From owner-metabolic-reg@net.bio.net Wed Feb 05 22:00:00 1997
Path: biosci!daresbury!not-for-mail
From: Pedro Mendes <prm@aber.ac.uk>
Newsgroups: bionet.metabolic-reg
Subject: Re: On direct simulation.
Date: 6 Feb 1997 17:34:45 -0000
Organization: University of Wales Aberystwyth
Lines: 38
Sender: lpddist@mserv1.dl.ac.uk
Distribution: bionet
Message-ID: <5dd4nl$osb@mserv1.dl.ac.uk>
Comments: Authenticated sender is <prm@pophost.aber.ac.uk>
X-mailer: Pegasus Mail for Win32 (v2.42a)
MIME-Version: 1.0
Original-To: btk-mca@dl.ac.uk

As everyone probably knows I am strong defender of computer simulation,
but read on...

On  6 Feb 97 at 7:02, Paul M. Schlosser wrote:

> [...]
> 1) in the case where one does not have equations for all the enzymes
>    involved, or you want to quantify the behavior of a system with
>    too many variables to develop a comprehensive model, they allow one to
>    analyze the system without building a formal model;
> 2) a historic lack of the compute-power and software needed to do the
>    fully dynamic stuff.
>[...]

A gem on point 2) (using computers to help our understanding of metabolic 
regulation) is:

Kacser, H. and Burns, J. A. (1968) Causality, complexity and computers. In
Quantitative biology of metabolism., (ed. A. Locker), pp. 11-23, Springer
Verlag, Berlin.

Yes, 1968!

There is one third (and probably the strongest) argument for that type of
approach: the properties derived with that approach are independent of the
kinetics. I see the two approaches (kinetic modelling and steady-state
sensitivity analyses) as complementary. Of course the kinetic model
displays all the properties that one would find with the sensitivity
analyses (and even with just the structural analysis of the Reder type)
but it is nice to be able to identify what are the properties that are
independent of the kinetics.

Pedro 

Pedro Mendes                                     Inst. Biological Sciences
prm@aber.ac.uk (home: pedro@enzyme.demon.co.uk)  Univ. Wales, Aberystwyth,
http://gepasi.dbs.aber.ac.uk/pedro/prmhome.htm   Dyfed SY23 3DA, U.K.
http://gepasi.dbs.aber.ac.uk/softw/gepasi.html   FAX: +44 (0)1970 622350

.