In article <1993Mar24.205757.7892 at leland.Stanford.EDU> arkin at leland.Stanford.EDU (Adam P. Arkin) writes:
>Greetings,
>> I am looking for Unix and Mac based programs which are set up to
>accurately simulate the kinetics of large portions of metabolism or, for
^^^^^^^^^^
>that matter, any multiply branched chemical reaction network. I am also
>interested in knowing the exact enzyme models used in each portion of the
^^^^^^^^^^^^^^^^^^^
>pathway.
> Currently, I have built my own model of the TCA and Glycolytic/
>Gluconeogenic systems and would like to extend the models to include more
>of the surrounding biochemistry and to better imitate reality (Ha!).
> I would be grateful for any help anyone can give!
>
May I ask what values do you use for the hundreds of parameters that your
model has? I'm afraid the route you are taking is the same as David Garfinkel
took in the 60s and it led us to a dead-end. He was able to simulate
glycolysis in very good detail (with the exception of the level of phosphate)
although his model was missing what we now know is one very important element
of the pathway: Fructose-2,6-BisPhosphate.
What we can learn with this example is that if we have a sufficiently
complex model, we can adjust the parameters to obtain virtually any behaviour
we want (well, not _any_ but a very wide range, anyway).
Also, the question of the numerical values for the parameters is a very
difficult one as there is no complete set available that was determined for
the same cells (frequently you'll have to use data from hepatocytes, some
times from E. coli. etc.)
Finally, this approach is very weak (to say the least) as by using the
data obtained in vitro with isolated enzymes, it misses all the enzyme-enzyme
interactions that are present in all cells.
Now, to answer your question, I do not know of any such program for the MAC
(I mean a speciallized one, as you may use STELLA for this purpose). I would
be interested to know if you get any positive answer. You might have seen my
previous posting announcing my own simulator, GEPASI, which presently only
has a front-end for Windows-3.
I wish you the best on your immitation of reality (HA!)
Pedro Mendes
prm at aber.ac.uk
