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                G E N E S I S
        The GEneral NEural Simulation System
                   Version 2.4
Last edited: $Date: Tue Nov 11 13:00:14 MST 2014 $

Introduction

This directory contains the distribution of GENESIS version 2.4.

A detailed list of source code changes from previous versions is provided in ChangeLog.txt. New features of version 2.3 and 2.4 are described in 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.

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. 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, such as scripts and utilities are in contrib.

Obtaining GENESIS

GENESIS source and binary distributions can be obtained from: http://genesis-sim.org, or from the Sourceforge GENESIS 2 development site http://sourceforge.net/projects/genesis-sim.

Machine dependence

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, X11R6, Xorg), as well as OSX and Windows with Cygwin. Most recent experiences are with Fedora and Ubuntu. It has also been used under various MS Windows virtual environments for running Linux.

The current GENESIS 2.4 version has been tested on various recent Linux distributions including Debian, Ubuntu, and Fedora, on Mac OSX (intel), and Cygwin (32 bit version, which works with 64 bit Windows).

Here is a partial list of older platforms tested for version 2.3:

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:

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.

GENESIS Users Mailing List

Serious users of GENESIS are advised to join the GENESIS genesis-sim-users mailing list at https://lists.sourceforge.net/lists/listinfo/genesis-sim-users. Find the latest new simulations, libraries of cells and channels, additional simulator components, new documentation and tutorials, and patches at the main GENESIS web site http://genesis-sim.org.

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.

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