Subject: Summary: BioInformatics. (fwd)

From: Iraj Daizadeh <[email-masked]>
Date: Thu, 29 Oct 1998 18:46:09 -0500 (EST)

Hello.

I did not get a wide response concerning Bioinformatics software.  I am
slightly disappointed, but I believe it to be understandable.

My hypothesis is this: 

Computational Chemistry has recently split into the following three 
sub-areas:

		Computational 		Chemistry
		/		|	    \
	  Traditional       Biogenomics    Combinatorial
			    Bioinformatics

By Traditional, I mean: quantum chemistry, dynamics, etc...
By Biogenomics/Bioinformatics: I mean: genome/protein database analysis
By Combinatorial, I mean: molecular diversity, molecular similarity,
etc..
There are of course ``interdisciplinary'' fields as well: quantum
molecular similarity, etc...

I have been ``brought'' up in the left-most branch of the above tree, viz.
``traditional'' computational chemistry.  My dissertation, entitled
``Theoretical Study of Electron Transfer Reactions in Biological and
Chemical Systems'', examined long-distance electron transfer reactions
using semi-empirical, ab initio, and molecular dynamics techniques (and
their combinations). My post-doctoral work is in Combinatorial Chemistry,
my interest lies more in BioGenomics, however.  The question I submitted
to the CCL was meant to introduce me (and through this summary hopefully 
others) to the software resources that are available in the biogenomics
area of research.

>From the few responses to my query, I see that maybe the Computational
Chemistry Communittee (or at least members of this list) is
focused on the more traditional areas of research.  Yet, when I explore
www.altavista.com with the keyword bioinformatics, I find many, many hits
that correspond to software packages (free or commercial). [There is a
chance that few people actually took the time to read my email!]

The importance of this field has been quickly realized.  Journals such as
Science and Nature are loaded with employment opportunities for
Bioinformatics experts. Indeed, there is a strong trend for those in
industry to invest in Bioinformatics.  A recent article was posted in
C&EN: (Oct. 19, 1998 pp.29-33 ``Bioinformatics begins to buzz'' Ronald S.
Rogers); and also in the notebook section of The Scientist ( ``...But
don't forget about bioinformatics'' September 28,1998 pp 31) attribute to
this phenomena. 

The question is why are the molecular biologists and the computer
scientists having all the fun! Why has the Computational Chemistry
Communittee been so slow to respond to these new branches of study when
they deal in a most direct way to what is happening on a molecular level.
I feel as though our contributions to this field may be enormous!

Your thoughts on any of the above statements would be acknowledged.

Sincerely, Iraj.

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The outline of this summary is as follows:

	I. Main query.
	II. Responses from the communittee.

Sincerely,

Iraj.

I)

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Hello.

I am interested in obtaining codes (written in any language) that are free
or relatively free (< $500.00) for members in academia that can visualize
and manipulate Genetic Database Information (nucleic acid sequences,
etc...) for problems in BioInformatics.  I will summarize all respones as
is traditional on the CCL.

Sincerely,

Iraj.

Iraj Daizadeh, Ph.D.
Harvard University
Department of Chemistry and Chemical Biology
12 Oxford Street, Box #35
Cambridge, MA 02138-2902
Phone:  617-495-2654
Fax:   	617-495-1823
email:  [email-masked]

II)

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Hi,

Have a look at AntheProt and AntheNuc:

     ftp://ibcp.fr/pub/

There are also lists of PD software at

     http://mbisg2.sbc.man.ac.uk/soft4.html
     http://www.ebi.ac.uk/biocat/

- there's a lot of it out there; I'll be very interested to read your 
summary.

Good luck,

Nick
*****************************************************************
Nick Rhodes, Chemical Information Systems Research Group, 
Department of Information Studies, University of Sheffield, 
Regent Court, 211 Portobello Street, Sheffield, 
South Yorkshire, S1 4DP, United Kingdom.

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You may want to try CuraTools, our sequence analysis package
which is freely available for use on the World Wide Web. Visit 
"http://www.curagen.com" and choose "CuraTools".

Andreas Windemuth
CuraGen Corporation
555 Long Wharf Drive
New Haven, CT 06511

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Hello, Iraj!

One of my colleagues forwarded me your question on CCL.  You may be interested
in the Silicon Graphics MineSet product, which has been used by Incyte
Pharmaceuticals to visualize genomic databases.  You can see, for example, our
"MineSet for Discovery Research Report" for various examples of how MineSet has
been used in bioinformatics and cheminformatics:

http://www.sgi.com/chembio/resources/mineset/index.html

The specific example of Incyte Pharmaceuticals is here:

http://www.sgi.com/chembio/resources/mineset/bioinfo/genomic_database/index.html

I am afraid though that the price of MineSet is beyond what you specified.  You
can, however, obtain a 30 day free evaluation license for MineSet:

http://www.sgi.com/Products/Evaluation/#mineset

May I ask what you are interested in being able to do?  Alan Robinson
([email-masked]) at the European Bioinformatics Insitute may be able to give
you some pointers.

-- Haruna  :)

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