[Bioperl-l] clustering algorithms in BioPerl

Hilmar Lapp lapp@gnf.org
Fri, 23 Feb 2001 09:52:46 -0800

Frank Gibbons 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.

In my opinion they are perfectly appropriate for Bioperl. 

> * If so, does any one know of other work that may have been done in this area,
> on which I could build/integrate with?

There is PDL (http://pdl.perl.org/), but I haven't seen clustering on
their pages. No idea whether they're working on it.

> * 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

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).

As for naming, I don't understand clearly yet the scope of your
project. The best thing usually is to come up with a proposal and post

You will also need write-access to the repository (Chris?).


Hilmar Lapp                            email: lapp@gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757