-
Notifications
You must be signed in to change notification settings - Fork 1
/
readme.txt
520 lines (496 loc) · 19.1 KB
/
readme.txt
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
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
README: Cerebellar Nucleus (CN) Neuron modeling project.
Abbasi et. al. PLOS Computational Biology 2017
A) There are 3 types of code:
1) Matlab code to prepare artificial spike trains (ASTs) as input to CN neuron model.
2) CN model code to run different combinations of ASTs and model parameter settings.
3) Matlab code to analyze the simulation output files.
Note: a paperFigures folder is large and included separately from
https://senselab.med.yale.edu/modeldb/data/229279/paperFigures.zip
Please download and extract this zip file within the top level folder of this archive.
Re. 1) The AST code is located in subdirectory AST-DCN-ProjectCode/ASTgeneration. The main script is MAIN_ASTcreation.m.
The recorded physiological spike trains that are used as templates are located in subdirectory NumberedData, where each number represents data from a recording session, including respiratory event times. The spike trains of the recorded neurons come in 3 formats. 1) [name].txt. The raw spike times in one column in units 0.1 ms, i.e. the number '30' is equivalent to 3 ms. 2) [name]_refp3.txt. All spikes preceding a previous spike by less than 3 ms (the assumed absolute refractory period) are removed. 3) [name]_refp3_sub.txt. The absolute refractory period of 3 ms between spike times is removed in order to generate the best match to a gamma distribution.
The subdirectory AST-DCN_ProjectCode/ModelData includes a set of ASTs generated using our algorithm and also those same ASTs after removing the refractory period.
Re. 2) The CN model code is located under AST-DCN-ProjectCode/Genesis model. The main script is located in DCN-Runs (Main_Samira.g).
'DCN-Common' directory contains common scripts of both model and 'DCN-Runs' contains main script to run the model. Note that this model is an adaptation from our previously shared model available in ModelDB (Steuber, V., N. W. Schultheiss, R. A. Silver, E. De Schutter and D. Jaeger (2011). "Determinants of synaptic integration and heterogeneity in rebound firing explored with data driven models of deep cerebellar nucleus cells." Journal of Computational Neuroscience 30: 633-658.).
Note: The GENESIS simulator source code was changed in order to allow for the biologically correct formulation of the short-term plasticity rule for Purkinje cell input to the CN (see PLOS Comp. Biology paper). In order to replicate our simulations exactly the source code for GENESIS needs to be recompiled with the changed synchan.c code. The synchan object now has a field called std_on, which is set to 0 for a classical synchan, and to 1 for the CN specific STD rule. The Genesis archive genesis2.3_std.zip in folder AST-DCN-ProjectCode/GenesisModel/GenesisSource contains this code in its src/newconn subfolder. It also contains the precompiled nxgenesis_std executable, which may work on any given Linux machine (or not).
Re. 3) The analysis code is primarily located in subfolder paperFigures/AnalysisScripts. Some custom code may also be in each Figure directory, and the analysis code draws from the chronux toolbox (http://chronux.org/) (copy of the version used here provided in chronux subdirectory). See section C) below for more detail.
Our analysis strategy uses the database approach published by Cengiz Gunay (Gunay, C., J. R. Edgerton, S. Li, T. Sangrey, A. A. Prinz and D. Jaeger (2009). "Database Analysis of Simulated and Recorded Electrophysiological Datasets with PANDORA's Toolbox." Neuroinformatics 7(2): 93-111.) and available under https://github.com/cengique/pandora-matlab. We include a copy of the version we used here under 'pandora-matlab-1.4compat2':
B) The figures from the publication can be reproduced from the paperFigures subdirectory.
Note, however, that figure panels were post-processed with Adobe Illustrator and axis labels, colors, and dot sizes in raster plots for example will not match the published figures.
Before running the .m files from each figure directory, please add the root codes directory with all subdirectories to your Matlab path.
Figure 1:
- 'figure1_A_B_C_D.m': this script plots panels A to D of figure 1.
- 'figure1_E_F.m': this script plots panels E to F of figure 1.
Figure 2:
This figure compares original and improved DCN model for Gex = 2 and Gin = 6.
- 'figure2_A_B.m': this script plots panels A to B of figure 2.
- 'figure2_C_D_E_F.m': this script plots panels C to F of figure 2.
- 'DatabaseGeneration.m': this script creates database for simulated DCN outputs. Its output is 'figure2_db'.
Figure 3:
This figure shows FR vs Gex and CV and LV vs FR for DCN simulations.
- 'Figure3.m': this script plots panels of figure 3.
Figure 4:
This figure shows CV vs FR and LV vs CV for recorded DCN data and simulations results.
- 'figure4.m': this script plots panels of figure 4.
Figure 5:
This figure shows input and output PSTHs and respiratory raster plots for recorded and simulated PC and DCN.
- 'figure5.m': this script plots panels of figure 5.
- 'codes\AST-DCN-ProjectCode\ModelData\ASTcell30withFRfromCell43\Shift0_BehMod1_BehModStrength1': ASTs in this directory are used in figure 5.
Figure 6:
This figure shows PSTHs for low and high Gex for three values of Behavior Modulation Strength (BMS), also it shows CV, LV and change in mean PSTH peak frequency vs BMS for different values of Behavior Modulation Fraction (BMF), Gex and Shift Fraction.
- 'figure6_A.m': this script plots panel A of figure 6.
- 'figure6_B_C_D.m': this script plots panels B to D of figure 6.
Figure 7:
This figure shows results of simulation with 500 ASTs, and also differences between these results and simulation results with 50 ASTs.
- 'figure7_A.m': this script plots panel A of figure 7.
- 'figure7_B_C_E_F.m': this script plots panels B to C and E to F of figure 7.
- 'figure7_D.m': this script plots panel D of figure 7.
Figure 8:
This figure shows results of simulations with different values of SK conductance.
- 'figure8_A.m': this script plots panel A of figure 8.
- 'figure8_B_C_D_F.m': this script plots panels B to D and F of figure 8.
- 'figure8_E.m': this script plots panel E of figure 8.
Supplemental Figure 1:
This figure shows spike train statistics of recorded neurons.
'SuppFigure1.m': this script plots figure S1.
Supplemental Figure 2:
This figure shows PSTHs and respiratory cycles for MFs, PCs, and DCNs.
- 'SuppFigure2.m': this script plots panels of figure S2.
Supplemental Figure 3:
This figure shows PSTH population properties.
- 'SuppFigure3.m': this script plots panels of figure S3.
Supplemental Figure 4:
This figure shows results for simulation without STD (std off), and also differences between std off and on.
- 'SuppFigure4.m': this script plots figure S4.
Supplemental Figure 5:
This figure shows results of simulation with ASTs constructed with half value of original firing rate, and also differences between these results and original results.
- 'SuppFigure5_A.m': this script plots panel A of figure S5.
- 'SuppFigure5_B.m': this script plots panel B of figure S5.
- 'SuppFigure5_C_D_E_F.m': this script plots panels C to F of figure S5.
Supplemental Figure 6:
This figure shows results of simulation with ASTs constructed with twice value of original firing rate, and also differences between these results and original results.
- 'SuppFigure 6_A.m': this script plots panel A of figure S6.
- 'SuppFigure 6.m': this script plots panel B of figure S6.
- 'SuppFigure 6_C_D_E_F.m': this script plots panels C to F of figure S6.
Supplemental Figure 7:
This figure shows results of simulations with ASTs constructed from recorded firing rate distribution. It also shows differences between original simulations and current results.
Firing rate distribution used to construct ASTs= 50:25:175
- 'SuppFigure7_A.m': this script plots panel A of figure S7.
- 'SuppFigure7_B.m': this script plots panel B of figure S7.
- 'SuppFigure7_C_D_E_F.m': this script plots panels C to F of figure S7.
Supplemental Figure 8:
This figure shows results of simulations with ASTs from different recorded PC (cell with lower CV). It also demonstrates differences between original simulations and current simulations.
- 'SuppFigure8_A.m': this script plots panel A of figure S8.
- 'SuppFigure8_B.m': this script plots panel B of figure S8.
- 'SuppFigure8_C_D_E_F.m': this script plots panels C to F of figure S8.
Supplemental Figure 9:
This figure shows results of simulation with manipulation of slow and fast rate template.
SRM: slow rate modulation
FRM: fast rate modulation
- 'SuppFigure9.m': this script plots panels of figure S9.
C) 'AnalysisScripts' directory:
This directory includes functions and scripts required to do simulations and plot figures. It also includes codes to make databases from simulation output of DCN model and generated databases. For making a database one deals with the following parameters i.e. you must change them according to your desire database:
- 'filesetGenesisAnalysis.m':
In this mfile one finds:
start_time = 0;
end_time = 110;
These are start and end time of spike times that you want to use in your analysis to make a database.
- 'GenesisOutputAnalysis.m':
This script is the main script to make a database. In this script one must change the following parameters according to each database:
nums : this is the recorded PC ID that you used for generating ASTs (for example I used PC numbered 30). It is used to load behavior event times to calculate PSTH.
DCNmodel_rundur: genesis run duration is second (in our simulations it was 110)
ASTnums: number of ASTs (50 or 500)
- 'getPSTHsDCN.m':
This script calculates PSTH. You must determine directory of your ASTs in "base". For example:
These were parameters that one should pay attention to them for making a database. Then to make a database there is script entitled "DatabaseGeneration.m". By running this mfile one can make a database.
Databases which were made from different batches of simulations are placed in this directory and explanation of them goes here:
"ParamFile1_db": this was made from results of the first batch of simulations using the following values for the parameters:
num_contact: number of contacts in DCN model, g_ampa : ampa conductance, g_gaba: gaba conductance, g_sks: somatic SK channel conductance, g_skd: dendritic SK channel conductance, pcct: number of PCs synapses on the DCN model dendrites, mfct: number of MFs synapses on the DCN model dendrites, mfASTfolder: ID identifying directory of MF ASTs, ShiftFrac: shift fraction parameter in the AST generation algorithm, BehMod: behavior modulation parameter in the AST generation algorithm.
num_contact [ 1 ]
g_ampa [ 0 1 2 3 4 5 6 7 8 9 10 ]
g_gaba [ 0 2 4 6 8 10 12 14 16 18 20 ]
g_sks [ 2 ]
g_skd [ 0.6 ]
pcct [ 48 ]
mfct [ 48 ]
mfASTfolder [ 1 ]
ShiftFrac [ 0:0.25: 1 ]
BehMod [ 0 ]
'
"ParamFile2_db":
This is results of simulations with adding behavior modulation. These simulations were run with two values of g-gaba and two values of g-ampa for each g-gaba.
1)
num_contact [ 1 ]
g_ampa [ 3.5 6 ]
g_gaba [ 16 ]
g_sks [ 2 ]
g_skd [ 0.6 ]
pcct [ 48 ]
mfct [ 48 ]
mfASTfolder [ 1 ]
ShiftFrac [ 0.5 1 ]
BehMod [ 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1 ]
BehModStrength [ 0 0.2 0.4 0.6 0.8 1 1.2 1.4 1.6 1.8 2]
2)
num_contact [ 1 ]
g_ampa [ 1.1 2.15 ]
g_gaba [ 4 ]
g_sks [ 2 ]
g_skd [ 0.6 ]
pcct [ 48 ]
mfct [ 48 ]
mfASTfolder [ 1 ]
ShiftFrac [ 0.5 1 ]
BehMod [ 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1 ]
BehModStrength [ 0 0.2 0.4 0.6 0.8 1 1.2 1.4 1.6 1.8 2]
'
'std_off_db':
This is previous simulations but without STD.
1)
num_contact [ 1 ]
g_ampa [ 3.5 6 ]
g_gaba [ 7.2 ]
g_sks [ 2 ]
g_skd [ 0.6 ]
pcct [ 48 ]
mfct [ 48 ]
mfASTfolder [ 1 ]
ShiftFrac [ 0.5 1 ]
BehMod [ 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1 ]
BehModStrength [ 0 0.2 0.4 0.6 0.8 1 1.2 1.4 1.6 1.8 2]
2)
num_contact [ 1 ]
g_ampa [ 1.1 2.15 ]
g_gaba [ 1.8 ]
g_sks [ 2 ]
g_skd [ 0.6 ]
pcct [ 48 ]
mfct [ 48 ]
mfASTfolder [ 1 ]
ShiftFrac [ 0.5 1 ]
BehMod [ 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1 ]
BehModStrength [ 0 0.2 0.4 0.6 0.8 1 1.2 1.4 1.6 1.8 2]
'
'FR_twice_half_db':
This is simulations with ASTs constructed with twice and half values of original FR.
1. FR twice
num_contact [ 1 ]
g_ampa [ 3.5 6 ]
g_gaba [ 8 ]
g_sks [ 2 ]
g_skd [ 0.6 ]
pcct [ 48 ]
mfct [ 48 ]
mfASTfolder [ 1 ]
ShiftFrac [ 0.5 1 ]
BehMod [ 0 0.2 0.4 0.6 0.8 1 ]
BehModStrength [ 0 0.4 0.8 1.2 1.6 2]
2. FR twice
num_contact [ 1 ]
g_ampa [ 1.1 2.15 ]
g_gaba [2 ]
g_sks [ 2 ]
g_skd [ 0.6 ]
pcct [ 48 ]
mfct [ 48 ]
mfASTfolder [ 1 ]
ShiftFrac [ 0.5 1 ]
BehMod [ 0 0.2 0.4 0.6 0.8 1 ]
BehModStrength [ 0 0.4 0.8 1.2 1.6 2]
3. FR half
num_contact [ 1 ]
g_ampa [ 3.5 6 ]
g_gaba [ 32 ]
g_sks [ 2 ]
g_skd [ 0.6 ]
pcct [ 48 ]
mfct [ 48 ]
mfASTfolder [ 1 ]
ShiftFrac [ 0.5 1 ]
BehMod [ 0 0.2 0.4 0.6 0.8 1 ]
BehModStrength [ 0 0.4 0.8 1.2 1.6 2]
4. FR half
num_contact [ 1 ]
g_ampa [ 1.1 2.15 ]
g_gaba [8 ]
g_sks [ 2 ]
g_skd [ 0.6 ]
pcct [ 48 ]
mfct [ 48 ]
mfASTfolder [ 1 ]
ShiftFrac [ 0.5 1 ]
BehMod [ 0 0.2 0.4 0.6 0.8 1 ]
BehModStrength [ 0 0.4 0.8 1.2 1.6 2]
'
After this set of simulations we realized that we should modify g-gaba. So, I ran this set with modifies values for g-gaba. Results are in the following directory:
'NewFR_twice_half_db':
1. FR twice
num_contact [ 1 ]
g_ampa [ 3.5 6 ]
g_gaba [ 9.84 ]
g_sks [ 2 ]
g_skd [ 0.6 ]
pcct [ 48 ]
mfct [ 48 ]
mfASTfolder [ 1 ]
ShiftFrac [ 0.5 1 ]
BehMod [ 0 0.2 0.4 0.6 0.8 1 ]
BehModStrength [ 0 0.4 0.8 1.2 1.6 2]
2. FR twice
num_contact [ 1 ]
g_ampa [ 1.1 2.15 ]
g_gaba [2.46 ]
g_sks [ 2 ]
g_skd [ 0.6 ]
pcct [ 48 ]
mfct [ 48 ]
mfASTfolder [ 1 ]
ShiftFrac [ 0.5 1 ]
BehMod [ 0 0.2 0.4 0.6 0.8 1 ]
BehModStrength [ 0 0.4 0.8 1.2 1.6 2]
3. FR half
num_contact [ 1 ]
g_ampa [ 3.5 6 ]
g_gaba [ 27.52 ]
g_sks [ 2 ]
g_skd [ 0.6 ]
pcct [ 48 ]
mfct [ 48 ]
mfASTfolder [ 1 ]
ShiftFrac [ 0.5 1 ]
BehMod [ 0 0.2 0.4 0.6 0.8 1 ]
BehModStrength [ 0 0.4 0.8 1.2 1.6 2]
4. FR half
num_contact [ 1 ]
g_ampa [ 1.1 2.15 ]
g_gaba [6.88 ]
g_sks [ 2 ]
g_skd [ 0.6 ]
pcct [ 48 ]
mfct [ 48 ]
mfASTfolder [ 1 ]
ShiftFrac [ 0.5 1 ]
BehMod [ 0 0.2 0.4 0.6 0.8 1 ]
BehModStrength [ 0 0.4 0.8 1.2 1.6 2]
'
' SK_db.mat':
This is simulations with different values of SK conductances.
1)
num_contact [ 1 ]
g_ampa [ 3.5 6 ]
g_gaba [ 16 ]
g_sks [ 0 ]
g_skd [ 0 ]
pcct [ 48 ]
mfct [ 48 ]
mfASTfolder [ 1 ]
ShiftFrac [ 0.5 1 ]
BehMod [ 0 0.2 0.4 0.6 0.8 1 ]
BehModStrength [ 0 0.4 0.8 1.2 1.6 2]
2)
num_contact [ 1 ]
g_ampa [ 1.1 2.15 ]
g_gaba [ 4 ]
g_sks [ 0 ]
g_skd [ 0 ]
pcct [ 48 ]
mfct [ 48 ]
mfASTfolder [ 1 ]
ShiftFrac [ 0.5 1 ]
BehMod [ 0 0.2 0.4 0.6 0.8 1 ]
BehModStrength [ 0 0.4 0.8 1.2 1.6 2]
3)
num_contact [ 1 ]
g_ampa [ 3.5 6 ]
g_gaba [ 16 ]
g_sks [ 0.5 ]
g_skd [ 0.15 ]
pcct [ 48 ]
mfct [ 48 ]
mfASTfolder [ 1 ]
ShiftFrac [ 0.5 1 ]
BehMod [ 0 0.2 0.4 0.6 0.8 1 ]
BehModStrength [ 0 0.4 0.8 1.2 1.6 2]
4)
num_contact [ 1 ]
g_ampa [ 1.1 2.15 ]
g_gaba [ 4 ]
g_sks [ 0.5 ]
g_skd [ 0.15 ]
pcct [ 48 ]
mfct [ 48 ]
mfASTfolder [ 1 ]
ShiftFrac [ 0.5 1 ]
BehMod [ 0 0.2 0.4 0.6 0.8 1 ]
BehModStrength [ 0 0.4 0.8 1.2 1.6 2]
5)
num_contact [ 1 ]
g_ampa [ 3.5 6 ]
g_gaba [ 16 ]
g_sks [ 4 ]
g_skd [ 1.2 ]
pcct [ 48 ]
mfct [ 48 ]
mfASTfolder [ 1 ]
ShiftFrac [ 0.5 1 ]
BehMod [ 0 0.2 0.4 0.6 0.8 1 ]
BehModStrength [ 0 0.4 0.8 1.2 1.6 2]
6)
num_contact [ 1 ]
g_ampa [ 1.1 2.15 ]
g_gaba [ 4 ]
g_sks [ 4 ]
g_skd [ 1.2 ]
pcct [ 48 ]
mfct [ 48 ]
mfASTfolder [ 1 ]
ShiftFrac [ 0.5 1 ]
BehMod [ 0 0.2 0.4 0.6 0.8 1 ]
BehModStrength [ 0 0.4 0.8 1.2 1.6 2]
7)
num_contact [ 1 ]
g_ampa [ 3.5 6 ]
g_gaba [ 16 ]
g_sks [ 8 ]
g_skd [ 2.4 ]
pcct [ 48 ]
mfct [ 48 ]
mfASTfolder [ 1 ]
ShiftFrac [ 0.5 1 ]
BehMod [ 0 0.2 0.4 0.6 0.8 1 ]
BehModStrength [ 0 0.4 0.8 1.2 1.6 2]
8)
num_contact [ 1 ]
g_ampa [ 1.1 2.15 ]
g_gaba [ 4 ]
g_sks [ 8 ]
g_skd [ 2.4 ]
pcct [ 48 ]
mfct [ 48 ]
mfASTfolder [ 1 ]
ShiftFrac [ 0.5 1 ]
BehMod [ 0 0.2 0.4 0.6 0.8 1 ]
BehModStrength [ 0 0.4 0.8 1.2 1.6 2]
'
' modifyFRdistribution_db.mat':
This is simulations with ASTs constructed from recorded PC firing rate distribution.
1)
num_contact [ 1 ]
g_ampa [ 3.5 6 ]
g_gaba [ 12.37 ]
g_sks [ 2 ]
g_skd [ 0.6 ]
pcct [ 48 ]
mfct [ 48 ]
mfASTfolder [ 1 ]
ShiftFrac [ 0.5 1 ]
BehMod [ 0 0.2 0.4 0.6 0.8 1 ]
BehModStrength [ 0 0.4 0.8 1.2 1.6 2]
2)
num_contact [ 1 ]
g_ampa [ 1.1 2.15 ]
g_gaba [ 3.1 ]
g_sks [ 2 ]
g_skd [ 0.6 ]
pcct [ 48 ]
mfct [ 48 ]
mfASTfolder [ 1 ]
ShiftFrac [ 0.5 1 ]
BehMod [ 0 0.2 0.4 0.6 0.8 1 ]
BehModStrength [ 0 0.4 0.8 1.2 1.6 2]
'
'AST500_db.mat':
This is simulations with 500 ASTs.
1)
num_contact [ 1 ]
g_ampa [ 3.5 6 ]
g_gaba [ 1.6 ]
g_sks [ 2 ]
g_skd [ 0.6 ]
pcct [ 480 ]
mfct [ 48 ]
mfASTfolder [ 1 ]
ShiftFrac [ 0.5 1 ]
BehMod [ 0 0.2 0.4 0.6 0.8 1 ]
BehModStrength [ 0 0.4 0.8 1.2 1.6 2 ]
2)
num_contact [ 1 ]
g_ampa [ 1.1 2.15 ]
g_gaba [ 0.4 ]
g_sks [ 2 ]
g_skd [ 0.6 ]
pcct [ 480 ]
mfct [ 48 ]
mfASTfolder [ 1 ]
ShiftFrac [ 0.5 1 ]
BehMod [ 0 0.2 0.4 0.6 0.8 1 ]
BehModStrength [ 0 0.4 0.8 1.2 1.6 2 ]
'
'gains_db.mat':
This is simulations with different values of slow and fast rate modulation gains.
1)
num_contact [ 1 ]
g_ampa [ 3.5 6 ]
g_gaba [ 16 ]
g_sks [ 2 ]
g_skd [ 0.6 ]
pcct [ 48 ]
mfct [ 48 ]
mfASTfolder [ 1 ]
ShiftFrac [ 0.5 1 ]
BehMod [ 0.2 0.8 ]
BehModStrength [ 0.8 1.6 ]
GainFa [0 0.5 1.5 2]
GainSa [0 0.5 1.5 2]
2)
num_contact [ 1 ]
g_ampa [ 1.1 2.15 ]
g_gaba [ 4 ]
g_sks [ 2 ]
g_skd [ 0.6 ]
pcct [ 48 ]
mfct [ 48 ]
mfASTfolder [ 1 ]
ShiftFrac [ 0.5 1 ]
BehMod [ 0.2 0.8 ]
BehModStrength [ 0.8 1.6]
GainFa [0 0.5 1.5 2]
GainSa [0 0.5 1.5 2]
'cell32_db.mat':
This is results of simulations with ASTs constructed from recorded PC with lower CV.
1)
num_contact [ 1 ]
g_ampa [ 3.5 6 ]
g_gaba [ 16 ]
g_sks [ 2 ]
g_skd [ 0.6 ]
pcct [ 48 ]
mfct [ 48 ]
mfASTfolder [ 1 ]
ShiftFrac [ 0.5 1 ]
BehMod [ 0 0.2 0.4 0.6 0.8 1 ]
BehModStrength [ 0 0.4 0.8 1.2 1.6 2]
2)
num_contact [ 1 ]
g_ampa [ 1.1 2.15 ]
g_gaba [ 4 ]
g_sks [ 2 ]
g_skd [ 0.6 ]
pcct [ 48 ]
mfct [ 48 ]
mfASTfolder [ 1 ]
ShiftFrac [ 0.5 1 ]
BehMod [ 0 0.2 0.4 0.6 0.8 1 ]
BehModStrength [ 0 0.4 0.8 1.2 1.6 2]
'FR50HZ-175HzResults':
This directory contains some of the simulation results used to plot figure 2.
D) 'AST-DCN-ProjectCode' directory:
This directory includes 3 subdirectory as follows:
'ASTgeneration':
- This directory contains functions and scripts required to generate ASTs population and 'MAIN_ASTcreation.m' is the main script for generating ASTs and in this script one should set the following parameters:
* BehModFrac: fraction of ASTs which have behavior modulation, its range is [0-1]
* BehModStren: strength of added behavior modulation or its amplitude
* ShiftFrac : fraction of shifted rate template to make noisy template, its range is [0-1]
* numAST: number of ASTSs you are going to generate.
* Savedir: directory to save ASTs
* i: ID of recorded PC, we used cell number 30 if you are going to use another cell you must change it. And also change "popstat" according to your desire.