[Bioperl-l] Call to users/developers -- user cases that bringBioperl to its knees

[Kevin Brown]

Try loading the Genbank file or files for the human genome.

ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/

Last time I tried to load them each chromosome took 30+ minutes to load
and chewed up lots of memory to hold onto them. 

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org 
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of 
> Albert Vilella
> Sent: Monday, February 23, 2009 9:06 AM
> To: bioperl-l
> Subject: [Bioperl-l] Call to users/developers -- user cases 
> that bringBioperl to its knees
> 
> Hi all,
> 
> I've discovered the profiling wonders of "perl -d:NYTProf -S" and I
> would like to play with it and Bioperl.
> 
> Can interested users/developers provide a URL with a dataset that
> brings bioperl to its knees in
> terms of CPU usage for say, about 1h?
> 
> Preferably no net access, no calling external programs or other
> complications, just data churning within Bioperl.
> And the data must be public, of course.
> 
> The idea would be to try to identify optimizations in the code that
> could benefit us all,
> 
> Cheers,
> 
>     Albert.
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