This directory contains the October 9, 2000, beta release of the General Neural Simulation System (GENESIS), version 2.2. GENESIS runs under most varieties of UNIX, including Linux. It also contains additional files that may be used to create a customized version of GENESIS that may be used to run the Leech Tutorial contained in the calabrese directory on this CDROM, and described in Chapter 10.
In addition to containing the usual source code distribution, the CDROM has precompiled binaries for Sun Microsystems computers running Solaris, SGI systems running IRIX 6, and Intel x86 compatible systems running Linux (Linux 2.x ELF). The binaries may be run directly off the CDROM without installation, or may be installed to a hard disk. They have been compiled with the additional libraries needed for the Leech Tutorial.
We do not anticipate any significant changes to GENESIS 2.2 between
this beta release and the final release, other than changes to allow it to
reliably compile and run on UNIX systems other than the three listed
above. Nevertheless, 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.
Parallel GENESIS (PGENESIS 2.2) will also be available with the final
GENESIS release. The final release will be available by the time of
publication of this book and CDROM.
See the file genesis/README for a list of platforms on which GENESIS is expected to compile and run. You will need one of the listed UNIX systems in order to run the GENESIS software. Note that some non-UNIX systems may be used to browse the contents of this CDROM directory.
This directory contains the following files and directories:
README - The UNIX formatted version of this README file
README.txt - A DOS/Windows formatted version of the README file
README.html - The hypertext version of the README file
LEECH.txt - Further information about the Leech Tutorial
leech-genesis - The directory conaining source code to make the customized
GENESIS version used for the Leech Tutorial.
leech-genesis.tar.Z - A compressed tar archive of leech-genesis
genesis - The directory containing the full GENESIS distribution
genesis.tar.Z - A compressed tar archive of the genesis directory
bin.Linux-ELF - The directory containing the Linux binary of genesis
bin.Solaris - The directory containing the Solaris binary of genesis
bin.IRIX - The directory containing the IRIX binary of genesis
More information about GENESIS is contained in genesis/README. The plain text and printed GENESIS documentation is in the directory genesis/Doc. Directions for printing and using the documentation may be found in genesis/Doc/README. The hypertext version of the GENESIS Reference Manual is in genesis/Hyperdoc/Manual.html.
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.
In addition to demonstrations that 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.
Note that the Purkinje cell tutorial described in Chapter 9 of this book is contained in genesis/Scripts/purkinje. The Leech Tutorial described in Chapter 10 is contained in the calabrese directory of this CDROM. To run the leech tutorial, you may use the precompiled genesis binaries, or compile your own customized version of genesis. Further details are given in LEECH.txt.
The safest and most reliable way to install and run GENESIS is to copy the genesis.tar.Z archive to your hard drive and to compile GENESIS yourself, rather than using binaries compiled under a different computing environment.
The GENESIS distribution may be installed in whatever directory is most convenient. You do not need "root" privileges to install within your home directory. On the other hand, if you want a system-wide installation, /usr/local is a good place to install GENESIS. The distributed compressed tar file unpacks to produce the directory named "genesis" and its subdirectories. This will be the same as the genesis directory in this CDROM directory.
After changing to the directory in which you wish the GENESIS directory tree to reside, give the unix command "zcat genesis.tar.Z | tar xvf -". Begin by reading the README file in the genesis directory, and then follow the compilation instructions in genesis/src/README.
NOTE: If you experience any problems using these binaries, please follow the instructions above for compiling your own GENESIS binary.
GENESIS may be run directly from the CDROM. Let us suppose that the CDROM is mounted on your Linux/Solaris/IRIX system as the directory
/cdrom
and that the file that you are reading is in
/cdrom/genesis-dist
(If the CDROM is mounted using a different path, occurrences of /cdrom in the instructions below must be modified accordingly.) You can run GENESIS simply by typing
/cdrom/genesis-dist/genesis/genesis
The above is a front-end shell script. The script will attempt to determine what operating system is present and run the appropriate precompiled executable. The user may control which executables are run by setting the GENESIS_OS environment variable to one of Solaris, IRIX or Linux-ELF.
Some systems by default prevent running programs from a mounted CDROM. On these systems, it will be necessary to add a mount option to enable running executables, including installation scripts. Check with your system administrator or system documentation for information on how to properly mount the CDROM file system.
Some of the scripts provided under the Scripts directory require write access to the directory from which the scripts are run. To run these scripts, you must either set the SIMPATH to include the particular script directory, or copy the entire script directory to a writable directory on your hard disk.
Visit the GENESIS web page at http://www.bbb.caltech.edu/GENESIS for more information about GENESIS, as well as access to the latest version. This will also allow you to see "snapshots" of GENESIS simulations and find information about research which has been conducted with GENESIS.
Email inquiries concerning GENESIS should be addressed to genesis@bbb.caltech.edu.