## This is the README file for the GENESIS downloads directory

(Updated May 28, 2009.)

This directory contains the March 2006 distribution of GENESIS version 2.3.

GENESIS 2.3 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, Version 2 of the Purkinje cell tutorial, some new objects and enhancements of existing ones, plus revised and updated documentation.

We expect that GENESIS 2.3 will be the last GENESIS 2 release, before we begin preliminary releases of GENESIS 3. Therefore we encourage all GENESIS users to upgrade to this (hopefully) final GENESIS 2 release.

This directory also contains the latest release of Parallel GENESIS (PGENESIS 2.3.1), which now has support for MPI as well as PVM. It should run on almost any multiple core PC, parallel cluster, SMP, supercomputer, or network of workstations where MPI and/or PVM is supported, and on which serial GENESIS itself is runnable. For further information about the use and installation of PGENESIS, please see README.pgenesis, which is a copy of the the README file in the PGENESIS distribution. There is also additional hypertext documentation in the PGENESIS distribution. Note that older versions of PGENESIS will not work with GENESIS 2.3 or later.

# Downloading GENESIS and PGENESIS

This directory contains several different forms of the GENESIS 2.3 distribution.

The GENESIS source distribution contains full source code and documentation for both GENESIS and XODUS as well as a large number of tutorial and example simulations. Documentation for these tutorials is included along with online GENESIS help files and the hypertext GENESIS Reference Manual.

It is available in the following compressed archive formats:

- genesis-2.3-src.tar.gz - A gzipped tar archive that unpacks (with gunzip and tar) to genesis-2.3/genesis.
- genesis-2.3-src.tar.bz - A more highly compressed form of the archive, that is recommended it you have the bunzip2 utility installed.
- genesis-2.3-src.tar.Z - A less highly compressed form of the archive, to be used if you have only the old UNIX uncompress utility.
- pgenesis-2.3-src.tar.gz - A gzipped tar archive for PGENESIS. Note that the GENESIS source distribution must also be installed to use PGENESIS.

MD5 checksum files are also provided to check the integrity of the downloaded files. For example, after downloading the archive file and the corresponding file with the ".md5" extension, type

        md5sum -c genesis-2.3-src.tar.gz.md5

Binary distributions are also available that include precompiled versions of both genesis (with XODUS, dependent on X11 installation) and nxgenesis (non-X genesis, without the XODUS GUI, hence no X11 dependence). These contain all the contents of the full source distribution, except for the source code. They also unpack to form the directories genesis-2.3/genesis. After unpacking the distribution, please consult the file README.bindist for installation instructions.

The genesis executables have been linked with certain versions of dynamic libraries. These libraries must be available at run time, so the binary versions are not guaranteed to work on all operating system versions. If you have problems running a binary distribution, or want to compile your own version of GENESIS, please get the source distribution.

The binary distributions currently available are:

- genesis-2.3-linux-bin.tar.gz - A gzipped tar archive for Linux. This should run under most recent Linux distributions.
- genesis-2.3-cygwin-bin.tar.gz - A gzipped tar archive for Windows, using Cygwin. Cygwin (http://cygwin.com) is a free Windows application that provides a UNIX-like environment for Windows. It is easy to install directly from the Cygwin site, and provides much of the functionality of UNIX or Linux, complete with X-windows support, under Windows. Installing Cygwin will let you use Windows to run GENESIS and other UNIX programs that have been compiled to run under Cygwin.
- genesis-2.3-cygwin-bin.zip - The Windows/Cygin binary distribution packaged for use with the zip utilty, commonly used with Windows.
- genesis-2.3-osx-bin.tar.gz - A gzipped tar archive for the Mac with OS/X. This should run under recent versions of OS/X.

NOTE for Windows users:

If you are using a computer with Windows to install the GENESIS binary for Windows, you can download genesis-2.3-cygwin-bin.zip, and use Winzip or a similar utility to extract it. Then, read the file genesis/README.bindist for information about installing Cygwin. If you are planning on installing the source "tar.gz" distribution, you will need to install Cygwin first, in order to have a terminal window to enter the "tar" commands above for extracting the files. Here is a link to README.bindist with the instructions.

If you experience any trouble compiling or running GENESIS, be sure to see the README file in the Bug-fixes directory for any patches or changes since the release of the 2.3 distribution. The LATEST.NEWS file also contains information on recent developments and changes.

# Installation

After downloading the distribution that you plan to install, change to the directory in which you wish the GENESIS directory tree to reside. For a system-wide installation, it is common to use /usr/local/. If this is a system directory such as /usr/local, you will probably need to have root privileges to do this. However, you can install it on one of your own directories with no special privileges.

If you have downloaded the file genesis-2.3-src.tar.gz, it should be uncompressed with the gnu "gunzip" utility, then extracted with tar. This can be done with:

        gunzip -c genesis-2.3-src.tar.gz | tar xvf -

On most Linux systems, and those with GNU tar, it is possible to simply use:

        tar xvzf genesis-2.3-src.tar.gz

If genesis-2.3-src.tar.gz, is not in this directory, give the full path to it, e.g.

        gunzip -c ~joeuser/downloads/genesis-2.3-src.tar.gz | tar xvf -.

Note that genesis-2.3-src.tar.gz cannot be uncompressed with the UNIX compress utility. If you do not have gunzip, use the genesis-2.3-src.tar.Z file instead, with the command "zcat genesis-2.3-src.tar.Z | tar xvf -".

These commands will create the directory tree 'genesis-2.3/genesis' with 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. Also, be sure to carefully read the comments in 'src/Makefile'. In the case of a binary distribution, there will be a file 'README.bindist'.

Directions for 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. The 'Tutorials' directory contains additional hypertext documentation, including a beginners guide to UNIX/Linux commands. This directory also serves as a "place holder" for supplemental hypertext GENESIS modeling tutorials and documentation, including the GENESIS Neural Modeling Tutorials package. The latest version of this package is offered as a separate download from the GENESIS web site, http://www.genesis-sim.org/GENESIS. The downloaded file (Tutorials.tar.gz or Tutorials.zip) should be unpacked in the 'genesis' directory in order to augment the files that are already provided there.

The PGENESIS source distribution is unpacked in a similar manner, to produce the directory tree genesis-2.3/pgenesis. The 'pgenesis/README' file gives installation instructions for PGENESIS. To use PGENESIS, you will need to have PVM or MPI installed. If you do not have PVM installed on your computer, you can get the latest version, as well as more information about PVM from the PVM home page:

http://www.epm.ornl.gov/pvm/pvm_home.html.

A PVM distribution and manual is also available from the GENESIS site, but it is not guaranteed to be the most recent version.

# GENESIS Description

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 Caltech, the Marine Biological Laboratory, the Bangalore, European Union, and Latin American (LASCON) short courses in Computational Neuroscience, and at least 49 universities of which we are aware. 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.

# 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 or X11R6), as well as OSX and Windows with Cygwin. This is a partial list of tested UNIX/Linux platforms:

- x86-based Linux systems:
  - Debian Linux with kernel 2.x
  - Fedora Core 2, 3, and 4
  - Gentoo
  - Ubuntu
  - Mandrake Linux 7, 8, and 9.1 (but not 9.0)
  - Red Hat Linux 5, 6, 7, 8, and 9
  - Slackware 10
- 64 bit Linux:
  - 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-based 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.

# GENESIS Scripts

In addition to demonstrations which illustrate GENESIS features and techniques for programming simulations, the genesis/Scripts direcctory contains 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. In addition there are a number of example simulation scripts to illustrate the use of various GENESIS features. These simulations are described in detail in "The Book of GENESIS" by James M. Bower and David Beeman, which is available for download from the GENESIS web site.

# The GENESIS Neural Modeling Tutorials

The genesis/Tutorials directory in the GENESIS distribution is provided as a "place holder" for supplemental hypertext GENESIS modeling tutorials and documentation, including the GENESIS Neural Modeling Tutorials package. These are an evolving set of HTML tutorials intended to teach the process of constructing biologically realistic neural models with the GENESIS simulator. The latest version of this package is offered as a separate download from the GENESIS web site. The Tutorials directory that comes with the GENESIS distribution contains a short guide to getting around in the UNIX command line environment that may be helpful to new users who are unfamiliar with entering commands into a terminal window.

# GENESIS Users Group (BABEL)

Due to the large number of requests for GENESIS, we are only able to provide limited help or support for those who acquire GENESIS through the GENESIS web site. Therefore, we strongly encourage serious users of GENESIS to join the GENESIS Users Group (BABEL) mailing list "genesis-sim-users" and to subscribe to the user forums on the GENESIS web site.

## How to subscribe

In order to subscribe to the mailing list, go to the web page at

https://lists.sourceforge.net/lists/listinfo/genesis-sim-users

and enter the address from which you will post and receive email, and a password of your choice.

In order to subscribe to the forums, go to the GENESIS web page at

http://genesis-sim.org

and create an account. As we move towards GENESIS 3, this will become the main entry point for access to GENESIS distributions and information about GENESIS 3 development.

Although it is not required, the GENESIS development team would like to know something about your intended or present use of GENESIS through the forums.

Although this description need not be lengthy, please try to be as specific as possible in your statement of what types of models you intend to construct with GENESIS. If you have used GENESIS in teaching or research in the past, we would like to hear about it, with references for any publications or conference papers related to your use of GENESIS. This introduction of yourself will not only help GENESIS developers to support your needs, but will also enable other GENESIS users to share information and ideas with those who have similar modeling interests.

The Sourceforge project page

http://sourceforge.net/projects/genesis-sim

is the CVS repository for GENESIS 2 versions.

# Copyright Notice

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.