HHsim: Graphical Hodgkin-Huxley Simulator

David S. Touretzky, Mark V. Albert, Nathaniel D. Daw, Alok Ladsariya and Mahtiyar Bonakdarpour

HHsim is a graphical simulation of a section of excitable neuronal membrane using the Hodgkin-Huxley equations. It provides full access to the Hodgkin-Huxley parameters, membrane parameters, stimulus parameters, and ion concentrations. To learn about the Hodgkin-Huxley equations, see:

Channeling with Bard, an online tutorial by G. Bard Ermentrout.
Biophysics of Computation: Information Processing in Single Neurons, by Christof Koch. (See chapter 6.)
Theoretical Neuroscience, by Peter Dayan and Larry F. Abbott. (See chapter 5.)
A Simple Sodium - Potassium Gate Model, by James K. Peterson.

In contrast with NEURON or GENESIS, which are vastly more sophisticated research tools, HHsim is simple educational software designed specifically for graduate or undergraduate neurophysiology courses. The user interface can be mastered in a couple of minutes and provides many ways for the student to experiment.

HHsim is free software distributed under the GNU General Public License. The official HHsim web site is at http://www.cs.cmu.edu/~dst/HHsim. The online documentation, including sample screen shots, is available on this web site, and also included with the program when you download it. Also included are sample exercises that use the simulator.

Download HHsim Now

HHsim is available as a Windows, Mac, or Unix executable file that does not require a Matlab license. Source code is included. It is also available in source-only form if you have Matlab R2007a or later. The latest release of HHsim is version 3.1, released February 16, 2008. Notes for Mac users: (1) HHsim requires that X11 be installed; it's available in /Applications/Utilities/X11.app. (2)There is a known graphics error in Leopard (Mac OS 10.5) that fails to display button labels. We're working on a fix for this; for now, please see the screenshot below for the labels. The functionality is the same.

Windows/Pentium (Windows XP) Version 3.1 - Feb 16, 2008 hhsim_31_win.zip	Linux/Pentium Version 3.1 - Feb 16, 2008 hhsim_31_linux.zip
Mac OS X (Intel Architecture) Version 3.1 - Feb 16, 2008 hhsim_31_macIntel.zip	Mac OS X (PowerPC Architecture) Version 3.1 - Aug 23, 2008 hhsim_31_macPPC.zip
Matlab source code only Version 3.1 - Dec 20, 2007 hhsim_31_source.zip or browse the code online

Installation Instructions (version 3.1)

Windows:

Unzip hhsim_31_win.zip to a directory of your choice.
Run MCRInstaller.exe, this installs the MATLAB Runtime Component allowing you to run standalone MATLAB applications. You are now ready to use HHSim.
Run hhsim.exe.

Linux:

Unzip hhsim_31_linux.zip into a the directory of your choice.
cd into that directory and run ./hhsim

Mac (Intel Architecture):

Unzip hhsim_31_macIntel.zip into the directory of your choice
Use the MCR_Installer dmg to install the MATLAB Runtime Component, allowing you to run standalone MATLAB applications. NOTE: be sure to use the default location: /Applications/MATLAB/MATLAB_Component_Runtime/v76
Use the HHSim dmg to install HHsim.

Mac (PowerPC Architecture):

Unzip hhsim_31_macPPC.zip into the directory of your choice
Use the Matlab_Component_Runtime dmg to install the MATLAB Runtime Component, allowing you to run standalone MATLAB applications.
Use 'Terminal' and, while in the hhsim_31_macPPC directory, type (assuming you installed MCR in the default location):
./run_hhsim.sh /Applications/MATLAB/MATLAB_Component_Runtime/v76

Sample screen shot:

Click here for HHsim User's Guide

This work was supported in part by National Science Foundation grant DGE-9987588. Any opinions, conclusions, or recommendations expressed herein are those of the authors and do not necessarily reflect the views of the National Science Foundation.

Dave Touretzky

Last modified: Fri Oct 24 19:28:47 EDT 2008