Instruction for demo simulations that generate the simulation figures in
Tomokazu Doi, Shinya Kuroda, Takayuki Michikawa, and Mitsuo Kawato 
Inositol 1,4,5-Trisphophate-Dependent Ca2+ Threshold Dynamics Detect Spike Timing in
Cerebellar Purkinje Cells. 
The Journal of Neuroscience (2005) 25(4):950-961.

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 xtomdoi@atr.jp.


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HOW TO RUN DEMOS


To extract doiJNSdemo.tar.gz, type

tar zxvf doiJNSdemo.tar.gz


The created directory has several files named fig*.g. To run demos, just type

genesis fig3.g
(or choose other files named fig*.g)

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.

Some simulations take enormous time (several months). Here is a list of expected time for simulation on a 2 GHz Pentium 4 PC.

fig3.g         4 min
fig4.g        12 min
fig5.g        20 min
fig6B.g        7 hrs
fig6C.g        3 min
fig7A.g       12 min
fig7B.g        9 hrs
fig8CDE.g     80 min
fig8F.g       10 days
fig9.g        25 min
fig11A.g       4 min
figS2A.g      12 min
figS2BCDE.g    1 day
figS2F.g      27 hrs
figS2G.g       4 hrs
figS2GHIJ.g  120 days (strongly recommended to use a PC cluster)


To load the model scripts without demos, type
genesis DoiCaModel.g

All of the model parameters have notes in the scripts, which are identical to Supplemental Tables 1-3. 

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Tomoakazu Doi, 
ATR Computational Neuroscience Labs,
26 Jan 2005
xtomdoi@atr.jp