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Bioinformatics + OCaml
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Date: 2007-03-29 (10:23)
From: Ramon Diaz-Uriarte <rdiaz02@g...>
Subject: Re: [Caml-list] Bioinformatics + OCaml
On 3/29/07, Jon Harrop <> wrote:
> On Saturday 10 March 2007 21:15, Oliver Bandel wrote:
> > Look for Perl & Bioinformatics at O'Reilly#s Homepage
> > and rewrite the examples in Ocaml or F# ;-)
> I already did that but OCaml and F# have very different strengths compared to
> Perl (and all other languages currently used in bioinformatics). So I really
> need fresh examples that leverage these languages more, which typically means
> rewriting research that is currently almost impossible to code in Perl/Python
> as an easy ML program.

Not sure this adds anything, but the kind of bioinformatics I do is
mostly statistics and similar with genomic/proteomic data sets. And
many (most ?) people seem to do that via R (and maybe C, and to a
lesser extent Fortran, called from R). We also tend to use
parallelization quite a bit via MPI (from this list, I understand some
of the latter might fit some of F#'s strengths).

Python usage, for us, is limited to some initial data cleaning, error
checking, etc, (we also use some sed and awk) and the CGI interfaces.

I am not sure how OCaml would fit here but it'd be great to see
examples of usage.



> --
> Dr Jon D Harrop, Flying Frog Consultancy Ltd.
> OCaml for Scientists
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Ramon Diaz-Uriarte
Statistical Computing Team
Structural Biology and Biocomputing Programme
Spanish National Cancer Centre (CNIO)