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Bioinformatics

Rob Miller rmiller at bsm.bioc.ucl.ac.uk
Thu Apr 4 21:33:31 EST 1996


Keith Bradnam (keith at evol.gene.nottingham.ac.uk) wrote:
: Leonard F. Kuehner wrote:
: > I have searched high and low for some information on bioinformatics and have
: > so far come up with nothing....snipped...Does anyone in this group know what 
: > bioinformatics is exactly.  

: Well seeing as I did my MSc in Bioinformatics and am now doing my PhD in it, 
: I guess I should know.
: Taken in its most literal sense, bioinformatics deals with biological information.
: The information in question is DNA, RNA, and protein sequence information.

... <snip>


: amino acids to look at.  At the end of the day, all the bioinformatician (if that
: is the word?) deals with is this raw sequence information, usually stored as
: a string on their computer.

... <snip>


bzzzzzt!  (note lower case, not shouting - I only disagree a *little* with Keith's
well thought out and very good comments :-)

I'm also a `bioinformaticist', my Ph.D. is interdisciplinary in biochem, chem, 
and computer science.  My disagreement with Keith's definition is that it's 
not sequence data *alone* we work with - my specialty is protein *structure* 
bioinformatics, so there's a lot of 3D modelling work and data - can't do much 
structure prediction without it !  

Others would probably claim their own subfield is included in `bioinformatics'.
`Informatics' covers what you can learn from databases, so analysis of evolution
at an organismal level might be included as well (though I'm more familiar with 
the term being limited to *molecular* bioinformatics).

It hasn't been brought up that I've seen, but I'd further point out that 
bioinformatics is distinct from `computational (bio)chemistry' in that the 
bioinformaticist normally is trying to do work from databases whereas the 
computational chemist has a mathematical model to be programmed and computed.
A good example might be the difference between Manfred Sippls `Potentials of
Mean Force' (PMF), a statistical/empirical potential based on observed distances
between amino acid pairs in 3D protein structures, versus the AMBER potential.

Maybe it's just that the (structure) bioinformaticists couldn't handle their 
quantum chem courses :-) :-) :-) :-) :-) :-)   (or just couldn't handle the 
problems in scaling the theory up to protein size molecules).


One more possible definition - I used this as one of several for the intro to 
a talk - What is bioinformatics ?  My wife's calendar.


					rob.  

(not married any more, but again soon :-)


--
-----------------------------------------------------
Rob Miller, Ph.D.  

Biomolecular Structure and Modelling Unit (BSM),
Department of Biochemistry and Molecular Biology,
University College / Gower Street / London WC1E 6BT.
United Kingdom.

Tel: +44 171419 3890           Fax: +44 171380 7193

Internet: rmiller at bsm.bioc.ucl.ac.uk 
http://www.biochem.ucl.ac.uk/~rmiller

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