[Bioperl-l] Any volunteers for doing a Nested Containment List implementation?

Chris Fields cjfields at uiuc.edu
Mon Jul 21 21:27:58 EDT 2008


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 at oicr.on.ca>
>
> Cold Spring Harbor Laboratory
> 1 Bungtown Road
> Cold Spring Harbor, NY 11724 USA
> (516) 367-8380
> Assistant: Sandra Michelsen <michelse at cshl.edu>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Marie-Claude Hofmann
College of Veterinary Medicine
University of Illinois Urbana-Champaign






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