* Readme

** What is this program?

This is our re-implementation of the cerebellar model presented in the
following paper:

    Tadashi Yamazaki and Shigeru Tanaka (2005),
    Neural Modeling of an Internal Clock.
    Neural Computation 17(5) 1032--1058.

One can set parameters arbitrarily and simulate the network dynamics.

Please notice that this program is independent of the original version
developed by Yamazaki and Tanaka (2005).

** Files

This folder contains the following files:

readme.txt :: This file

Makefile :: Makefile

internalclock.c :: The model

similarity.c :: Calculation of the similarity index.  This program
                uses libgd(*) for generating the PNG file of the
                similarity matrix.
                (*) http://www.libgd.org/

activity.dat :: Activity of model neurons (z_{i}(t)).

raster.dat :: Indices of active neurons {i| z_{i}(t) > 0} at t.

readout.dat :: Net input for given inter-stimulus interval, as shown
               in Fig. 14, p.1048.

s.png (below):: PNG file of similarity matrix generated by similarity.c:

s.png would have normally been displayed in your browser

s.dat :: the 200, 400, 600, 800th rows of the similarity matrix

** Usage

1. Modify parameters in internalclock.c if necessary.
2. Install libgd to compile similarity.c.
3. make
4. ./internalclock   The
   value of inter-stimulus interval is used to compute the Net input.
   You can use for example "./internalclock 1234 10"
5. The program generates activity.dat, raster.dat, readout.dat.
6. ./similarity activity.dat s

7. The program computes the similarity index and generates s.png and

** How to plot data using gnuplot

gnuplot (http://gnuplot.info/) is a data and function plotting

Active neurons are plotted by 

gnuplot> plot 'raster.dat'

X and Y axes represent time and neuron index, respectively.

Net input for given inter-stimulus interval is plotted by

gnuplot> plot 'readout.dat' with line

X and Y axes represent time and the value, respectively.

Similarity indices at t=200,400,600,800 are plotted by

gnuplot> plot 's.dat' with line

X and Y axes represent time and the value, respectively.

** Authors

Takeru Honda and Tadashi Yamazaki

TH: Dept. of Information and Communication Engineering, University of
Electro-communications. TY: Lab. for Motor Learning Control, RIKEN
Brain Science Institute.

** Copyright

Copyright (c) 2007 RIKEN (The Institute of Physical and Chemical
Research) Some rights reversed.

** License


This work is licensed under the Creative Commons Attribution 3.0
License. To view a copy of this license, visit
or send a letter to
Creative Commons, 171 Second Street, Suite 300, San Francisco,
California, 94105, USA.

Note from ModelDB administrator: This model is also available at:

The model can be run online at the sim.neuinf.jp simulation platform: