Bioinformatics + OCaml

Bioinformatics + OCaml

[Martin Jambon]

Hello,

I am helping a person to find someone who knows both OCaml and
bioinformatics (proteomics if possible) for a short "project" in the
United States.

I will give you more details privately, but I can tell you it is pretty
interesting and visa issues are the only reason why I don't do it myself.

Anyway, I'd be glad to talk with other OCaml-bioinformaticians.


Thanks for your help,


Martin


--
Martin Jambon
http://martin.jambon.free.fr

Re: [Caml-list] Bioinformatics + OCaml

[Jon Harrop]

On Friday 09 March 2007 19:08, Martin Jambon wrote:
> Hello,
>
> I am helping a person to find someone who knows both OCaml and
> bioinformatics (proteomics if possible) for a short "project" in the
> United States.
>
> I will give you more details privately, but I can tell you it is pretty
> interesting and visa issues are the only reason why I don't do it myself.
>
> Anyway, I'd be glad to talk with other OCaml-bioinformaticians.

I'm looking for bioinformatics examples for my new book on F#, so they might 
like to collaborate and get some free consultancy. :-)

-- 
Dr Jon D Harrop, Flying Frog Consultancy Ltd.
OCaml for Scientists
http://www.ffconsultancy.com/products/ocaml_for_scientists

Re: [Caml-list] Bioinformatics + OCaml

[Oliver Bandel]

On Sat, Mar 10, 2007 at 02:57:03PM +0000, Jon Harrop wrote:
> On Friday 09 March 2007 19:08, Martin Jambon wrote:                                                         
> > Hello,                                                                                                    
> >                                                                                                           
> > I am helping a person to find someone who knows both OCaml and                                            
> > bioinformatics (proteomics if possible) for a short "project" in the                                      
> > United States.                                                                                            
> >                                                                                                           
> > I will give you more details privately, but I can tell you it is pretty                                   
> > interesting and visa issues are the only reason why I don't do it myself.                                 
> >                                                                                                           
> > Anyway, I'd be glad to talk with other OCaml-bioinformaticians.                                           
>                                                                                                             
> I'm looking for bioinformatics examples for my new book on F#, so they might                                
> like to collaborate and get some free consultancy. :-)                                                      
>                                                                                                             


Look for Perl & Bioinformatics at O'Reilly#s Homepage
and rewrite the examples in Ocaml or F# ;-)


Ciao,
  Oliver

Re: [Caml-list] Bioinformatics + OCaml

[Jon Harrop]

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.

-- 
Dr Jon D Harrop, Flying Frog Consultancy Ltd.
OCaml for Scientists
http://www.ffconsultancy.com/products/ocaml_for_scientists

Re: [Caml-list] Bioinformatics + OCaml

[Ramon Diaz-Uriarte]

On 3/29/07, Jon Harrop <jon@ffconsultancy.com> 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.

Best,

R.


> --
> Dr Jon D Harrop, Flying Frog Consultancy Ltd.
> OCaml for Scientists
> http://www.ffconsultancy.com/products/ocaml_for_scientists
>
> _______________________________________________
> Caml-list mailing list. Subscription management:
> http://yquem.inria.fr/cgi-bin/mailman/listinfo/caml-list
> Archives: http://caml.inria.fr
> Beginner's list: http://groups.yahoo.com/group/ocaml_beginners
> Bug reports: http://caml.inria.fr/bin/caml-bugs
>


-- 
Ramon Diaz-Uriarte
Statistical Computing Team
Structural Biology and Biocomputing Programme
Spanish National Cancer Centre (CNIO)
http://ligarto.org/rdiaz