This is the reference manual for GENESIS version 2.4. As there will be continuing updates and additions to the manual, please be sure that you have the most recent version. Information about the latest version of GENESIS and its documentation may be found on the GENESIS WWW site, http://www.genesis-sim.org/GENESIS/.
The help files in the on-line version (in the genesis/Docs
directory) may be viewed with the GENESIS command "
help topic |
more", where "topic" is the name of a file with the extension
".txt". As they are ASCII files, they may also be printed. In
order to view the documentation in these help files in the
recommended order, type ``
help CONTENTS | more'', or print out
the file ``CONTENTS.txt''.
Beginning with GENESIS 2.0.2, we have also incorporated these files into a hypertext documentation system, which may be viewed with a web browser. The HTML hypertext documentation for GENESIS is in a separate directory, genesis/Hyperdoc. The main file is "Manual.html", and there is a README file giving further information.
Some of the new features in GENESIS 2 are not yet documented here.
You may find a brief summary of these and the significant differences
from previous versions of GENESIS under
If there is no documentation for a particular GENESIS command, give
the name of the command followed by ``
-usage'' from within
GENESIS. Likewise, you may obtain a brief description of a GENESIS
object by typing ``showobject'' followed by the name of the object.
The GENESIS Reference Manual is primarily a summary of the syntax used by the GENESIS Script Language Interpreter, the commands which it recognizes, and of the main GENESIS ``objects'' which are available for constructing simulations. However, it will not tell you very much about the use of GENESIS for the construction of neural simulations. For a ``Users guide'' to GENESIS, we recommend ``The Book of GENESIS'', 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.
Part II of this book provides a detailed tutorial guide to the process of constructing neural simulations with GENESIS. These tutorials progress from the construction of simple cell models to detailed cell and network models with a sophisticated XODUS interface. For further information, see The Book of GENESIS.
The GENESIS/XODUS documentation (Revelations) is contained within the genesis/Doc and genesis/man directories. The former contains the main GENESIS documentation, and the latter contains UNIX man pages for external utilities (such as convert), which are used with GENESIS. The README file in the Doc directory explains the use of the on-line help facility.
The genesis/Scripts directory has a README file which describes the the database of simulations and its library of channels and other simulation components (Numbers).
In addition to containing the C source code for GENESIS, the genesis/src directory contains a README file and a commented Makefile. These files (Leviticus) give detailed instructions for the compilation and installation of GENESIS. They also suggest ways to avoid common mistakes when installing GENESIS. (For example, an incorrect pathname to a system library is an abomination to the compiler.) We still haven't thought of a good excuse to call something Deuteronomy, but are working on it.
After installing GENESIS, start the simulator with the command ``genesis''. (In some cases, you may wish to use one of the command options described in the documentation for genesis.) After experimenting with the on-line help, your first step should be to try out one of the demonstrations or tutorials in the Scripts directory, following the directions in its README file. You may create your own simulations by modifying these simulation scripts.
The GENESIS Reference Manual and other documentation were written by Dave Beeman, Upi Bhalla, Dave Bilitch, Jim Bower, Kevin Cunningham, Erik De Schutter, John Uhley, and Matt Wilson, with contributions from Dieter Jaeger, Venkat Jagadish, Maurice Lee, Reinoud Maex, Mark Nelson, Alex Protopapas, Mike Vanier, and many others.
GENESIS and XODUS are the result of the work of many users and developers. The principal contributors are:
Upinder S. Bhalla David H. Bilitch Erik De Schutter Michael Hucka Venkat Jagadish Mark E. Nelson John D. Uhley Michael Vanier Matthew A. Wilson
under the direction of James M. Bower
XODUS graphical interface:
Upinder S. Bhalla Venkat Jagadish Jason Leigh Maneesh Sahani
Parallel library development:
Upinder S. Bhalla Erik De Schutter Nigel Goddard Greg Hood
Development work for Intel i860-based Parallel Machines:
Michael D. Speight
X11R4 upgrade modifications:
Randall D. Smith
X11R5 and X11R6 upgrade modifications:
Rich Murphey Diana K. Smetters
Upinder S. Bhalla Erik De Schutter Dieter Jaeger Venkat Jagadish Mark E. Nelson Adam Strassberg Matt Wilson
Numerical methods enhancements:
Upinder S. Bhalla Hugo Cornelis Erik De Schutter Bruce P. Graham
Synapse and Parameter Search Library development:
Modifications to run under Microsoft Windows with Cygwin by:
Modifications to run on the Apple under Mac OS X:
Alfonso Delgado-Reyes Josef Svitak
Script Demos and Tutorials:
Dave Beeman Upinder S. Bhalla Sharon Crook Erik De Schutter Mark E. Nelson Alex Protopapas Michael Vanier Matt Wilson
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.
For a statement of the GPL, see the file "GPLicense". For a statement of the LGPL, see the file "LGPLicense".
Most software has bugs, and GENESIS is no exception. If you believe you have found a bug, please follow the procedure outlined below. Doing so will vastly increase the speed with which the bug gets fixed.