [DAS2] Notes from the biweekly DAS/2 teleconference, 14 May 2007 Message-ID: Notes from the biweekly DAS/2 teleconference, 14 May 2007 $Id: das2-teleconf-2007-05-14.txt,v 1.1 2007/06/08 17:41:21 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 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 --------------------- sc: Finished configuring the new machine that will host the Affy public DAS servers. Migrated data from current box, set up local mirrors for affy data and public data on internal machines to enable easy syncing with the box when it moves to the colo. Need to investigate potential issues with the DAS server and affymetrix.com traffic. There has been a spate of dropped downloads lately (e.g., Netaffx annotation files). If DAS traffic has been high, this could be a possible source of trouble. [Note added post facto: DAS traffic was not the issue. It was a client-side problem.] Now that we have memory, we can add support for other arrays and organisms that have UCSC genome assemblies (cow, dog, chicken, rhesus, zebrafish, anopheles). [A] Steve add support on Affy das server for other affy arrays and orgs with UCSC genomes Have also been considering how to support organisms with non-UCSC hosted assembled genomes for which we have arrays (e.g., arabidopsis, rice, poplar) and for other orgs like drosophila where we use an assembly not supported by UCSC (drosophila flybase R5.x, for example). Possible plan: We can we generate psl files for the annotations we have and then convert into a format igb can read (bps). The transcriptome group has interest in this for the mod-encode work, targetting Drosophila release 5. [A] Steve add support on Affy das server for arrays and orgs with non-UCSC genomes gh: das2 code modificatios. have das2 server on internal affy server serving up graph slices for transcriptome tiling array data. practice for public version. Has been up for 1.5 weeks, so far so good. Clever indexing on server to retrieve graph slices out of graph files, mods on igb side to stitch slices together to make them look like one graph in igb. Dynamic type instantiation. request for graph slice, needs to request something that server doesn't yet know about. Names are initially randomly generated -- based on file name. Not meaningful for display. transcriptome db stores where file resides, igb has a plugin tie to transcriptome db, looks up file, tells server where to go to get it. Public server will have structure for where file resides. das2 server will determine typename for each graph based on directory names, will support types query. same idea for dir structure as now for genome annotations. some tricks getting server to view a set of files as one type. don't load into memory, just indexes files. should support many graphs before it impacts memory. Also have worked on overhaul of GUI in igb for selecting/loading type information. planning phase now. previously - panel to navigate genome choice, then switches genome view to that source, then can select the available types based on current view or whole sequence. messy because 1) you always see all possible genomes you can select. - confusing. and 2) types available was only per version, awkward. genome selection is a separate UI, pop up tree you can navigate. tree does not show all servers, sources, versions that igb knows about, it will filter to show only leafs that appropriate to the version you are looking at. So it's a filtered view, any source user could pick is appropriate to the selection. types displayed below, can select checkboxes for what you're interested in. Table view panel will look across all versioned sources for the particular version you are looking at. E.g. versioned source from affy, hapmap, biopackages for may 2004 human, you will see types for all versions. Current way doesn't lend itself to overlay annotations in the same view. Other work: less about UI, working on getting IGB to retain more prefs across sessions. IGB should remember all types you selected in current session, remembers, loads. Now it requires you to select versioned sources individually. One big refresh data button that will trigger loading of all types from every genome based on current view. Universal way to reload data based on current view. Topic: Next meeting ------------------- 28 May 2007 (this is a US holiday, attendance optional) From Steve_Chervitz at affymetrix.com Fri Jun 8 18:26:49 2007 From: Steve_Chervitz at affymetrix.com (Steve Chervitz) Date: Fri, 08 Jun 2007 11:26:49 -0700 Subject: [DAS2] DAS reminders Message-ID: The next DAS/2 teleconference will take place on Monday 11 Jun 2007. Access info is available here: http://www.biodas.org/wiki/BioDAS:Community_Portal#Teleconference_Schedule_a nd_Phone_numbers Tentative agenda: * General discussion * Status updates * DAS/2 publication plans Also, I?d like to remind folks about the BOSC meeting next month in Vienna. It?s too late to submit an abstract, but it would be good to have some DAS representatives there. (I see we do already: Rafael C. Jimenez talking about Dasty2). darin.london at duke.edu wrote: > > The BOSC Organizing Committee are proud to announce BOSC 2007, occurring > in Vienna, Austria on July 19th, 20th. The conference this year > promises to be exciting, as the BOSC developers attempt to define and > solve currently intractable problems in Bioinformatics. Please refer to > the following website for complete information, and requests for > submissions. Thank you, and we hope to see you in Vienna. > > http://open-bio.org/wiki/BOSC_2007 > > > The BOSC organizing Committee > Steve From Steve_Chervitz at affymetrix.com Tue Jun 12 01:28:53 2007 From: Steve_Chervitz at affymetrix.com (Steve Chervitz) Date: Mon, 11 Jun 2007 18:28:53 -0700 Subject: [DAS2] DAS meeting missed Message-ID: Sorry I missed today's DAS teleconf. I was caught up in chaos at home until ~10:30. If folks can sent me a summary of their status updates, I can pull together some meeting notes. As for my status, the new machine for hosting the public Affy DAS servers is now installed and online at http://netaffxdas.affymetrix.com (same address as old server). The number of arrays supported is now significantly larger, thanks to the increased memory on the new box. The array features that we are serving up (probe, probe set locations on various genome builds) are mostly coming from a DAS/1 server, though we hope to move to a single DAS/2 server eventually, once we resolve some data format issues for the 3?-IVT arrays (the DAS/2 server currently only supports the newer exon/gene arrays). There would of course be a generous transition period to allow clients to switch their DAS/1-based code to use DAS/2. Cheers, Steve From Steve_Chervitz at affymetrix.com Tue Jun 26 00:20:39 2007 From: Steve_Chervitz at affymetrix.com (Steve Chervitz) Date: Mon, 25 Jun 2007 17:20:39 -0700 Subject: [DAS2] Accelerating interval queries Message-ID: Of potential interest to genome DAS server implementers: Nested Containment List (NCList): a new algorithm for accelerating interval query of genome alignment and interval databases http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/11/1386 Any comments on this approach or comparison with other methods? Steve From aloraine at gmail.com Tue Jun 26 03:58:13 2007 From: aloraine at gmail.com (Ann Loraine) Date: Mon, 25 Jun 2007 22:58:13 -0500 Subject: [DAS2] Accelerating interval queries In-Reply-To: References: Message-ID: <83722dde0706252058v44900604g263cc7c82ed439d5@mail.gmail.com> Interesting! This is definitely needed. How do we incorporate this into our own schema? On 6/25/07, Steve Chervitz wrote: > Of potential interest to genome DAS server implementers: > > Nested Containment List (NCList): a new algorithm for accelerating interval > query of genome alignment and interval databases > > http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/11/1386 > > Any comments on this approach or comparison with other methods? > > Steve > > _______________________________________________ > DAS2 mailing list > DAS2 at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/das2 > -- Ann Loraine Assistant Professor University of Alabama at Birmingham http://www.transvar.org 205-996-4155 From allenday at ucla.edu Tue Jun 26 06:42:18 2007 From: allenday at ucla.edu (Allen Day) Date: Mon, 25 Jun 2007 23:42:18 -0700 Subject: [DAS2] Fwd: Accelerating interval queries In-Reply-To: <5c24dcc30706252341u7eb58wcc2b12d6a835b1a2@mail.gmail.com> References: <83722dde0706252058v44900604g263cc7c82ed439d5@mail.gmail.com> <5c24dcc30706252341u7eb58wcc2b12d6a835b1a2@mail.gmail.com> Message-ID: <5c24dcc30706252342i2746794eifa651c9d907b8224@mail.gmail.com> And again, from my ucla.edu address :) -Allen ---------- Forwarded message ---------- From: Allen Day Date: Jun 25, 2007 11:41 PM Subject: Re: [DAS2] Accelerating interval queries To: Ann Loraine Cc: Steve Chervitz , DAS/2 Discussion , Scott Cain I see Alex occasionally in my building, I'll ask him next time I see him. Without looking closely at the data structure in the paper, I am thinking we may be able to implement this indexing scheme with the PostgreSQL GiST mechanism for new index strategies. -Allen On 6/25/07, Ann Loraine wrote: > Interesting! > > This is definitely needed. > > How do we incorporate this into our own schema? > > On 6/25/07, Steve Chervitz wrote: > > Of potential interest to genome DAS server implementers: > > > > Nested Containment List (NCList): a new algorithm for accelerating interval > > query of genome alignment and interval databases > > > > http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/11/1386 > > > > Any comments on this approach or comparison with other methods? > > > > Steve > > > > _______________________________________________ > > DAS2 mailing list > > DAS2 at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/das2 > > > > > -- > Ann Loraine > Assistant Professor > University of Alabama at Birmingham > http://www.transvar.org > 205-996-4155 > _______________________________________________ > DAS2 mailing list > DAS2 at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/das2 > -- allenday.skype o: +1 (415) 335-4654 m: +1 (310) 804-5304 -- allenday.skype o: +1 (415) 335-4654 m: +1 (310) 804-5304 From aloraine at gmail.com Tue Jun 26 13:19:00 2007 From: aloraine at gmail.com (Ann Loraine) Date: Tue, 26 Jun 2007 08:19:00 -0500 Subject: [DAS2] Accelerating interval queries In-Reply-To: <5c24dcc30706252341u7eb58wcc2b12d6a835b1a2@mail.gmail.com> References: <83722dde0706252058v44900604g263cc7c82ed439d5@mail.gmail.com> <5c24dcc30706252341u7eb58wcc2b12d6a835b1a2@mail.gmail.com> Message-ID: <83722dde0706260619o7842d2fexdc845adf8d3b0972@mail.gmail.com> Sorry this is so naive... Would implementing this schema require re-building your database, or could you layer it on top an existing schema somehow? -Ann On 6/26/07, Allen Day wrote: > I see Alex occasionally in my building, I'll ask him next time I see > him. Without looking closely at the data structure in the paper, I am > thinking we may be able to implement this indexing scheme with the > PostgreSQL GiST mechanism for new index strategies. > > -Allen > > On 6/25/07, Ann Loraine wrote: > > Interesting! > > > > This is definitely needed. > > > > How do we incorporate this into our own schema? > > > > On 6/25/07, Steve Chervitz wrote: > > > Of potential interest to genome DAS server implementers: > > > > > > Nested Containment List (NCList): a new algorithm for accelerating interval > > > query of genome alignment and interval databases > > > > > > http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/11/1386 > > > > > > Any comments on this approach or comparison with other methods? > > > > > > Steve > > > > > > _______________________________________________ > > > DAS2 mailing list > > > DAS2 at lists.open-bio.org > > > http://lists.open-bio.org/mailman/listinfo/das2 > > > > > > > > > -- > > Ann Loraine > > Assistant Professor > > University of Alabama at Birmingham > > http://www.transvar.org > > 205-996-4155 > > _______________________________________________ > > DAS2 mailing list > > DAS2 at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/das2 > > > > > -- > allenday.skype > o: +1 (415) 335-4654 > m: +1 (310) 804-5304 > -- Ann Loraine Assistant Professor University of Alabama at Birmingham http://www.transvar.org 205-996-4155