G E N E S I S
The GEneral NEural Simulation System
Version 2.3 - final release
Last edited: $Date: 2006/03/17 17:00:08 $
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Introduction
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This directory contains the distribution of GENESIS version 2.3.
This release supercedes version 2.2.1, and has a number of changes in
the simulator source code to allow use on a greater variety of platforms,
including Intel and AMD 64 bit processors, MacIntosh with OS/X, and
Microsoft Windows with the Cygwin environment. It includes Kinetikit
Version 11, and revised documentation.
A detailed list of source code changes from previous versions is provided in
genesis/ChangeLog. New features of version 2.3 are described in
genesis/Doc/Changes.txt.
Directions for installing binary distributions may be found in README.bindist
in this directory. Directions for building and installing source distributions
are in src/README. Be sure to read the directions
concerning the installation of the ".simrc" file. Directions for printing
and using the documentation may be found in Doc/README. The
Scripts/README file describes the demonstration and tutorial simulations
which are included with this distribution.
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Description of GENESIS
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GENESIS is a general purpose simulation platform which 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. Most current GENESIS applications involve realistic
simulations of biological neural systems. Although the software can also
model more abstract networks, there exist other simulation packages that
are more suitable for backpropagation and similar connectionist modeling.
A detailed guide to the GENESIS neuroscience tutorials and the construction
of GENESIS simulations is given in:
The Book of GENESIS: Exploring Realistic Neural Models with the GEneral
NEural SImulation System, Second Edition, by James M. Bower and David
Beeman, Springer-Verlag (1998). The free Internet Edition is available
at http://www.genesis-sim.org/GENESIS/bog/bog.html
Additional hypertext documentation, including a beginners guide to
UNIX/Linux commands, can be found in genesis/Tutorials.
Source code contributed by GENESIS users which must be compiled is found in
src/contrib; other contributions are in contrib.
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Obtaining Genesis
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GENESIS source and binary distributions can be obtained from:
http://sourceforge.net/projects/genesis-sim.
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Machine dependence
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GENESIS and its graphical front-end XODUS are written in C and are known to
run under many UNIX-based systems with the X Window System (X11R5 or X11R6),
as well as OSX and Windows with Cygwin. Here's a partial list of tested
platforms:
* x86-based Linux systems:
+ Debian Linux with kernel 2.x
+ Fedora Core 2, 3, and 4
+ Gentoo
+ Mandrake Linux 7, 8, and 9.1 (but not 9.0)
+ Red Hat Linux 5, 6, 7, 8, and 9
+ Slackware 10
* 64 bit Linuces:
+ Fedora Core 3 and 4
+ Red Hat Enterprise
* x86-based FreeBSD 4.1
* Alpha with Debian 3.0
* IBM SP2 systems running AIX 4.2 and 4.3
* PPC-based Linux systems running LinuxPPC, SUSE 7.0, and OSX
* SGI MIPS-based systems running IRIX 5.x and 6.5.x
* Sun SPARC and x86 systems running Solaris 2.6, and 2.7
It is quite likely that GENESIS will also work on systems running other
versions of the operating systems listed above; however, the GENESIS
developers only have direct experience with the particular systems listed.
GENESIS may *fail* to work on DEC Alpha-based systems. Please let us know of
any experiences with this platform.
GENESIS has in the past worked on the following systems, but the developers
do not have these systems available for full testing and have not been able
to adequately verify that GENESIS 2.3 compiles and runs properly:
* Sun SPARC-based systems running SunOS 4.1.x
* Sun SPARC-based running Solaris 2.5/2.5.1
* HP-UX systems
* Intel Paragon
* DECStation running Ultrix 4.x or 3.x
* Cray T3E and T3D
We welcome feedback on experiences with these platforms. If you attempt to
use GENESIS on these systems and have problem reports (or even better,
fixes), please contact the GENESIS maintainers.
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GENESIS Users Group
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Serious users of GENESIS are advised to join the users group, BABEL.
Members of BABEL are entitled to access the BABEL directories and email
newsgroup. These are used as a repository for the latest contributions by
GENESIS users and developers. These include new simulations, libraries of
cells and channels, additional simulator components, new documentation and
tutorials, bug reports and fixes, and the posting of questions and hints
for setting up GENESIS simulations. As the results of GENESIS research
simulations are published, many of these simulations are being made
available through BABEL. New developments are announced via the
BABEL mailing list. Members are able to access the BABEL directories via
the passworded BABEL web page.
Inquiries concerning GENESIS should be addressed to genesis@genesis-sim.org.
Inquiries concerning BABEL memberships should be sent to
babel@genesis-sim.org. Other information concerning GENESIS, including
"snapshots" of GENESIS simulations and descriptions of research which has been
conducted with GENESIS may be found on the GENESIS World Wide Web Server at
the following URL:
http://www.genesis-sim.org/GENESIS
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Disclaimer
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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.
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Copyright Notice
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Copyright 1988 - 2001 by the California Institute of Technology
This program is free software; you can redistribute it and/or modify it
under the terms of the GNU General Public License as published by the Free
Software Foundation. Portions of this program are in library form. The
libraries are also free software; you can redistribute them and/or modify
them under the terms of the GNU Lesser General Public License as published
by the Free Software Foundation; either version 2.1 of the License, or (at
your option) any later version.
This program is distributed in the hope that it will be useful, but
WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
General Public License for more details.
You should have received a copy of the GNU General Public License and the
GNU Lesser General Public License along with this program; if not, write to
the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor,
Boston, MA 02110-1301 USA.
Recent additions to the GENESIS libraries are copyrighted by other
institutions or authors, and are covered by the GNU General Public
License (GPL), GNU Lesser General Public License (LGPL), or by other
licenses that are compatible with the GPL and that do not restrict the
free distribution of GENESIS. These licenses appear with these modules.
For a statement of the GPL, see the file "GPLicense".
For a statement of the LGPL, see the file "LGPLicense".