GitHub - ModelDBRepository/49305: Spike timing detection in different forms of LTD (Doi et al 2005)

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Spike timing detection in different forms of LTD (Doi et al 2005)

modeldb.science/49305

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readme.html		readme.html

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Note: 
<a href="http://www.cns.atr.jp/neuroinfo/doi/doiJNSdemo.tar.gz">Click here for the model tar.gz file</a> available from <a href="http://www.cns.atr.jp/neuroinfo/doi/indexE.html">http://www.cns.atr.jp/neuroinfo/doi/indexE.html</a>
<hr/>Note from the ModelDB administrator:  here are some notes from an original readme supplied by the authors:
<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. <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>
<br>
</p>
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