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 $
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.
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.
GENESIS source and binary distributions can be obtained from: http://sourceforge.net/projects/genesis-sim.
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.
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
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.
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".