From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: X-Spam-Checker-Version: SpamAssassin 3.1.3 (2006-06-01) on yquem.inria.fr X-Spam-Level: * X-Spam-Status: No, score=1.4 required=5.0 tests=SPF_NEUTRAL autolearn=disabled version=3.1.3 X-Original-To: caml-list@yquem.inria.fr Delivered-To: caml-list@yquem.inria.fr Received: from discorde.inria.fr (discorde.inria.fr [192.93.2.38]) by yquem.inria.fr (Postfix) with ESMTP id B691BBC69 for ; Thu, 29 Mar 2007 12:23:53 +0200 (CEST) Received: from ug-out-1314.google.com (ug-out-1314.google.com [66.249.92.172]) by discorde.inria.fr (8.13.6/8.13.6) with ESMTP id l2TANrHX025524 for ; Thu, 29 Mar 2007 12:23:53 +0200 Received: by ug-out-1314.google.com with SMTP id q2so532497uge for ; Thu, 29 Mar 2007 03:23:53 -0700 (PDT) DKIM-Signature: a=rsa-sha1; c=relaxed/relaxed; d=gmail.com; s=beta; h=domainkey-signature:received:received:message-id:date:from:to:subject:cc:in-reply-to:mime-version:content-type:content-transfer-encoding:content-disposition:references; b=oWlLSTEB9/egbc9IUF3CGfyTR3fp83sD1dwxtiVrTL1D3iMwKzot/Ufcs1Vp0fDUHOG2KUSTvzET3XlaGvmXK+AsmJNUJtY1Sh/3yM4CvBMEnaQLi/Vv/skxwZi/ifhmbUW7H1iNFYW9vugOhfHIA2uj3Z7HYFRQzP1ZKJUkgNM= DomainKey-Signature: a=rsa-sha1; c=nofws; d=gmail.com; s=beta; h=received:message-id:date:from:to:subject:cc:in-reply-to:mime-version:content-type:content-transfer-encoding:content-disposition:references; b=H3ewvoLrYUi0JT11PnkOS4isnj/cD8tYFHQxPu+6qfe6mLYH42GFHKPGYxVdT1RvVpqKe2SFKdCn4gIPhbX4+bzeEhHdsJaJSepsVCXO0bVPHjPeU0doZP/UqJn+T/vsVNpJXETSH4oGJff8Upe35PV9AaGjciUTtOcbH1e0HAA= Received: by 10.114.14.1 with SMTP id 1mr199257wan.1175163832144; Thu, 29 Mar 2007 03:23:52 -0700 (PDT) Received: by 10.114.56.6 with HTTP; Thu, 29 Mar 2007 03:23:52 -0700 (PDT) Message-ID: <624934630703290323l68039b3qf6c489d674872e65@mail.gmail.com> Date: Thu, 29 Mar 2007 12:23:52 +0200 From: "Ramon Diaz-Uriarte" To: "Jon Harrop" Subject: Re: [Caml-list] Bioinformatics + OCaml Cc: caml-list@yquem.inria.fr In-Reply-To: <200703290131.05083.jon@ffconsultancy.com> MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Content-Disposition: inline References: <200703101457.03860.jon@ffconsultancy.com> <20070310211505.GA492@first.in-berlin.de> <200703290131.05083.jon@ffconsultancy.com> X-j-chkmail-Score: MSGID : 460B93B9.000 on discorde : j-chkmail score : X : 0/20 1 0.000 -> 1 X-Miltered: at discorde with ID 460B93B9.000 by Joe's j-chkmail (http://j-chkmail . ensmp . fr)! X-Spam: no; 0.00; ocaml:01 bandel:01 o'reilly:01 ocaml:01 rewriting:01 beginner's:01 bug:01 ramon:98 frog:98 ramon:98 beginners:01 wrote:01 wrote:01 sed:01 oliver:01 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. 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