The directories beneath /usr/genesis/Scripts include a series of simple
simulations built on the GENESIS platform.  They are intended as tutorial
examples of simulations which can be built with the package.  The demos
currently include:

MultiCell
neurokit
orient_tut
helpdemo
channels
vclamp
int_methods
examples

neuron
cable
squid
burster
traub91
piriform

To try out the GENESIS demos, cd to the desired directory and look at the
README file for information on running the simulation.  It is best to do
this from a terminal window at the bottom of the screen, so that that it will
not be completely covered up by the displays created by the simulations.

MultiCell simulates two simple neurons in a feedback configuration.  It has
no built-in documentation, but has extensive documentation in the file
MultiCell.doc, explaining the syntax used in the GENESIS scripts for the
simulation.  This is a good one to study if you would like to learn to
construct your own GENESIS simulations.

helpdemo consists of a very short script (helpdemo.g) which illustrates the
use of the GENESIS ximage and xtext widgets.  These are useful for
constructing help windows which display bitmapped images or scrollable text.

The demonstration in "orient_tut" gives an example of how one would set up
arrays of many interconnected neurons in a simulation.  In this case, the
simulation is a simplified model of the Hubel and Weisel orientation
selectivity circuit.  The scripts illustrate the use of a number of
sophisticated features of the draw widget.  The text file "orient_tut.notes"
gives a description of someof the GENESIS commands which are used to set up
the network.  Take a look at the README file before running the simulation,
then issue the command "genesis orient_all".  

The "neurokit" directory contains the most elaborate of the simulations.  It
provides a number of tools for building and editting complex neurons and
uses a sophisticated graphical interface.  Although the scripts are quite
complicated, the program is easy to use.  Type "genesis Neurokit" to start
the simulation and, after a while, a command bar will appear at the top of
the screen.  Click the left mouse button on "help" and follow the
directions.  This version of neurokit takes advantage of new features found
in GENESIS version 1.4.1.

The files in /usr/genesis/Scripts/channels provide an introduction to the
channel editing facilities provided by neurokit, and illustrate the use of
the library of prototype channels. This tutorial should be run after the
user has tried out neurokit itself.

The /usr/genesis/Scripts/vclamp directory has paradigm files for doing a
voltage clamp analysis of ion channels. It is meant as a tutorial on how
neurokit can be used to simulate electrophysiological experiments.
Familiarity with neurokit is assumed.

The Scripts/int_methods tutorial is a tutorial in the different integration
methods accessible through neurokit and available for use in your
simulations.

The Scripts/examples directory contains a few short demonstration scripts
giving examples of simulations involving new GENESIS features. 

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The following simulations were designed as 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.

Further details of these tutorials and the theory behind them will be given
in "The Book of GENESIS" by James M. Bower and David Beeman, to be published
in early 1994 by TELOS/Springer.

The tutorial on single neuron behavior in "Scripts/neuron" is a good one to
start with, as it has fairly extensive built-in help available.  To run it,
give the command "genesis Neuron" and click the left mouse button on the box
labeled "help" once it appears.

The "cable" tutorial simulates an extensible neuronal cable.  Current
injection or synaptic input may be provided to any one of the compartments,
and all relevant parameters are adjustable from "pop-up" menus.

"Scripts/squid" contains a simulation of voltage and current clamp
experiments on the giant squid axon.  The tutorial also provides the ability
to block channels, to plot the Hodgkin-Huxley activation variables, and to
generate phase plots.  The accompanying exercises help the student
understand the Hodgkin-Huxley model and the procedure used to calculate rate
parameters from voltage clamp experiments.  Other exercises elucidate the
basis of post-inhibitory rebound and refractory period.  Documentation is
contained in the file squid.text.  Give the command "genesis Squid" to run
the tutorial and then click on "help".

The "burster" tutorial examines mechanisms which lead to burst firing in
molluscan neurons and the effects of the various types of ionic channels
which are commonly found.  The simulation is implemented within the Neurokit
cell builder environment and can also serve as an introduction to Neurokit.
This allows the user to modify most of the relevant parameters and
assumptions used in the model and to investigate the causes of many of the
features seen in molluscan pacemaker firing patterns.  The cell which is
modeled is a ``generic burster'', loosely modeled after the Aplysia R15
cell, although it contains channel models fitted to measurements on bursting
neurons in several different molluscs.  The README file gives instructions
for running the tutorial.

The "traub91" tutorial is based upon a GENESIS recreation of the hippocampal
pyramidal cell model of Traub, et. al.  [R.D.Traub, R. K. S.  Wong, R.
Miles, and H. Michelson, Journal of Neurophysiology, Vol. 66, p.  635
(1991)] This tutorial also uses Neurokit to explore some of the properties
of the model.  The file "traub91proto.g" may also be used as an example of
the implementation of Ca concentration dependent channels in GENESIS.  The
README file gives instructions for running the tutorial.

The "Scripts/piriform" directory contains a ``user-friendly'' adaptation of
the research simulation used by Wilson and Bower to model the processing of
olfactory inputs to the piriform cortex.  This scaled-down version of the
original simulation uses 135 each of pyramidal cells, feedforward and
feedback inhibitory interneurons, arranged in a 9 x 15 array.  To run the
simulation, type "genesis Piriform" and click on the box labeled "help" when
it appears.

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NOTE:
	Before running these simulations, make sure that you have added the
	directory in which GENESIS resides to your path.  (This is normally
	/usr/genesis, unless it has been installed elsewhere.)  You will
	also need to have a copy of .simrc in your home directory.  This
	file will need to be edited if GENESIS has not been installed in
	/usr/genesis.  In order to access the Neurokit simulation, your
	.simrc file should use the SIMPATH environment variable to set a
	path to the neurokit and neurokit/prototypes directories.  (This is
	done in the usual default .simrc which is provided with GENESIS.)

	Some of these simulations will write data to files.  In this case,
	you will need to run the simulation from a directory for which you
	have "write" permission.  The README file which accompanies the
	simulation will tell you if this is necessary.
