G E N E S I S The General Neural Simulation System Version 2.2 beta ------------ Introduction ------------ This directory contains the distribution of the beta test version of GENESIS version 2.2. When the development process has reached a stable point, this code will be released as GENESIS version 2.2. If you experience any problems with this beta version, or intend to make any serious use of GENESIS, please obtain the final release version from the GENESIS web site: http://www.bbb.caltech.edu/GENESIS. This release represents a significant upgrade from the previous version, 2.1. A detailed list of source code changes from previous versions is provided in genesis/src/CHANGES. New features are described in genesis/Doc/Changes.doc. Directions for installing the software may be found in the README file contained in the 'src' subdirectory. 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. ---------------------- Description of GENESIS ---------------------- 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. GENESIS has provided the basis for laboratory courses in neural simulation at both Caltech in Pasadena, California, and the Marine Biological Laboratory in Woods Hole, Massachusetts. 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. ------------------ Machine dependence ------------------ GENESIS and its graphical front-end XODUS are written in C and run under UNIX on Sun (SunOS 4.x or Solaris 2.x), DECstation (Ultrix), Silicon Graphics (IRIX 4.0.1 and up), and x86 PC (Linux or FreeBSD) machines with the X Window System (versions X11R4, X11R5, and X11R6). DEC Alphas (OSF v2 and v3, and Digital UNIX v4), IBM RS6000s (AIX) and HPs (HPUX) have been successful in compiling and running, though our experience with these platforms is limited. We have received reports of use of GENESIS on the Power Macintosh with Mac Linux, but have not tested it ourselves. We welcome feedback on experiences with these platforms. Other platforms may be capable of running GENESIS, but the software has not been tested by Caltech outside of these environments. 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, published by TELOS/Springer-Verlag -- ISBN 0-387-94938-0 ------------------- GENESIS Users Group ------------------- 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 in a newsletter which is sent by email to all members. Members are able to access the BABEL directories and transfer files to and from their host machines using a passworded ftp account. Inquiries concerning GENESIS should be addressed to genesis@bbb.caltech.edu. Inquiries concerning BABEL memberships should be sent to babel@bbb.caltech.edu. 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.bbb.caltech.edu/GENESIS ---------- Disclaimer ---------- 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 Notice ---------------- Copyright 1988 - 2000 by the California Institute of Technology Permission to use, copy, modify, and distribute this software and its documentation for any purpose and without fee is hereby granted, provided that the above copyright notice appear in all copies and that both that copyright notice and this permission notice appear in supporting documentation, and that the name of the California Institute of Technology not be used in advertising or publicity pertaining to distribution of the software without specific, written prior permission. The California Institute of Technology makes no representations about the suitability of this software for any purpose. It is provided "as is" without express or implied warranty. Some components are copyright by the originating institution and are used with the permission of the authors. The conditions of these copyrights (none of which restrict the free distribution of GENESIS) appear with these modules.