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

Lincoln Stein lstein at cshl.edu
Mon Jul 21 21:49:00 EDT 2008


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 at uiuc.edu> 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?
>
> 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>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> 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
>
>
>
>
>


-- 
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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