[Bioperl-l] clustering algorithms in BioPerl

Ewan Birney birney@ebi.ac.uk
Fri, 23 Feb 2001 17:53:13 +0000 (GMT)

On Fri, 23 Feb 2001, Frank Gibbons wrote:

> Hi,
> I've been lurking for about a month. I've checked out the BioPerl homepage, 
> including the list of projects. I notice that the bias is heavily towards 
> sequence analysis (naturally).
> Right now I'm working on implementing a few clustering algorithms
> (priority #3 on the list of projects) in Perl, for use with DNA
> microarray data (priority #4 on the list!). The algorithms themselves
> are quite general, and have been around for a while, but I can find
> few references to implementations of them in Perl. (I have seen
> mention of Jong Park's Geanfammer package, as a possible source for
> clustering, but as far as I can see he implements only single-linkage
> clustering there.) I think they would be quite useful to the Perl
> community as a whole, and I would like to write them in as generic a
> way as possible, which is why I'm writing to the list now, having
> implemented only one particular algorithm, before I write any more!

I think we would love this...

> 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.

> * If so, does any one know of other work that may have been done in
> this area, on which I could build/integrate with?
> * Do you have any suggestions? I'm thinking in terms of
> 	- Naming schemes
> 	- Particular algorithms which should be implemented as a priority
> 	- Other possible applications, which I should keep in mind
> 	- Pitfalls I should look out for
> Thanks for your input,
> Frank Gibbons
> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
> PhD, Computational Biologist, Harvard Medical School
> Dept of Biological Chemistry and Molecular Pharmacology
> 240 Longwood Avenue, C-125, Boston, MA 02115
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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420