Graphical Hodgkin-Huxley Simulator
This program is a graphical simulation of a section of excitable
neuronal membrane, using the Hodgkin-Huxley equations.
To run the program:
- start up MATLAB
- cd to the directory holding the source code
- type "run"
Click on the purple S1 or S2 buttons to inject a depolarizing or
hyperpolarizing current stimulus. Click on the Membrane, Channels, or
Stimuli buttons to view and modify the simulation parameters.
Running the Program on the CNBC System
If you're logged in to a console on one of the CNBC computer systems
(EAGLE, CONDOR, or the Pentium or Alpha clusters), you can run the
program on that machine. Simply start up MATLAB and then type:
cd ~dst/Matlab/hh/code
run
Running the Program on a Remote Unix System
If you have an account on a Unix system that runs MATLAB (such as one
of the CNBC computers), but you want to run the program from another
location, using a machine that does not have MATLAB installed, you can
do so provided that the machine is either a) another Unix system
running X Windows, or b) a PC running an X-Windows emulator like
Exceed.
To run the program on a remote Unix system, you first need to know the
name of your display. From a Unix shell, type echo $DISPLAY to
seey your display name. It should look like your machine name
followed by a colon and some digits, e.g.,
skinner.boltz.cs.cmu.edu:0.0. (If it says localhost:0.0 then
substitute your true machine name for the localhost part.)
- On your machine, type xhost + to allow remote connections.
- Log in to the remote system you wish to use to run MATLAB.
- On the remote system, type setenv DISPLAY display-name.
- On the remote system, start up MATLAB. You should see a little
graphical window with the MATLAB logo appear briefly on your display.
- Now cd to the directory containing the Hodgkin-Huxley simulator and
type "run" to being the simulation.
When the simulation is run remotely it runs more slowly, because all
the graphics have to be transmitted over the network. However, it is
still quite usable even at the reduced speed.
Running the Program on the Pitt unixs-eval System
- Before telneting to unixs-eval from another Unix system, type:
xhost +unixs-eval.cis.pitt.edu
- Then: telnet unixs-eval.cis.pitt.edu
- On unixs-eval type, setenv DISPLAY name_of_your_local_machine:0.0
- To run matlab, first type setup matlab and then type
matlab
Downloading the Program to Your Own Machine
You can download the source as a zip file.
Or you can browse the code directly.
The inner loop that computes the membrane voltage at each timestep is
in file iterate.m.
This software and accompanying documentation are copyright (c) 2000, 2001 by
David S. Touretzky. Nathaniel Daw and Mark Albert contributed to the implementation.
Dave Touretzky
Last modified: Thu Nov 22 03:17:53 EST 2001