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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html><head>
<meta name="GENERATOR" content="IBM WebSphere Studio Homepage Builder Version 6.5.0.0 for Windows">
<meta http-equiv="Content-Type" content="text/html; charset=Shift_JIS">
<meta http-equiv="Content-Style-Type" content="text/css"><title>Purkinje Ca, LTD</title></head>
<body alink="#ff0000" background="" bgcolor="#f0ffe6" link="#0000ff" text="#0f3700" vlink="#990099">
Note: <a href="http://hawaii.naist.jp/~tomoka-d/doiJNS/index.html">
Click here for the model tar.gz file (available under a link from this next page)</a>. <p/><hr>
<p align="center">[<a href="http://hawaii.naist.jp/%7Etomoka-d/index.html">Top</a>]
[<a href="http://www.cns.atr.jp/%7Edoi/research/index.html">Research</a>]
[<a href="http://www.cns.atr.jp/%7Edoi/GENESIS/index.html">GENESIS</a>]
[<a href="http://www.cns.atr.jp/%7Edoi/keihanna/index.html">Keihanna</a>]
[<a href="http://www.cns.atr.jp/%7Edoi/biography/index.html">Biography</a>]
[<a href="http://www.cns.atr.jp/%7Edoi/links/index.html">Links</a>]</p>
<hr>
<p>Instruction for demo simulations that generate the simulation figures in<br>
<br>
Tomokazu Doi, Shinya Kuroda, Takayuki Michikawa, and Mitsuo Kawato<br>
Inositol 1,4,5-Tripshosphate-Dependent Ca2+ Threshold Dynamics Detect Spike Timing in Cerebellar Purkinje Cells.<br>
The Journal of Neuroscience 25(4): 950-961, 2005<br>
<br>
<br>
The simulation requires GENESIS version 2.2 and kinetikit version 9 or
higher. Both of which are included in the compressed file you have
downloaded. We have confirmed that our simulation scripts run on Red
Hat Linux version 8 and Pentium 4 PCs. If you have a problem, please
contact at <a href="mailto:xtomdoi@atr.jp">xtomdoi@atr.jp</a>.<br>
<br>
<br>
////////////////////////////////////////////////////////////////<br>
<br>
HOW TO RUN DEMOS<br>
<br>
<br>
To extract doiJNSdemo.tar.gz, type<br>
<br>
tar zxvf doiJNSdemo.tar.gz<br>
<br>
<br>
The created directory has several files named fig*.g. To run demos, just type<br>
<br>
genesis fig3.g<br>
(or choose other files named fig*.g)<br>
<br>
GENESIS/kinetikit includes model scripts for the simulation, and displays
and saves simulation results in 'simresult/fig*/'. In simresult/fig*/,
there are MALTAB scripts files (*.m) which display the simulation results
as in the JNS paper. Comments in fig*.g might be useful to understand how
GENESIS/kinetikit works.<br>
<br>
Some simulations take enormous time, more than months. Here is a list of expected time for simulation on a 2 GHz Pentium 4 PC.<br>
<br>
<br>
</p>
<table border="1">
<tbody>
<tr>
<td>fig3.g</td>
<td align="right">4 min</td>
</tr>
<tr>
<td>fig4.g</td>
<td align="right">12 min</td>
</tr>
<tr>
<td>fig5.g</td>
<td align="right">20 min</td>
</tr>
<tr>
<td>fig6A.g</td>
<td align="right">3 min</td>
</tr>
<tr>
<td>fig6B.g</td>
<td align="right">7 hrs</td>
</tr>
<tr>
<td>fig6C.g</td>
<td align="right">3 min</td>
</tr>
<tr>
<td>fig7A.g</td>
<td align="right">12 min</td>
</tr>
<tr>
<td>fig7B.g</td>
<td align="right">9 hrs</td>
</tr>
<tr>
<td>fig8CDE.g</td>
<td align="right">80 min</td>
</tr>
<tr>
<td>fig8F.g</td>
<td align="right">10 days</td>
</tr>
<tr>
<td>fig9.g</td>
<td align="right">25 min</td>
</tr>
<tr>
<td>fig11A.g</td>
<td align="right">4 min</td>
</tr>
<tr>
<td>figS2A.g</td>
<td align="right">12 min</td>
</tr>
<tr>
<td>figS2BCDE.g</td>
<td align="right">1 day</td>
</tr>
<tr>
<td>figS2F.g</td>
<td align="right">27 hrs</td>
</tr>
<tr>
<td>figS2G.g</td>
<td align="right">4 hrs</td>
</tr>
<tr>
<td>figS2HIJK.g</td>
<td align="right">120 days</td>
</tr>
</tbody>
</table>
<p><br>
<br>To load the model scripts without demos, type<br>
genesis DoiCaModel.g<br>
<br>
All of the model parameters has notes in the scripts, which are identical to Supplemental Tables 1-3. <br>
<br>
////////////////////////////////////////////////////////////////<br>
<br>
Tomoakazu Doi, <br>
ATR Computational Neuroscience Labs,<br>
26 Jan 2005<br>
<a href="mailto:xtomdoi@atr.jp">xtomdoi@atr.jp</a><br>
</p>
</body></html>