Version 2002-08-30 contains modifications for variable time step method.

This readme file gives usage instructions for patdemo2.zip (essentially
patdemo.zip at http://www.cnl.salk.edu/~zach/methods.html by Z. F. Mainen
and T. J. Sejnowski)

This model contains compartmental models of four reconstructed neocortical
neurons (Layer 3 Aspiny, layer 4 Stellate, layer 3 and layer 5 Pyramidal
neurons) with active dendritic currents using NEURON. It is shown here that
an entire spectrum of firing patterns can be reproduced in this set of model
neurons which share a common distribution of ion channels and differ only in
their dendritic geometry.

The reference paper is:
Z. F. Mainen and T. J. Sejnowski (1996) Influence of dendritic structure
on firing pattern in model neocortical neurons. Nature 382: 363-366.

See also http://www.cnl.salk.edu/~zach/methods.html and
http://www.cnl.salk.edu/~zach/


This package is written in the NEURON simulation program written by Michael
Hines and available on internet at:
http://www.neuron.yale.edu/


  HOW TO RUN (under NEURON version 4 and higher)
  =========================================

To compile the demo, NEURON and INTERVIEWS must be installed and working on
the machine you are using.

When the patdemo1.zip file is unzipped it creates a patdemo directory which
contains the hoc and mod NEURON program files.  Change directory to patdemo.

under UNIX:
===========

Just type "nrnivmodl" to compile the mechanisms
given in the mod files in the patdemo directory.

Execute the first figure demo program by typing:

nrngui demofig1.hoc

continue below under back to any platform:

under MS WINDOWS (PC):
======================

Press Start button (lower left corner) and then press Programs and then
NEURON and then mknrndll DOS box.  Change directory to where the zip file was
unzipped and enter the directory that came with the zip file (patdemo). Type
mknrndll and press the Enter key.

Execute the first figure demo program by typing:

nrngui

In the NEURON main menu click on file and open and then double click on
demofig1.hoc

continue below:

back to any platform:
=====================

For each of the cells, click on one of the cell buttons in the
figure 1 window - for example

a. L3 Aspiny

and then click on the Init & Run button to observe the voltage trace.

to explore the figure 2 model quit (click on file and then quit in the NEURON main
menu) and start up again using the command:

nrngui demofig2.hoc

To explore parameters in these models, on the NEURON main menu click on
Tools, Distributed Mechanisms, Viewers, and Name Values

When the special window comes up double click on one of the sections in the
left hand column, e.g. soma and then finally you can observe/change the
parameters of the model.  Note for example that changing the morphology of
the model, e.g. changing L, will cause the model to change shape in the
Shape window.  If you closed the shape window press one of the cell buttons
again in the Figure 1 window.  At any time you can test how any of your modifications
change the electrical excitability by pressing Init & Run.

If you wish to change the current injected into the model, on the NEURON main
menu click on Tools, Point Processes, Viewers, and IClamp.  Then on the new
IClamp window double click on "soma(0.5)".  The on the "IClamp[] at soma(.5)"
modify the protocol by for example changing the amplitude (amp) of the current
to a value that is for example .02 nA larger.  To compare with the previous
run of the model right click on the graph of v(.5), and select the menu item
"Keep Lines".  Notice that there are many ways to to zoom/scroll the graph by
right clicking on the graph and slide to the top of the pop-up menu to the
View... menu and then slide off to the right and select one of these items.

