Neuron simulator set-up and running.
Neuroscience 500 Demo 2000-09-28.
Copyright © 1999-2000 N. T. Carnevale and
M. L. Hines
To set-up Neuron
4.3.1 on set-up file and follow instructions. Get
file from install CD or at website:
A single file
setup.exe (almost 6 MB long) is required. Save this
file to an empty directory, then use the
"Add/Remove Programs" item in MSWin's Control Panel
to install or download five pkzipped files, each of
which is small enough to fit on a 1.44 MB floppy
set-up and install into the C:\NRN directory.
Neuron works best on Pentium level computers
probably greater than 100 MHz. After installing
neuron remember to restart computer.
Double click on
Neuron demo icon. From Neuron demonstrations menu
select a demo. First select the patch: HH (Hodgkin
Huxley). To reduce congestion on the screen
minimize Neuron command line menu. Also change the
temperature default to 22 °C. Whenever
changes are made (to parameters) one needs to click
the box to the left of the value insuring that a
red check mark is present.
To run the demo
find the Run Control window and press
Init and Run the second entry. On the window
termed V (voltage) a single action potential is
apparent. Click on the window called IV clamp
electrode on I clamp. Increase the delay in ms to
better see baseline and remember to click on the
left box so you see a red check. In the window
designated IV clamp electrode decrease the
amplitude of the current pulse to 0.1 and 0.5 nA.
At each setting hit Init and Run again to see the
effect. If the action potential is now off the
window go back to the run control window and change
the duration of the simulation. For example in each
place where 5 ms appears substitute with 10 ms.
Make sure to check the boxes.
Now alter the
amount of Na and K conductance. In the tools
menu select distributed mechanisms and then select
viewers, shape name, soma. Double-click on soma and
menu will come up with parameters for the soma. In
that Menu go down and adjust gNaBAR the amount of
Hodgkin-Huxley Na current. Reduce the
conductance and observe what happens to the
excitability of the cell and the action potential
amplitude. Now try increasing the K conductance and
decreasing K conductance. What happens if K
conductance is decreased by a factor of 5? What
happens to the action potential in zero K conductance
and varied Na conductance? Now try to adjust the
leak conductance gL. Try increasing the leak
by a factor of 5. What happens to excitability? In
the soma parameters menu you can also adjust
concentrations of permeant ions such as Na and K.
Try adjusting the capacitance of the cell, increase
it by a factor of 5 and see what happens to
excitability. Now examine the Na and K currents
directly. Go to Neuron main menu select graph,
current axes, and then right mouse-click on the
window of the graph, select plot what, double-click
on soma, scroll down until you find INa (0.5),
double-click on it, click accept. Now run the
simulation. If the peak is overshooting the range
of the graph right mouse-click on the legend that
says soma.INa and then scroll up to view and
then over to view = plot and it will autoscale.
Follow the same procedure and graph the K current
graph current axes.
Close Neuron and
start another demo. This one would be on
demonstrating principles of synaptic transmission.
Choose stylized neuron. This is a myelinated
neuron with 3 synapses. Click on Init and
Run and observe action potentials being plotted
at the soma and at the first node of Ranvier. In
this demo there are 3 synapses on dendrite of a
myelinated neuron and in the simulation window
designated synaptic parameters it is possible to
adjust the location of the 3 different synapses as
well as the delays between them. Adjust these and
examine what effect they have on action potential