README file for the Tutorial Simulation of a CA3 Hippocampal Neuron

This is a preliminary version of tutorial based upon a GENESIS simulation 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 paper should be consulted while using the tutorial.  The
tutorial serves as an introduction to the 'Neurokit' simulation environment
and explores some of the properties of this model.  A future version of the
text of the tutorial will explore the properties of the various types of
ionic channels used in the model.  The file "traub91proto.g" may also be
used as an example of the use of tabchannels and tabgates to implement Ca
concentration dependent channels.

In order to run the simulation, carry out the following steps:

1) In order to allow room for the graphical display, move a terminal window
   into the lower left hand corner of your screen.  (This is normally done
   by using the left mouse button to click and drag on the title bar of the
   window.)

2) After changing into the directory in which this file resides, (usually
   "traub91"), type "genesis" to the unix prompt.

3) After the "genesis #0>" prompt appears, type "Neurokit", in order to load
   the Neurokit simulation.  (Don't forget that unix is case sensistive!)
   There will be a delay while the simulation is being set up, and a few
   obscure messages will appear.  If all goes well, a title bar with various
   options will eventually appear at the top of the screen.  (If not, consult
   the notes below on "installing the simulation".)

4) Click the left mouse button on the box labeled 'help' and follow the
   instructions which appear.  (This on-line documentation is in the file
   "traub_tut.help", which may also be printed.)

INSTALLING THE SIMULATION

If GENESIS has not yet been installed on your machine, refer to the main
README file accompanying GENESIS or the printed documentation for GENESIS.
The paths to necessary files should be set up as specified in the GENESIS
README file, the necessary ".simrc" file should exist in your home
directory, and X-windows should be started.  In order to access the 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.)
Finally, you should be using Neurokit version 1.4 or later.  (This version
of Neurokit is provided with GENESIS version 1.4.  It will run under GENESIS
versions 1.3 and later, however.)

Dave Beeman - dbeeman@boulder.colorado.edu
