Any volunteers for doing a Nested Containment List implementation?
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Any volunteers for doing a Nested Containment List implementation?
by Lincoln Stein
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Hi Folks,
This paper describes an indexing algorithm for genome feature databases called Nested Containment Lists. Apparently it is substantially faster than the indexing systems we use in BioPerl for the Bio::DB::GFF, Bio::DB::SeqFeature::Store, and Chado. The concept and data structures are quite simple, and I think it would be straightforward to implement this system in MySQL tables. Would anybody be interested in taking this on as a summer project? Lincoln -- Lincoln D. Stein Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Stacey Fairfield <Stacey.Fairfield@...> Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 USA (516) 367-8380 Assistant: Sandra Michelsen <michelse@...> ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: [Bioperl-l] Any volunteers for doing a Nested Containment List implementation?
by Chris Fields
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It's definitely worth exploring. Might be nice to sort a few things
out, for instance, do we want to use their C library, or role our own data structures? And would we want this to retain a similar interface to Bio::DB::SeqFeature::Store? chris On Jul 21, 2008, at 7:02 PM, Lincoln Stein wrote: > Hi Folks, > > This paper describes an indexing algorithm for genome feature > databases > called Nested Containment Lists. Apparently it is substantially > faster than > the indexing systems we use in BioPerl for the Bio::DB::GFF, > Bio::DB::SeqFeature::Store, and Chado. > > http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btl647v1?papetoc > > The concept and data structures are quite simple, and I think it > would be > straightforward to implement this system in MySQL tables. Would > anybody be > interested in taking this on as a summer project? > > Lincoln > > -- > Lincoln D. Stein > > Ontario Institute for Cancer Research > 101 College St., Suite 800 > Toronto, ON, Canada M5G0A3 > 416 673-8514 > Assistant: Stacey Fairfield <Stacey.Fairfield@...> > > Cold Spring Harbor Laboratory > 1 Bungtown Road > Cold Spring Harbor, NY 11724 USA > (516) 367-8380 > Assistant: Sandra Michelsen <michelse@...> > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@... > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Marie-Claude Hofmann College of Veterinary Medicine University of Illinois Urbana-Champaign ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: [Bioperl-l] Any volunteers for doing a Nested Containment List implementation?
by Lincoln Stein
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I was thinking that the data structures could be reimplemented as MySQL tables. The main data structures are both fixed-width records. They do a binary search across the arrays, and MySQL can do the same thing with its B-tree indexing.
Lincoln On Mon, Jul 21, 2008 at 9:27 PM, Chris Fields <cjfields@...> wrote: It's definitely worth exploring. Might be nice to sort a few things out, for instance, do we want to use their C library, or role our own data structures? And would we want this to retain a similar interface to Bio::DB::SeqFeature::Store? -- Lincoln D. Stein Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Stacey Fairfield <Stacey.Fairfield@...> Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 USA (516) 367-8380 Assistant: Sandra Michelsen <michelse@...> ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: [Bioperl-l] Any volunteers for doing a Nested Containment List implementation?
by aaron.j.mackey
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FYI, there's also (native) support for RTREE-based spatial indices in
MySQL 5.1 and beyond ... http://dev.mysql.com/doc/refman/5.1/en/optimizing-spatial-analysis.html I once took a day to try to implement this NCL algorithm as a MySQL UDF (i.e. written entirely in C), but got bogged down and discouraged. The PostgreSQL implementation is available from the authors, if I remember correctly. -Aaron bioperl-l-bounces@... wrote on 07/21/2008 08:02:36 PM: > Hi Folks, > > This paper describes an indexing algorithm for genome feature databases > called Nested Containment Lists. Apparently it is substantially faster than > the indexing systems we use in BioPerl for the Bio::DB::GFF, > Bio::DB::SeqFeature::Store, and Chado. > > http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btl647v1?papetoc > > The concept and data structures are quite simple, and I think it would be > straightforward to implement this system in MySQL tables. Would anybody be > interested in taking this on as a summer project? > > Lincoln > > -- > Lincoln D. Stein > > Ontario Institute for Cancer Research > 101 College St., Suite 800 > Toronto, ON, Canada M5G0A3 > 416 673-8514 > Assistant: Stacey Fairfield <Stacey.Fairfield@...> > > Cold Spring Harbor Laboratory > 1 Bungtown Road > Cold Spring Harbor, NY 11724 USA > (516) 367-8380 > Assistant: Sandra Michelsen <michelse@...> > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@... > http://lists.open-bio.org/mailman/listinfo/bioperl-l > ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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