Notes on using the NEURON simulation environment for BIOL 378/478,
Computational Neuroscience.

These notes are subject to constant feedback and improvement based on
student input.  Please send the instructor your suggestions!

1. Download the current standard distribution of NEURON (version 6.1) from
the website,

	http://www.neuron.yale.edu/neuron/

by clicking on "Download and Install" and following the instructions for
your system.  You should end up with NEURON-6.1 installed wherever you
keep your other application programs (on the mac, it will be in the
folder /Applications/NEURON-6.1).  To test that things installed
correctly, run the neuron demo (on the mac, double click on the file
neurondemo.app, or in the mac's Terminal window, type: open
neurondemo.app/)  Several blue and white windows should open.  To run a
demonstration, click one of the buttons under "Choose one of the
demonstrations" and then click "Init & Run" in the "RunControl" window.
To leave NEURON, type quit() in the terminal window that appeared (it
should have an "oc>" prompt) or select "Quit" from NEURON's File menu.

To get a first look at NEURON via the demo, answer the following questions:

1.a. When you start the demo there should be a blue window titled
"Choose one of the demonstrations". Click the radio button next to
Patch:HH.  This runs a script to create a simulation of a neuron
consisting of a single compartment with Hodgkin-Huxley channels driven
by a current stimulus.  In the terminal window (titled "neurondemo")
there should be a prompt like this:

oc>

At this prompt, enter "topology()" (without the " marks) to see a
skeletal view of the simulated cell.  In this case there is only one
compartment, represented as |-|, called soma(0-1).

Now run the "Patch:HH" demo run NEURON by clicking the 'Init & Run'
button.  Under "I/V Clamp Electrode", click "IClamp" (current clamp) and
change the stimulus duration to 100 ms.  How does the shape of the
action potential change?  Extend the time range under "RunControl" by
setting "Tstop" to 200 ms.  Did the simulation behave as you expected? 
Reduce the driving amplitude from 250 picoAmps (0.25 nanoAmps) to 25
picoAmps. Now how does the simulation behave?

1.b. Run the "Stylized" demo using "Init & Run" on the Run Control
panel.  Now use "Init & Run" from the "Movie Run" panel to watch what
happens in slow motion.  The red and blue traces show the membrane
voltage at the middle of the soma (soma.v(.5)) and at the node of
Ranvier at the end of the long axon.  Type "topology()" in the command
window to see that this is a more complicated cell with a variety of
compartments.  Where does the action potential peak first?  Double the
delays of each synapse (under "Synaptic Parameters").  How does the
relative timing of incoming spikes appear to affect the simulated cell's
response?

1.c. Click on the synchronizing net (artificial cells) demo.  Under the
"Synchronizing network parameters" window, change "All to all connection
weight" to 0 and run the simulation.  Reset the connection weight to
-.1, -.2, and -.3.  How does the pattern of spikes change?

1.d. Click on the Stochastic Single Channels: HH demo.  How does the
behavior for N=10,000, N=1,000 and N=100 channels compare with
"Continuous" (effectively an infinite number of channels)?

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2. From the main NEURON page, go to "Course announcements" and click on
"Why not pick up the complete course archive?"  Put the download files
somewhere you can find them later.  For example, if your name is
"student", you might put them in a folder like

	~student/nrncourse/
	
If this is the first time you've used the command line interface on
your computer, please consult either another student in the course, the
course assistant, or the instructor for help.  See also an introduction
to the bash or linux command line, such as 
	http://linux.org.mt/article/terminal 
or
	http://www.itc.virginia.edu/achs/documents/intro_unix.html

For example, in Terminal (the bourne-again shell ("bash") environment
for mac/os x) you could move the directory "course" from your desktop to
the folder above by typing the following at the "$" prompt

	$ mv   ~student/Desktop/course/   ~/student/nrncourse/

To begin self-study of the NEURON environment, open the file
handson.html in your web browser, and begin with the first exercise,
Lipid Bilayer.  We will do this exercise together in class as well.

The course directory should contain bilayer.html as well as a directory
bilayer/, which in turn contains bilayer.hoc.  Open the file bilayer.hoc
in a basic text editor (such as WordTab in Windows, Emacs in Linux, or
TextEdit or BBedit in OS X), to see an example of the basic programming
language underlying NEURON.  We will not delve into details of the "hoc"
language yet, but those who are interested can look ahead at exercise 4
in the course directory.

Under Windows:

How to install the course pack
1) Go to http://www.neuron.yale.edu/neuron/courses.html
2) Click on "Why not pick up the complete course archive ?" to download
a Zip file of the examples
3) Use an unzipping program to unzip the course.zip file into your c:\
directory
   a) if you don't have Winzip or Winrar you can download a trial copy
   at http://www.rarlab.com/download.htm

How to start the bilayer and subsequent experiments
1) Open your NEURON 6.1 folder
2) Begin NEURON via the nrngui shortcut
3) In the toolbar click on File and then "load hoc"
4) In the directory list that appears double click on the course/ folder
5) In the new directory list double click on bilayer/ folder
6) Double click on bilayer.hoc to start the experiment