GENESIS Availability

David M. Senseman senseman at lucy.brainlab.utsa.edu
Mon Apr 5 20:39:47 EST 1993


Sometime ago, I posted some information about GENESIS, the Caltech
Neurosimulator program for REAL neurons (i.e. not back-prop stuff).
A rather large number of readers asked for additional information
so I offer the following:
 
 1) Software Title:     GENESIS (GEneral NEural SImulation System)
 
 2) Brief:         A simulation tool for neural network modelers.
 
 3) Description:

        Use:  GENESIS is a general purpose simulation platform that 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.  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.  Although the software
can also model more abstract networks, it is not an efficient way to perform
backpropagation and similar connectionist modeling.

        Machine dependence:   GENESIS and its graphical front-end XODUS are
written in C and run on SUN (SUN 3, 4, and Sparc stations 1 and 2) and DEC
(DECstation 2100, 3100, and 5000/200PX) graphics workstations under
UNIX (Sun & DEC OS 4.0 and up),  and X-windows (version 11.3 and 11.4).
The most recent version of GENESIS has also been used with Silicon Graphics
(Irix 4.0.1 and up) and the HP 700 series (HPUX).

The following papers give further information about GENESIS:

   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

   James M. Bower and John Hale, "Exploring Neuronal Circuits on Graphics
   Workstations", Scientific Computing and Automation, p. 35, March 1991

   Matthew A. Wilson and James M. Bower, "The Simulation of Large-Scale
Neural

Neural
   Networks", in Methods in Neuronal Modeling, Christof Koch and Idan Segev,
   editors. (MIT Press, 1989)

4) Examining GENESIS source via free FTP distribution:

        In order to allow examination of GENESIS, we have made the full
source for the simulator (version 1.1) available via FTP from
genesis.cns.caltech.edu (131.215.137.64).  The distributed compressed tar
file is just under 1Meg in size.  This original distribution includes full
source for both GENESIS and XODUS as well as five tutorial simulations (squid
axon, single nenuron behavior, multicell, visual cortex, and neurokit).
Documentation for these tutorials is included along with three papers that
describe the general organization of the simulator.  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 below.  Any other questions about the system or its
distribution should also be sent to genesis at cns.caltech.edu.
 
5) BABEL - GENESIS users group

        For those interested in seriously using GENESIS we have also
established a GENESIS users group (BABEL). 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.  In addition to providing
your name, institution, mailing address and phone number (optional), please
provide the email address at which you would like to receive communications
from BABEL.  In order to set up an account for you on the BABEL computer, we
will also need a user name of eight characters or less.

As a registered user, one is provided with the current version of GENESIS
(version 1.4).  access to documentation on the simulator itself, access to
 26 lines more (you've seen 81%) 

(version 1.4).  access to documentation on the simulator itself, access to
libraries of simulator components, educational tutorials, GENESIS
programming tutorials, published GENESIS-based models, other GENESIS support
software, bug reports, and an email newsgroup.  Serious users of GENESIS are
advised to join the users group, as the current version of GENESIS and its
documentation is much improved over the original public release version. 

6) Licensing agreement

         Although no formal licensing is necessary for the GENESIS package,
it should be understood that this software system 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.
 
7) Contact Person:
        Professor James Bower           email:  genesis at cns.caltech.edu
                                                genesis at caltech.bitnet
        Division of Biology  MS 216-76
        Caltech
        Pasadena, Ca. 91125

In general, inquiries concerning GENESIS should be addressed to
genesis at cns.caltech.edu.  Inquiries concerning BABEL memberships should be
sent to babel at babel.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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