Table of Contents

Giorgio Ascoli, Editor

Maciej Lazarewicz (mailto:mlazarew@hotmail.com)
(The programs and materials for chapter 7 have been compiled and run on a PC workstation: 1.2 Ghz Athlon, 256MB RAM, Linux Redhat 7.1. MPEG files should run on any major platform and Neuron Simulation files should run on any platform which NEURON is installed (currently available for Windows and a variety of Unix systems); AWK executable (swc2hoc.awk) should run on any Unix machine.)
M95_t3_i1.mpg
Behavior of the burst in the Migliore 1995 CA3 model with different compartmentalizations based on electrotonic length. The x axis is time [ms] and the y axis is membrane potential [mV]. Each time frame is a different compartmentalization, with the number of compartments visualized on the top. This simulation used variable time step. Note how even with very fine compartmentalization, the model is not completely stable.
M95_nseg_uniform.mpg
The same model as above. Compartmentalization is uniform instead of based on electrotonic length.
ML01_vdrop.mpg
This movie is based on the updated CA3 model (Lazarewicz, 2001) with fixed time step 25 [us]. Each frame is a different compartmentalization (based on the voltage drop compartmentalization algorithm described in the text). Note how the model becomes stable at ~6000 compartments.
swc2hoc.awk
A Unix AWK executable to parsimoniously convert SWC fromat morphology into NEURON HOC format. This is done by creating sections from interbranching sequence of compartments with the same diameter. Between sections with different diameters, the program creates a truncated cone section ("frustum") to approximate a smooth geometry. Usage: awk -f swc2hoc.awk input_file.swc > output_file.hoc input_file.sec - input file in SWC format output_file.hoc - output file in HOC format
Neuron Simulations
This directory of files may be accessed through your web browser from this page. Alternatively, you can access this folder by locating the Directory "Neuron Simulations" in the contents of your CD-ROM drive.