Metabolic modeling

Herbert M Sauro HSauro at
Sat Jan 25 14:52:03 EST 1997

In article <5c2csl$kds at>, Pedro Mendes
<prm at> writes
>In article <5bo5uv$3s2 at>, jeff at 
>>        I've got a poster on my wall that illustrates many of the major
>>metabolic pathways such as the citric acid cycle, pentose pathway, urea
>>cycle, etc.  It seems that there is a simulation waiting for me to code 
>>it in there somewhere and I'd like to hear from anyone who is working on
>>such a project.   
Your're only about about 50 to 60 years too late. Metabolic modelling
has been going on for quite some time. Some people have even tried to
model entire cells without much success however. The main problem seems
to be poor state of knowledge concerning the kinetic properties of
enzymes. To be honest I would bother. More profitable would be to model
hypothetical systems from which you can begin to gain an understanding
of the dynamics of metabolic systems. Once you've done a bit of that you
can start reading about Metabolic Control Analysis, in some ways a
response to the present futility of trying to model real pathways. If
you want a reallly up todate reference then I would go for:

"Understanding the Control of Metabolism" by D A Fell. (1997) Portland
Press, ISBN 1 85578 047 X

>see before you get busy
>duplicating a lot of code. (BTW there are a few other programs similar
>to Gepasi).
>I hope this helps.

Or even SCAMP, found at

Herbert M Sauro
Future Skill Software (Specialists in Science Software for Education)
email:     HSauro at
Telephone: 01974 282428
"He who cannot draw on 3000 years is living from hand to mouth" Goethe
"Ah, but a man's reach should exceed his grasp, or what's a heaven for?"
R Browning.

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