  1.  Introduction

  This is the reference manual for GENESIS version 2.3.  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 are not yet documented here.
  You may find a brief summary of these and the significant differences
  from previous versions of GENESIS under ``Changes'' (Changes.txt).  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'' (BoG.txt).

  1.1.  Getting Started with 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'' (genesis.txt).)
  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.

  1.2.  Credits and Copyright Notice

  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:

  GENESIS development:
            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

  Libraries:
            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:
            Michael Vanier
  Modifications to run under Microsoft Windows with Cygwin by:
            Sergio Daicz

  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

  1.2.1.  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.

  For a statement of the GPL, see the file "GPLicense".
  For a statement of the LGPL, see the file "LGPLicense".
