Description: GENESIS (GEneral NEural SImulation System) 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, other simulators are more suitable for backpropagation and similar connectionist modeling. GENESIS and its graphical front-end XODUS are written in C and run on SUN and DEC graphics work stations under UNIX (Sun version 4.0 and up, Ultrix 3.1, 4.0 and up), and X-windows (versions X11R3, X11R4, and X11R5). The current version of GENESIS has also been used with Silicon Graphics (Irix 4.0.1 and up) and the HP 700 series (HPUX). The distribution includes full source code and documentation for both GENESIS and XODUS as well as fourteen tutorial simulations. Documentation for these tutorials is included, along with three papers that describe the general organization of the simulator. Improvements and New Features: The version of GENESIS which you will find here (ver. 1.4.1, August 1993), is greatly improved over the original July 1990 distribution which was previously available at this site. Over the past two years, there have been significant improvements in the numerical methods which may be used with GENESIS. There are now eleven methods for numerical integration in GENESIS, including two fast implicit methods which use Hines' method. The use of these last two methods greatly increases the speed, stability and accuracy of GENESIS simulations. When choosing a neural simulator, the reliability and accuracy of the simulator is an even more important consideration than its speed. For this reason, we have developed the "Rallpacks" suite of benchmarks for speed and accuracy. [Bhalla, et al. (1992) Trends Neurosci. 15: 453-458.] These are also available on this ftp site. The three sets of benchmarks model a linear passive cable with many compartments, a highly branched cable, and a linear axon containing Hodgkin-Huxley channels. The simulator results may be compared to the exact analytic solutions (for the first two cases) and to the results given by GENESIS and by NEURON, another popular neural simulator. (The results for these two simulators show nearly identical speed and accuracy.) In addition to numerous bug fixes, this new GENESIS release has a printable reference manual and much-improved on-line help, the ability to be compiled with X11R5 and Openwindows, and an easier installation procedure than the old one. Many improvements have been made to the Neurokit cell building environment and the associated cell reader, which allows cells to be constructed from a data file. The library of channel models taken from experimental data has been greatly extended, and new features for channel editing have been added. There have been many additions to the libraries of basic simulation components ("objects") and built-in functions. Some of the more important ones are: table-driven channels and gates which allow one to create voltage-dependent channels with properties taken from experimetal data, rather than from approximate fits to functions of the Hodgkin-Huxley form, ojects for creating concentration-dependent channel conductances, such as Ca-dependent K channels, dendro-dendritic synapses, objects to provide magnesium blocking for NMDA channels, objects to simulate a population of ion channel proteins (pores) which undergo Markov kinetics, new routines for use in searches of large parameter spaces. Finally, there have been many additions to the collection of simulation scripts in the Scripts directory. In addition to demonstrations which illustrate GENESIS features and techniques for programming simulations, there are a number of interactive tutorials for teaching concepts in neurobiology and neural modeling. As their use requires no knowldge of GENESIS programming, they are suitable for use in a computer simulation laboratory which would accompany upper division undergraduate and graduate neuroscience courses. Each of these has on-line help and a number of suggested exercises or "experiments" which may be either assigned as homework or used for self-study. These tutorials may also be taken apart and modified to create your own simulations, as they are reasonably well commented. Several of them are derived from existing research simulations. These tutorial simulations form the basis of Part I of "The Book of GENESIS" by James M. Bower and David Beeman, to be published in early 1994 by TELOS/Springer-Verlag. Part II is intended to teach the use of the GENESIS script language for the construction of one's own simulations. This part will be useful for self-study by researchers who wish to do neural modeling, as well as by students. For a detailed listing of the changes from the original distribution, see the file README.changes in the unpacked GENESIS distribution. GENESIS Users Group (BABEL): Due to the large number of requests for GENESIS, we are not able to provide help or support for those who acquire GENESIS through this ftp site. Therefore, we strongly encourage serious users of GENESIS to join the GENESIS 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. Membership in BABEL requires that a one time $200 registration fee payable to the California Institute of Technology be sent 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. Installation: The first step is to use ftp to download the file 'genesis.tar.Z'. After using ftp to connect to genesis.cns.caltech.edu, and giving your login name and password, give the ftp command "binary". Then give the command "get genesis.tar.Z". The file may take a while to transfer if you do this at a time when networks are busy. You may download the 'rallpack.tar.Z' benchmark set in a similar manner. Finally, give the "quit" command. Next, change to the directory in which you wish the GENESIS directory tree to reside and give the unix command "zcat genesis.tar.Z | tar xvf -". This will create the directory 'genesis' and a number of subdirectories. Begin by reading the README file in the 'genesis' directory. Directions for compiling and installing the software may be found in the README file contained in the 'src' subdirectory. 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. Copyright notice: Copyright (c) 1993 by California Institute of Technology (Caltech). Permission to use, copy, modify, and distribute this software and 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 Caltech not be used in advertising or publicity pertaining to distribution of the software without specific, written prior permission. Caltech makes no representations about the suitability or merchantability of this software for any purpose. It is provided "as is" without express or implied warranty.