Metabolic Simulators

Sean MARRETT sean at pet.mni.mcgill.ca
Thu Mar 25 10:59:33 EST 1993


In article <1993Mar25.075107.493 at dxcern.cern.ch>, sendall at dxpt01.cern.ch (Mike Sendall) writes:
|> 
|> In article <1993Mar24.205757.7892 at leland.Stanford.EDU>, arkin at leland.Stanford.EDU (Adam P. Arkin) writes:
|> ..
|> >	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!
|> 
|> It would be nice if you could post a summary of any information you
|> get.  But when I tried to email you at this address I got:
|> 
|> 
|> While talking to leland.stanford.edu:
|> >>> RCPT To:<arkin at leland.stanford.edu>
|> <<< 550 <arkin at leland.stanford.edu>... Addressee unknown
|> 550 <arkin at leland.stanford.edu>... User unknown
|> 

I had the same problem in replying to this posting, so for better or
worse here is my reply.


To: arkin at leland.Stanford.EDU (Adam P. Arkin)
Subject: Re: Metabolic Simulators

Dear Adam:
In article <1993Mar24.205757.7892 at leland.Stanford.EDU>, you write:
|>  (deleted copy of message above)

The program GEP205 is almost exactly what you want, except that it is
set up to run on windows. However, i think the author of the program
set it up in such a way that the simulator can be easily separated
from the interface. There are also a number of reaction kinetic
solvers that I have tried out from a site in Oklahoma, but I should
recheck that before I get into any trouble. There is also a mailing
list (somewhat inactive) which has been set up to discuss these issues
- there is more info available on this in the .zip files i have listed
below.

SO, here are the files you want

Directory PD1:<MSDOS.BIOLOGY>
 Filename   Type Length   Date    Description
==============================================
GEP205B.ZIP   B  552087  930210  WIN31: Simulation of biochemical pathways
GSRC205B.ZIP  B  298963  930210  Source code of GEP205B.ZIP simulation program

(this translates into oak.oakland.edu:/pub/msdos/biology/gep205b.zip,
and gsrc205b.zip)

For Unix systems look at

kekule.osc.edu:/pub/chemistry/kinetics,kinetics2

Also, Archie shows several Macintosh files (such as
/micros/mac/umich/misc/biology: enzymekinetics1.0c.sit.hqx (presumably
the Umich Macintosh archives and also found in
fly.bio.indiana.edu:/molbio/mac/enzymekinetics.*)

there is also a Maple (symbolic algebra system similar to Mathematica) system
which will do symbolic solutions of enzyme systems.

Sean

--------------------------------------------------------
Sean Marrett                     email: sean at pet.mni.mcgill.ca 
wb213, PET Unit, Montreal Neurological Institute.
3801 University St., Montreal, Quebec.	H3A 2B4 
                                 tel:(514)-398-1537,1996 Fax: 8948 

P.S.

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