GENESIS Info

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 (131.215.135.253 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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