wallace@fmi.ch (05/28/88)
From: Andrew Wallace <wallace%fmi.ch@RELAY.CS.NET>
Does anyone have any information about computer modelling
of intracellular metabolic processes ? I am particularly interested
in making models of switching processes, negative/positive feedback
regulation of intracellular pathways etc. Is there any software
available ? Who should I be talking to about this subject ? Any
help would be appreciated.
Please reply to : WALLACE%FMI.CH@EAN-RELAY.CS.NET (ean-mail)
or : Dr. Andrew Wallace,
Friedrich Miescher Institute,
P.O. Box 2543,
CH-4002 Basel,
Switzerland.
Telephone : (+)-41-61-374531.
Thank you for reading this message.
Andrew Wallace,
Friedrich Miescher Institute, Basel, Switzerland.
-------BRUTLAG@BIONET-20.ARPA (05/30/88)
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. -------