[BiO BB] Re: Bioinformatic and the Smith-waterman

[Michael Liebman]

Fyi

Liebman, M. N. Molecular Modeling of Protein Structure and Function: A
Bioinformatic Approach, J. Comp.-Aided Molecular Design 1, 323-341 l987

Michael N. Liebman, Ph.D.
Executive Director
Windber Research Institute
 
President and Managing Director
Strategic Medicine, Inc
 
620 Seventh St
Windber, PA 15963
 
(814) 467-9844 
(814) 361-6932 Office
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-----Original Message-----
From:
bio_bulletin_board-bounces+m.liebman=wriwindber.org at bioinformatics.org
[mailto:bio_bulletin_board-bounces+m.liebman=wriwindber.org at bioinformati
cs.org] On Behalf Of J.W. Bizzaro
Sent: Tuesday, July 31, 2007 7:34 PM
To: Temple F. Smith
Cc: BiO_Bulletin_Board at bioinformatics.org
Subject: [BiO BB] Re: Bioinformatic and the Smith-waterman

Hi Temple!

(For those on the mailing list, the origins of the word "bioinformatics"
was brought up in this thread:
http://bioinformatics.org/pipermail/bio_bulletin_board/2002-April/000635
.html and we have a short wiki page on the topic:
http://wiki.bioinformatics.org/Origins_of_bioinformatics)

Thank you for clearing up some misconceptions about the origins of the
field, including some of my own.  I guess when we spoke about this
around 1998, you actually said that you were *incorrectly* credited with
having coined the word.  In any case, I agree that no one person or
group started the field.

And it seems there are as many different definitions as there are
practitioners.  To me, bioinformatics is a compound of "bio" and the
English/common word "informatics"
(http://en.wikipedia.org/wiki/Informatics), with the latter being a
subdiscipline of computer science, whereas the French "informatique"
will translate to "computer science" in general.

A Wikipedia contributor wrote the following about "informatics," and I
pretty much agree with it: "Used as a compound, in conjunction with the
name of a discipline, as in medical informatics, bioinformatics, etc.,
it denotes the specialization of informatics to the management and
processing of data, information and knowledge in the named discipline,
and the incorporation of informatic concepts and theories to enrich the
other discipline."

So, I think of bioinformatics as a subdiscipline of computational
biology, the same way that informatics is a subdiscipline of computer
science.  But, I will cede that most people think that the terms are
synonymous.  And maybe it just doesn't matter.

I will integrate most of what you've written into our wiki, which will
hopefully help clear up some of the confusion about where things
started.

Cheers,
Jeff

Temple F. Smith wrote:
> Jeff for the record:
> 
>       Jean-Michel Claverie of France used the term "bio-informatik"
> in some email at the time of the "Waterville Valley computational
> biology meetings in the mid to late 80's. However in his book,
> Bioinformatics for Dummies I do not recall that he discusses the
> origin of the term? Recall that the term Informatik is the French
> word for computer science and Jean-Michel was one of the early guys
> in this "field" but true computational biology goes back to Haldane
> (1908) and D'arcy Thompson (1942), Dayhoff (1966) etc ..... to say
> nothing about the x-ray crystal guys of the last 1950's!! Clearly the
> term was not used in 1980 to 1982 when Dr. Waterman and I were
> starting out!! And no one "started the Field of Bioinformatics" it
> grow out of the molecular biology with protein sequencing and then
> DNA/RNA sequencing's need for databases and computer analysis. The
> first such recognized early work was by people like Zuckerkandl and
> Pauling (1965) and Fitch and Margolisash (1967) and then Needleman
> and Wuchsch (1977)! Thus unless the Dr. Hwa A.Lim can claim to have
> been doing sequence comparative analysis in the late 1960's he is not
> a founder!
>        While I was the organizer of the three Waterville Valley Genes
> and Machines meetings to which Jean-Michel attended, I did not use
> the term for at least another two years if I remember correctly. Also
> on my visits with Dayhoff and later Fitch they both agreed that it
> was likely Jean-Michel then at the FRENCH Institute Pasture who
> surely used it first --particularly given his use in email as 
> something he had been using at home in the Paris Institute. Thus
> unless Jean-Michel says other wise all others making such claims
> should stop! This is an old discussion which I find not funny any
> more. In fact the terms is a bit out of date these days and the
> better term is computational biology in any case.
> 
> Please pass this on to who ever is still asking this now unimportant
> question.
> 
> Temple F. Smith, PhD
> BMERC
> Boston University
> 

-- 
J.W. Bizzaro
Bioinformatics Organization, Inc. (Bioinformatics.Org)
E-mail: jeff at bioinformatics.org
Phone:  +1 508 890 8600
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