-
Notifications
You must be signed in to change notification settings - Fork 1
/
readme.html
130 lines (129 loc) · 3.46 KB
/
readme.html
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
<html><body>
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>
</body></html>