Instruction for demo simulations that generate the simulation figures in
Tomokazu Doi, Shinya Kuroda, Takayuki Michikawa, and Mitsuo Kawato
Inositol 1,4,5-Tripshosphate-Dependent Ca2+ Threshold 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 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.
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
(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.
To load the model scripts without demos, type
All of the model parameters has notes in the scripts, which are identical to Supplemental Tables 1-3.
ATR Computational Neuroscience Labs,
26 Jan 2005