[Bioperl-l] clustering algorithms in BioPerl

[Heikki Lehvaslaiho]

Frank,

I think you should contact Jaak Vilo (mailto:vilo@ebi.ac.uk) at EBI. He
works in the microarray group <http://www.ebi.ac.uk/microarray/>. Check his
programs at http://industry.ebi.ac.uk/~vilo/

	-Heikki

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!
> 
> 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.
> 
> * 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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______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
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