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Purkinje Ca, LTD
Note:
Click here for the model tar.gz file (available under a link from this next page).
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[GENESIS]
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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. 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, 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.
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Tomoakazu Doi,
ATR Computational Neuroscience Labs,
26 Jan 2005
xtomdoi@atr.jp
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