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GENESIS: GEneral NEural SImulation System

GENESIS (GEneral NEural SImulation System) is a general purpose simulation platform which supports 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. XODUS is a graphical front end for GENESIS. The distribution includes full source code and documentation for both GENESIS and XODUS as well as fourteen demonstration and tutorial simulations. Documentation for these simulations is included, along with three papers that describe the general organization of the simulator. Also included is a set of "Rallpacks" benchmarks for speed and accuracy of the simulation. 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.) The GENESIS Users Group, BABEL, provides some informal support to GENESIS users. BABEL members have access to an email list, a repository of contributions by GENESIS users and developers, new simulations, libraries of cells and channels, additional simulator components, new documentation and tutorials, and bug reports and fixes. Membership requires a one-time $200 registration fee made payable to the California Institute of Technology and sent to Jim Bower, Computational Neural Systems Program, 216-76, Caltech, Pasadena, CA, 91125. Please provide name, institution, mailing address, phone number, an email address for the mailing list, and an account name for use on the BABEL computer.
Origin: (
   Before using ftp, you must telnet to
   and login as the user "genesis" (no password required) to
   register.  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.

Version: GENESIS 1.4.1 (August 1993); RALLPACKS 1.1 (July 1992) Requires: C X-windows (versions X11R3, X11R4, and X11R5) UNIX (Sun version 4.0 and up, DEC Ultrix 3.1, 4.0 and up) Ports: The current version of GENESIS has also been used with Silicon Graphics (Irix 4.0.1 and up) and the HP 700 series (HPUX). Copying: Copyright (c) 1988-93 by California Institute of Technology (Caltech). Use, copying, modification, and distribution permitted. CD-ROM: Prime Time Freeware for AI, Issue 1-1 Author(s): Genesis -- Matt A. Wilson Upinder S. Bhalla John D. Uhley David H. Bilitch Mark E. Nelson James M. Bower Rallpacks -- Upinder S. Bhalla, David H. Bilitch, James M. Bower, Frank Eeckman, Erik De Schutter, John Miller, Michael Hines, Mark Nelson, Tony Zador, Wilfrid Rall Contact: Keywords: Artificial Life, Authors!Bhalla, Authors!Bilitch, Authors!Bower, Authors!Nelson, Authors!Uhley, Authors!Wilson, BABEL, Benchmarks!Neural Systems, Biological Simulation, CalTech, GENESIS, Neural Networks!Simulators, Neural Systems!Benchmarks, Neural Systems!Simulators, Rallpacks, XODUS References: 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 Matthew A. Wilson and James M. Bower, "The Simulation of Large-Scale Neural Networks", in Methods in Neuronal Modeling, Christof Koch and Idan Segev, editors. (MIT Press, 1989) Bhalla, et al. (1992) Trends Neurosci. 15: 453-458. James M. Bower and David Beeman, "The Book of GENESIS", TELOS/Springer-Verlag, 1994.
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