Instruction for simulation demos and reproduction of simulation figures

Tomokazu Doi, Shinya Kuroda, Takayuki Michikawa, Mitsuo Kawato:
Inositol 1,4,5-Trisphosphatate-Dependent Ca2+ Therehosld Dynamics Detect Spike Timing in Cerebellar Purkinje Cells.
The Journal of Neuroscience 25(4): 950-961, 2005


The simulation requires GENESIS version 2.2 and kinetikit version 9 or 10. 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



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, more than 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
fig6A.g 3 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
figS2HIJK.g 120 days

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

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


Tomoakazu Doi,
ATR Computational Neuroscience Labs,
16 Feb 2006