I think the following may be of some interest to this group.
Claude
Claude Aflalo ########################## Phones: Office 972-7-6472118 ####
Unit for Science Teaching/Dept. of Life Sciences Lab 972-7-6472119
Ben Gurion University of the Negev Fax 972-7-6472890
P.O.Box 653 email: aflaloc at bgumail.bgu.ac.il
Beer Sheva 84105 Israel ### URL: http://www.bgu.ac.il/~aflaloc/aflalo.html
---------- Forwarded message ----------
Date: Thu, 19 Oct 2000 09:52:49 +0100
From: Nicolas Le Novere <nl223 at cus.cam.ac.uk>
To: bio-software at hgmp.mrc.ac.uk
Subject: StochSim 1.2, new version of the STOCHastic SIMulator
StochSim is a discrete, stochastic simulator for (bio)chemical
reactions. It employs a simple, novel algorithm in which particles
(e.g. proteins, small molecules or ions) are represented as individual
software objects which react according to probabilities derived from
concentrations and rate constants. Formally, it is a mesoscopic
simulator, meaning that it stores an internal representation of every
molecule in the system as a unique object, but does not simulate
diffusion.
The original version of StochSim (1.0) treated the entire reaction
system as a uniformly mixed solution. In the current version of
StochSim (1.2), a simple two-dimensional spatial structure has been
implemented, in which nearest-neighbour interactions of molecules
(such as clustered receptors on a membrane) can be simulated.
The core program is written in standard C++. A graphical interface
written in Perl/Tk is provided, which permits to setup the simplest
simulations. Stochsim can be retreived via ftp from
at ftp://ftp.cds.caltech.edu/pub/dbray/
Authors:
--------
Carl Firth
Tom Shimizu
Nicolas Le Nov=E8re
For the original description of StochSim see:
- Morton-Firth, C. J. & Bray, D. (1998). Predicting temporal
fluctuations in=20
an intracellular signalling pathway. J. Theor. Biol. 192, 117-128.
- Morton-Firth, C. J., Shimizu, T. S. & Bray, D. (1999). A
free-energy-based=20
stochastic simulation of the Tar receptor complex.=20
J. Mol. Biol.286, 1059-1074.=20
--
Dr Nicolas Le Nov=E8re http://www-alt.pasteur.fr/~lenov
Dpt of Zoology, Univ of Cambridge, Downing street, Cambridge CB2 3EJ, UK
tel: +44 1223 336623 fax: +44 1223 336676 e-mail: nl223 at cus.cam.ac.uk
"Things have changed in the past two decades." Bill Gates (1995)
---
