CMU Artificial Intelligence Repository
GENESIS: GEneral NEural SImulation System
areas/alife/systems/genesis/
GENESIS (GEneral NEural SImulation System) is a general purpose
simulation platform which supports the simulation of neural systems
ranging from complex models of single neurons to simulations of large
networks made up of more abstract neuronal components. Most current
GENESIS applications involve realistic simulations of biological
neural systems. Although the software can also model more abstract
networks, other simulators are more suitable for backpropagation and
similar connectionist modeling. XODUS is a graphical front end for
GENESIS.
The distribution includes full source code and documentation for both
GENESIS and XODUS as well as fourteen demonstration and tutorial
simulations. Documentation for these simulations is included, along
with three papers that describe the general organization of the
simulator.
Also included is a set of "Rallpacks" benchmarks for speed
and accuracy of the simulation. The three sets of benchmarks model a
linear passive cable with many compartments, a highly branched cable, and
a linear axon containing Hodgkin-Huxley channels. The simulator results
may be compared to the exact analytic solutions (for the first two cases)
and to the results given by GENESIS and by NEURON, another popular neural
simulator. (The results for these two simulators show nearly identical
speed and accuracy.)
The GENESIS Users Group, BABEL, provides some informal support to
GENESIS users. BABEL members have access to an email list, a repository
of contributions by GENESIS users and developers, new simulations,
libraries of cells and channels, additional simulator components, new
documentation and tutorials, and bug reports and fixes. Membership
requires a one-time $200 registration fee made payable to the California
Institute of Technology and sent to Jim Bower, Computational Neural
Systems Program, 216-76, Caltech, Pasadena, CA, 91125. Please provide
name, institution, mailing address, phone number, an email address for
the mailing list, and an account name for use on the BABEL computer.
Origin:
genesis.cns.caltech.edu (131.215.137.64)
Before using ftp, you must telnet to genesis.cns.caltech.edu
and login as the user "genesis" (no password required) to
register. If you answer all the questions asked of you an
'ftp' account will automatically be created for you. You can
then 'ftp' back to the machine and download the software.
Version: GENESIS 1.4.1 (August 1993);
RALLPACKS 1.1 (July 1992)
Requires: C
X-windows (versions X11R3, X11R4, and X11R5)
UNIX (Sun version 4.0 and up, DEC Ultrix 3.1, 4.0 and up)
Ports: The current version of GENESIS has also been used with
Silicon Graphics (Irix 4.0.1 and up) and the HP 700
series (HPUX).
Copying: Copyright (c) 1988-93 by California Institute of Technology
(Caltech).
Use, copying, modification, and distribution permitted.
CD-ROM: Prime Time Freeware for AI, Issue 1-1
Author(s): Genesis --
Matt A. Wilson
Upinder S. Bhalla
John D. Uhley
David H. Bilitch
Mark E. Nelson
James M. Bower
Rallpacks --
Upinder S. Bhalla, David H. Bilitch, James M. Bower,
Frank Eeckman, Erik De Schutter, John Miller, Michael
Hines, Mark Nelson, Tony Zador, Wilfrid Rall
Contact: genesis@cns.caltech.edu
Keywords:
Artificial Life, Authors!Bhalla, Authors!Bilitch,
Authors!Bower, Authors!Nelson, Authors!Uhley, Authors!Wilson,
BABEL, Benchmarks!Neural Systems, Biological Simulation,
CalTech, GENESIS, Neural Networks!Simulators,
Neural Systems!Benchmarks, Neural Systems!Simulators,
Rallpacks, XODUS
References:
Wilson, M. A., Bhalla, U. S., Uhley, J. D., and Bower, J. M. (1989)
GENESIS: A system for simulating neural networks. In: Advances in Neural
Information Processing Systems. D. Touretzky, editor. Morgan Kaufmann,
San Mateo, CA. pp. 485-492
Matthew A. Wilson and James M. Bower, "The Simulation of Large-Scale
Neural Networks", in Methods in Neuronal Modeling, Christof Koch and Idan
Segev, editors. (MIT Press, 1989)
Bhalla, et al. (1992) Trends Neurosci. 15: 453-458.
James M. Bower and David Beeman, "The Book of GENESIS",
TELOS/Springer-Verlag, 1994.
Last Web update on Mon Feb 13 10:19:57 1995
AI.Repository@cs.cmu.edu