[Bioperl-l] FWD: Mail System Error - Returned Mail

Frank Gibbons francis_gibbons@hms.harvard.edu
Fri, 23 Feb 2001 16:01:22 -0500

Ewan Birney wrote:

>> So, my questions are:
>> * Is this appropriate for BioPerl in the first place? Would it be more
>> suitable for CPAN? The algorithms are general, but my focus is on
>> BioInformatics.
>Possible more suitable for a straight CPAN. Not sure. Perhaps CPAN modules
>with then a Bioperl stubs/docs to works things from there. Whatever you
>feel comfortable with.

Ewan, it sounds like I'd be better off going with CPAN, since it might also be
useful to somebody in PDL (which I had never heard of until you mentioned it).

Hilmar Lapp wrote:
>> I don't know how your code scales. Generally, computation-heavy code
>>     in pure perl tends to be slow. If you intend to write the core in C,
>>     this should then probably be moved to its own package (we already have
>>     bioperl-ext containing C-extensions, which is presently only Ewan's
>>     alignment algorithms), so as to keep it optional (C extensions can
>>     pose a problem to users on Win32 and Macs).

Hilmar, it won't be as fast as C, but then clustering is largely an
exploratory technique, rather than something you run routinely. You do it once
or twice to see what it gives you, then you go away and perform other kinds of
analyses/experiments based on your clustering results. Still, I may end up
having to write some of it in C, if it's unbearably slow. So, better to keep
it out of BioPerl.

Thanks for the input.


PhD, Computational Biologist, Harvard Medical School
Dept of Biological Chemistry and Molecular Pharmacology
240 Longwood Avenue, C-125, Boston, MA 02115