Fwd: Re: [Biosqueak] The germ of an idea (Bio Haskell library??)

[Galchin Vasili]

--0-63064052-999368721=:59076
Content-Type: text/plain; charset=us-ascii
Content-Disposition: inline


Note: forwarded message attached.


__________________________________________________
Do You Yahoo!?
Get email alerts & NEW webcam video instant messaging with Yahoo! Messenger
http://im.yahoo.com
--0-63064052-999368721=:59076
Content-Type: message/rfc822

X-Apparently-To: vngalchin@yahoo.com via web12203.mail.yahoo.com; 01 Sep 2001 00:21:21 -0700 (PDT)
Return-Path: <squeak-dev-admin@lists.squeakfoundation.org>
X-Track: 1: 40
Received: from sqf.theinternetone.net  (EHLO lnx-1.theinternetone.net) (62.4.94.12)
  by mta301.mail.yahoo.com with SMTP; 01 Sep 2001 00:21:18 -0700 (PDT)
Received: from lnx-1.theinternetone.net (localhost [127.0.0.1])
	by lnx-1.theinternetone.net (Postfix) with ESMTP
	id F1FE764D1F; Sat,  1 Sep 2001 09:10:24 +0200 (MEST)
Delivered-To: squeak-dev@lists.squeakfoundation.org
Received: from ns1.pmatrix.com (unknown [207.126.103.48])
	by lnx-1.theinternetone.net (Postfix) with ESMTP id D4F7B64C92
	for <squeak-dev@lists.squeakfoundation.org>; Sat,  1 Sep 2001 09:05:52 +0200 (MEST)
Received: from beth.pmatrix.com (c222217-a.plstn1.sfba.home.com [24.176.131.10]) by ns1.pmatrix.com (8.8.7/8.7.3) with ESMTP id AAA06486 for <squeak-dev@lists.squeakfoundation.org>; Sat, 1 Sep 2001 00:05:58 -0700
Message-Id: <4.3.2.7.2.20010831234438.036256c8@mailhost.pmatrix.com>
X-Sender: janb@mailhost.pmatrix.com
X-Mailer: QUALCOMM Windows Eudora Version 4.3.2
To: squeak-dev@lists.squeakfoundation.org
From: Jan Bottorff <janb@pmatrix.com>
Subject: Re: [Biosqueak] The germ of an idea
In-Reply-To: <3B904F50.D615E83C@telinco.co.uk>
References: <200108281919.f7SJJq027486@ike.ucdavis.edu>
 <m1zo8jzfyb.fsf@halfdome.holdit.com>
 <4.3.2.7.2.20010831131722.03ce2670@pop.mindspring.com>
Mime-Version: 1.0
Content-Type: text/plain; charset="us-ascii"; format=flowed
Sender: squeak-dev-admin@lists.squeakfoundation.org
Errors-To: squeak-dev-admin@lists.squeakfoundation.org
X-BeenThere: squeak-dev@lists.squeakfoundation.org
X-Mailman-Version: 2.0
Precedence: bulk
Reply-To: squeak-dev@lists.squeakfoundation.org
List-Help: <mailto:squeak-dev-request@lists.squeakfoundation.org?subject=help>
List-Post: <mailto:squeak-dev@lists.squeakfoundation.org>
List-Subscribe: <http://lists.squeakfoundation.org/listinfo/squeak-dev>,
	<mailto:squeak-dev-request@lists.squeakfoundation.org?subject=subscribe>
List-Id: The general-purpose Squeak developers list <squeak-dev.lists.squeakfoundation.org>
List-Unsubscribe: <http://lists.squeakfoundation.org/listinfo/squeak-dev>,
	<mailto:squeak-dev-request@lists.squeakfoundation.org?subject=unsubscribe>
List-Archive: <http://lists.squeakfoundation.org/pipermail/squeak-dev/>
Date: Sat, 01 Sep 2001 00:05:22 -0700
Content-Length: 903


>Mind you, if we're talking of stuff as intensive as the Human Genome,
>we're talking of very serious number crunching.

A friend of mine (who is quite into Bioinformatics) and I (who knows almost 
nothing about Bioinformatics) had a discussion a few weeks ago. It seemed 
like the thought was that many of the algorithms would be more efficient if 
fancy pattern matching logic was used instead of brute force compute power. 
For example, a multiple parallel state machine pattern search (i.e. a 
parser) might beat a bunch of passes with simple pattern match searches. It 
also seems possible the intersection of the bioinformatics wizards with the 
advanced parser wizards is almost an empty set.

Smalltalk is just super good at implementing fancy algorithms. I guess a 
question to ask: is it REALLY a very serious number cruncher problem, or is 
that just what current algorithms end up being.



--0-63064052-999368721=:59076--