
							June 30th, 1990


This directory contains the final release of the source code for the "free" 
version of the GENESIS simulation package.   This code is intended to give 
interested parties as taste of the GENESIS simulation package.  In addition 
to the source code which makes up the basic package, this distribution includes
a number of small simulations built with GENESIS (located beneath the directory
/usr/genesis/Scripts).   These are intended as tutorial examples which can 
demonstrate both the types of neurological simulations which can be 
modeled with the system as well as the look and feel of XODUS, the graphical 
front-end for the package.   These tutorials require that /usr/genesis/genesis
be built and installed, and that /usr/genesis be in the users path before
execution.

This distribution has been compiled and tested on Sun 3s, Sun 386is, Sun 4s, 
SPARCstation 1s, SPARCstation 1+'s, DECstation 3100s and DECstation 5000s.
It should function with either X11R3, X11R4 or DECwindows under SUN OS
4.0 (or greater) or Ultrix 3.1.

Over the coming years Caltech will continue to develop the simulation package.
Parties interested in using the package for neural modeling development
may wish join us in our development efforts.   We will supply such parties 
with updated source code, documentation, and additional computational models
as they become available.   A one time annoyance fee of $200.00 has been 
associated with "membership" in this group.   For more details see the 
remainder of this README file.

						John Uhley
						uhley@smaug.cns.caltech.edu

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 	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).  The interface will also
 be the subject of an oral presentation at the upcoming USENIX meeting in
 Washington D.C. 
 
 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), and X-windows 
 (version 11.3 and 11.4).

 	The software occupies clost to 20 meg of disk space during the
 compilation process on a SPARCstation 1+.  Non-SPARC machines will require
 less room to compile.  Once compilation and installation has been done the
 software only occupies 6 or 7 Meg of disk space.   The distributed 
 compressed tar file is just under 1Meg in size.    The current distribution 
 includes full source for both GENESIS and XODUS as well as four tutorial 
 simulations (squid axon, multicell, visual cortex, and neurokit).  
 Documentation for these tutorials is included along with three papers that 
 describe the general organization of the simulator. 
 
 GENESIS Users Group:

 	In addition to distributing GENESIS we have also established a GENESIS
 users group (BABEL) for those interested in developing new GENESIS
 applications.  Membership in BABEL requires that a one time $200
 registration fee payable to the California Institute of Technology be sent
 to BABEL, c/o Jim Bower, Computational Neural Systems Program, 216-76,
 Caltech, Pasadena, CA, 91125.  As a registered user, one is provided
 documentation on the simulator itself (currently in an early stage), has
 access to additional simulator components, bug reports, and a user's bulletin 
 board.  In addition we are establishing a depository for interesting
 completed simulations.   BABEL is still currently in it's early stages, but
 we plan to have a secondary release of the GENESIS system done by early 
 October, 1990.   This secondary release will only be distributed to BABEL
 users.

 Distribution Information:

 	Full source for the simulator is available via FTP from
 genesis.cns.caltech.edu (131.215.135.64).   To acquire the software
 use TELNET to connect to genesis.cns.caltech.edu and login as the
 user genesis (no password required).  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.  If you do
 not have network access the necessary tapes can be provided for a small 
 handling fee.  Those requiring tapes should send requests plus $50 payable to 
 Caltech at the address listed above.  Any other questions about the system or 
 its distribution should also be sent to genesis@caltech.bitnet.
 
 Disclaimer:

 	Finally, it should be understood that this software system, which
 currently consists of approximately 60,000 lines of code, and represents
 almost four years of programing effort, is being provided for general
 distribution as a public service to the neural network and computational
 neuroscience communities.  We make no claims as to the quality or
 functionality of this software for any purpose whatsoever and its release
 does not constitute a commitment on our part to provide support of any
 kind. 
 
 Jim Bower


