This directory contains the August 1997 distribution of GENESIS, version 2.1 in the compressed tar file genesis.tar.Z (a link to genesis2.1.tar.Z). If you have the gnu utility gunzip, you my download the smaller, more highly compressed version, genesis.tar.gz (a link to genesis2.1.tar.gz).
If you experience any trouble compiling or running GENESIS, be sure to see the README file in the Bug-fixes directory. The LATEST.NEWS file also contains information on recent developments and changes.
Versions 2.0 and later represent a major revision of GENESIS from the earlier GENESIS 1 version (1.4.2). If you have used a previous version of GENESIS, please read the file genesis/Doc/Changes.doc in the GENESIS distribution.
This directory also contains a much improved release of Parallel GENESIS (PGENESIS 2.1), designed for networks of workstations (NOW), symmetric multiprocessors (SMP) and massively parallel processors (MPP). This release, which replaces the experimental version which was previously available on this site, can be run on any platform which supports GENESIS 2.1 and the PVM (Parallel Virtual Machine) software. PGENESIS 2.1 has been tested extensively on IRIX 5.3, Digital UNIX, Unicos/mk (Cray T3E). It has been run on SunOS, Solaris, Linux, HPUX and Intel Paragon.
Parallel GENESIS is expected to be of use for simulations which must be run many times independently e.g., parameter-search, monte-carlo. It will also be of use for large scale models that do not fit in the memory of a single workstation, especially network models. The primary user-level changes are the extension of the script language to include some parallel programming constructs, the provision of GENESIS messages to cross cpu boundaries, and the use of the PVM parallel software layer.
If you wish to compile the parallel libraries for GENESIS, you will need to download the following files, in addition to the GENESIS 2.1 distribution:
Readme.pgenesis - top level instructions pgenesis.2.1.tgz - source including docs pvm3.3.11.tar.gz - pvm 3.3.11 sources pvm.ug.ps.gz - pvm userguide in postscript
If you do not have the gnu gunzip utility, you may download the larger files with the ".Z" extension which werre produced with UNIX compress.
Please see Readme.pgenesis and the README file and hypertext documentation in the PGENESIS distribution for further information about PGENESIS.
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 in Woods Hole, MA, the Crete Course in Computational Neuroscience, and at least 34 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.
GENESIS and its graphical front-end XODUS are written in C and run under UNIX on Sun (SunOS 4.x or Solaris 2.x), DECstation (Ultrix), Silicon Graphics (Irix 4.0.1 and up) or x86 PC (Linux or FreeBSD) machines with X-windows (versions X11R4, X11R5, and X11R6). DEC Alphas (OSF v2 and v3) IBM RS6000s (AIX) and HPs (HPUX) have been successful in compiling and running, though our experience is limited. We have received reports of use of GENESIS on the Power Macintosh with the current (ver. 2.1) developers release of Mac Linux, but have not tested it ourselves. We welcome feedback on experiences with these platforms.
Other platforms may be capable of running GENESIS, but the software has not been tested by Caltech outside of these environments.
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.
These tutorial simulations form the basis of Part I of "The Book of GENESIS" by James M. Bower and David Beeman, published 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.
In addition to many bug fixes, these are the most significant new features of GENESIS version 2.1:
Further details are given in genesis/src/CHANGES, and genesis/Doc/Changes.doc.
Due to the large number of requests for GENESIS, we only able to provide minimal help or support for those who acquire GENESIS through the ftp site described above. 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. BABEL operates from an Internet accessable SUN SPARCstation 2 at Caltech. Members are able to access the BABEL directories and transfer files to and from their host machines using ftp.
We have recently discontinued the requirement of a registration fee for BABEL membership. Now, all that we require is some assurance that you have a serious interest in using the GENESIS simulator. If you have not yet tried GENESIS, please try some of the demonstration simulations and tutorials, in order to determine if GENESIS is suitable for your purposes. If you then feel that membership in BABEL will be useful to you, you may apply for membership by sending the following information to firstname.lastname@example.org:
Your name, institution, mailing address and phone number (optional), the email address at which you would like to receive communications from BABEL, and a description of your present or intended uses of GENESIS. 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.
NOTE: If more than one person in your group is using GENESIS, you may wish to set up a local mail alias to a list of people who would like to receive BABEL news mailings. This will allow us to have a single email address on our mailing list, yet assure that everyone who uses GENESIS will get the mailings.
After your registration has been accepted, we will add you to the BABEL mailing list, and send you information on accessing the BABEL archives and posting to the BABEL newsgroup.
The first step is to download the file 'genesis.tar.Z', or if you have the gunzip utility, the smaller file 'genesis.tar.gz'. This may be done via the GENESIS WWW page (http://www.bbb.caltech.edu/GENESIS) or by anonymous ftp to genesis.bbb.caltech.edu.
When using ftp, give the username "anonymous" and your email address as the passwoed. Then, 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. If you have the gnu "gunzip" utility, you may get the smaller file "genesis.tar.gz", instead. You may download the parallel library files 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.
If you have downloaded the file genesis.tar.gz instead, it should be uncompressed with the gnu "gunzip" utility, then extracted with tar. This can be done with:
gunzip -c genesis.tar.gz | tar xvf -
On most Linux systems, it is possible to simply use:
tar xvzf genesis.tar.gz
Note that genesis.tar.gz *cannot* be uncompressed with the UNIX compress utility. If you do not have gunzip, use the genesis.tar.Z file, instead.
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. 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 1988, 1989, 1990, 1991, 1992, 1993, 1994, 1995, 1996, 1997 by the California Institute of Technology
Permission to use, copy, modify, and distribute this software and its 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 the California Institute of Technology not be used in advertising or publicity pertaining to distribution of the software without specific, written prior permission. The California Institute of Technology makes no representations about the suitability of this software for any purpose. It is provided "as is" without express or implied warranty.
Some components are copyright by the originating institution and are used with the permission of the authors. The conditions of these copyrights (none of which restrict the free distribution of GENESIS) appear with these modules.