Path: utzoo!utgpu!water!watmath!uunet!ig!daemon
From: BRUTLAG@BIONET-20.ARPA
Newsgroups: bionet.general
Subject: Re: Request for information
Message-ID: <6459@ig.ig.com>
Date: 30 May 88 15:53:26 GMT
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From: Doug Brutlag <brutlag@BIONET-20.ARPA>

To Andrew Wallace,

	Below I have listed a few references by groups involved in
simulating basic metabolism and viral multiplication using various
methods.  The classical quantitative approaches follow from the methods
of Britten Chance and David Garfinkel.  Recently other groups have been
applying more symbolic methods to simulating metabolism as described in
Myers and Friedland below.  There was also a seminal paper by a Belgium
group referenced in the Myers paper which I do not have at hand.  Peter
Karp in the Knowledge Systems laboratory at Stanford (KARP@SUMEX-AIM.
STANFORD.EDU) has continued in this tradition and has simulated gene
regulation phenomena known as attenuation as part of his Ph.D. project.

	I have also been developing rule-based simulations of DNA
metabolism using classical production rules and assumption-based truth
maintenance systems myself.  I will send you an abstract of our work in
the mail.  There is also an NIH supported Simulation group at Duke that
applies advanced computing methods and graph theory to the problem of
metabolic simulation but I do not have any references at hand.  Perhaps
others on the Net can fill in this list.

Doug Brutlag 

@find simulat in ai.bib

*@Article[meyers84,
*       Key=<Myers and Friedland>,
*       Author=<Meyers, S. and Friedland, P.>,
*       Journal=<Nucleic Acids Res.>,
>       Title=<Knowledge-based simulation of genetic regulation in
*bacteriophage lambda>,
*       Year=<1984>,
*       Volume=<12>,
*       Pages=<1-10>
*]

1 hit on key "simulat" in ai.bib.
@find simulat in computer.bib

*@article[franco84,
*       Key=<Franco and Canela>,
*       Author=<Franco, R. and Canela, E. I.>,
*       Journal=<Eur. J. Biochem.>,
>       Title=<Computer simulation of purine metabolism>,
*       Year=<1984>,
*       Volume=<144>,
*       Pages=<305-315>
*]

*@article[kohn83a,
*       Key=<Kohn and Garfinkel>,
*       Author=<Kohn, M. C. and Garfinkel, D.>,
*       Journal=<Ann. Biomed. Eng.>,
>       Title=<Computer simulation of metabolism in palmitate-perfused rat heart
. II.
*      Behavior of complete model.>,
*       Year=<1983>,
*       Volume=<11>,
*       Pages=<511-531>
*]

*@article[kohn83b,
*       Key=<Kohn and Garfinkel>,
*       Author=<Kohn, M. C. and Garfinkel, D.>,
*       Journal=<Ann. Biomed. Eng.>,
>       Title=<Computer simulation of metabolism in palmitate-perfused rat heart
. I.
*      Palmitate oxidation.>,
*       Year=<1983>,
*       Volume=<11>,
*       Pages=<361-384>
*]

3 hits on key "simulat" in computer.bib.
-------