David M. Senseman
senseman at lucy.brainlab.utsa.edu
Tue Mar 2 08:12:17 EST 1993
A relative large number of individuals asked for more details concerning
the Caltech Neurosimulator (GENESIS) so I am posting part of the GENESIS
"readme" file. There is/was a "free" verion of GENESIS that could be obtained
from Caltech (126.96.36.199 babel.cns.caltech.edu) as mentioned below.
However, it you are serious about neurosimulation, then you will want to join
the Babel user group (also see below). When I joined I think it cost $250
but it's been a while so the cost might be higher or lower.
GENESIS is not a game program! It is a serious modeling program for serious
research. It is a big program and requires a fair amount of hardware to run
at a reasonable speed. It will NOT run on PC's and Mac's.
GENESIS (GEneral NEural SImulation System) was developed to support
the simulation of neural systems ranging from complex models of single
neurons to simulations of large networks made up of more abstract
neuronal components. For the last two years GENESIS has provided the
basis for laboratory courses in neural simulation at both Caltech and the
Marine Biological Laboratory in Woods Hole, MA. Most current GENESIS
applications involve realistic simulations of biological neural systems,
however, the system has also been used to model more abstract networks.
The system is not, however, a particularly efficient way to construct and
run simple feedforward back propagation type simulations.
XODUS (X-windows Output and Display Utility for Simulations) was
written to provide a graphical interface for the GENESIS system. It was
written with both portability and flexibility in mind. It provides a
platform for modelers to construct an interface for particular simulations
using a high level interpretive language and an existing library of
graphical widgets. Although written in conjunction with the simulator,
XODUS comprises a standalone package potentially useful with a variety of
applications. More information on the simulator and its interface can be
obtained from an article by: Wilson, M.A., Bhalla, U.S., Uhley, J.D., and
Bower, J.M. titled: GENESIS: A system for simulating neural networks. In:
Advances in Neural information processing systems. D. Touretzky, editor.
Morgan Kaufmann, San Mateo, CA. 485-492, 1989).
Machine dependence and distribution details:
GENESIS and XODUS are written in C and run on SUN and DEC graphics
work stations under UNIX (Sun version 4.0 and up, Ultrix 3.1, 4.0 and up),
and X-windows (version 11.3 and 11.4). The present version will also run
on the SGI with Irix 4.0.1 and up and the HP 700 series.
The software occupies close to 25 MB of disk space during the
compilation process on a SPARCstation 2. Non-SPARC machines will require
less room to compile. Once compilation and installation has been done, the
software occupies about 10 MB of disk space, and can use as little as 4 MB
if user-written C code is not to be linked into the simulator. The
distributed compressed tar file is just under 2 MB in size. The current
distribution includes full source for both GENESIS and XODUS as well as nine
tutorial simulations (squid axon, multicell, visual cortex, neuron
tutorial, help screen demo, neurokit, channel, vclamp, int_methods).
Documentation for these tutorials is included along with three papers
that describe the general organization of the simulator.
GENESIS Users Group:
In addition to receiving this updated version of GENESIS, members of BABEL
are entitled to access the BABEL directories and bulletin board. These are
used as a depository for interesting simulations, additional simulator
components, bug reports and fixes, and the posting of questions and hints
for setting up GENESIS simulations. Inquiries concerning BABEL membership
may be sent to genesis at cns.caltech.edu.
David M. Senseman, Ph.D. | Imagine the Creator as a low
(senseman at lonestar.utsa.edu) | comedian, and at once the world
Life Sciences Visualization Lab | becomes explicable.
University of Texas at San Antonio | H.L. Mencken
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