ModelDB is moving. Check out our new site at https://modeldb.science. The corresponding page is https://modeldb.science/45539.

A single column thalamocortical network model (Traub et al 2005)

 Download zip file 
Help downloading and running models
Accession:45539
To better understand population phenomena in thalamocortical neuronal ensembles, we have constructed a preliminary network model with 3,560 multicompartment neurons (containing soma, branching dendrites, and a portion of axon). Types of neurons included superficial pyramids (with regular spiking [RS] and fast rhythmic bursting [FRB] firing behaviors); RS spiny stellates; fast spiking (FS) interneurons, with basket-type and axoaxonic types of connectivity, and located in superficial and deep cortical layers; low threshold spiking (LTS) interneurons, that contacted principal cell dendrites; deep pyramids, that could have RS or intrinsic bursting (IB) firing behaviors, and endowed either with non-tufted apical dendrites or with long tufted apical dendrites; thalamocortical relay (TCR) cells; and nucleus reticularis (nRT) cells. To the extent possible, both electrophysiology and synaptic connectivity were based on published data, although many arbitrary choices were necessary.
References:
1 . Traub RD, Contreras D, Cunningham MO, Murray H, LeBeau FE, Roopun A, Bibbig A, Wilent WB, Higley MJ, Whittington MA (2005) Single-column thalamocortical network model exhibiting gamma oscillations, sleep spindles, and epileptogenic bursts. J Neurophysiol 93:2194-232 [PubMed]
2 . Traub RD, Contreras D, Whittington MA (2005) Combined experimental/simulation studies of cellular and network mechanisms of epileptogenesis in vitro and in vivo. J Clin Neurophysiol 22:330-42 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network;
Brain Region(s)/Organism: Neocortex; Thalamus;
Cell Type(s): Thalamus geniculate nucleus/lateral principal GLU cell; Thalamus reticular nucleus GABA cell; Neocortex U1 L6 pyramidal corticalthalamic GLU cell; Neocortex U1 L2/6 pyramidal intratelencephalic GLU cell; Neocortex fast spiking (FS) interneuron; Neocortex spiking regular (RS) neuron; Neocortex spiking low threshold (LTS) neuron;
Channel(s): I Na,p; I Na,t; I L high threshold; I T low threshold; I A; I K; I M; I h; I K,Ca; I Calcium; I A, slow;
Gap Junctions: Gap junctions;
Receptor(s): GabaA; AMPA; NMDA;
Gene(s):
Transmitter(s):
Simulation Environment: NEURON; FORTRAN;
Model Concept(s): Activity Patterns; Bursting; Temporal Pattern Generation; Oscillations; Simplified Models; Epilepsy; Sleep; Spindles;
Implementer(s): Traub, Roger D [rtraub at us.ibm.com];
Search NeuronDB for information about:  Thalamus geniculate nucleus/lateral principal GLU cell; Thalamus reticular nucleus GABA cell; Neocortex U1 L2/6 pyramidal intratelencephalic GLU cell; Neocortex U1 L6 pyramidal corticalthalamic GLU cell; GabaA; AMPA; NMDA; I Na,p; I Na,t; I L high threshold; I T low threshold; I A; I K; I M; I h; I K,Ca; I Calcium; I A, slow;
Files displayed below are from the implementation
/
nrntraub
dat
deepaxax_v_F.dat *
deepbask_v_F.dat *
deepLTS_v_F.dat *
nointeraction.spk *
nontuftRS_v_F.dat *
nrntest.spk *
nRT_v_F.dat *
p2ctest.spk *
spinstell_v_F.dat *
supaxax_v_F.dat *
supbask_v_F.dat *
supLTS_v_F.dat *
suppyrFRB_v_F.dat *
suppyrRS_v_F.dat *
TCR_v_F.dat *
tuftIB_v_F.dat *
tuftRS_v_F.dat *
                            
    0.1000  -64.6585
    0.2000  -64.0741
    0.3000  -63.3925
    0.4000  -62.6366
    0.5000  -61.7985
    0.6000  -60.8452
    0.7000  -59.7048
    0.8000  -58.2369
    0.9000  -56.0639
    1.0000  -51.7423
    1.1000  -30.7222
    1.2000   47.7937
    1.3000   27.7379
    1.4000    0.9343
    1.5000  -17.2945
    1.6000  -38.9103
    1.7000  -84.9868
    1.8000  -86.4820
    1.9000  -82.3005
    2.0000  -77.7318
    2.1000  -74.5424
    2.2000  -72.4055
    2.3000  -70.9368
    2.4000  -69.8485
    2.5000  -68.9517
    2.6000  -68.1508
    2.7000  -67.4012
    2.8000  -66.6843
    2.9000  -65.9948
    3.0000  -65.3323
    3.1000  -64.6974
    3.2000  -64.0909
    3.3000  -63.5094
    3.4000  -62.9504
    3.5000  -62.4087
    3.6000  -61.8795
    3.7000  -61.3537
    3.8000  -60.8202
    3.9000  -60.2669
    4.0000  -59.6770
    4.1000  -59.0273
    4.2000  -58.2699
    4.3000  -57.3320
    4.4000  -56.0557
    4.5000  -54.0144
    4.6000  -49.4511
    4.7000  -25.4389
    4.8000   46.5761
    4.9000   22.5153
    5.0000   -3.0167
    5.1000  -21.5420
    5.2000  -48.9458
    5.3000  -83.0944
    5.4000  -82.8482
    5.5000  -77.6734
    5.6000  -73.0882
    5.7000  -69.5231
    5.8000  -67.6628
    5.9000  -66.8892
    6.0000  -66.6376
    6.1000  -66.5780
    6.2000  -66.5136
    6.3000  -66.3684
    6.4000  -66.1243
    6.5000  -65.8040
    6.6000  -65.4325
    6.7000  -65.0342
    6.8000  -64.6257
    6.9000  -64.2183
    7.0000  -63.8223
    7.1000  -63.4376
    7.2000  -63.0708
    7.3000  -62.7167
    7.4000  -62.3794
    7.5000  -62.0528
    7.6000  -61.7357
    7.7000  -61.4274
    7.8000  -61.1258
    7.9000  -60.8252
    8.0000  -60.5196
    8.1000  -60.2065
    8.2000  -59.8855
    8.3000  -59.5435
    8.4000  -59.1709
    8.5000  -58.7581
    8.6000  -58.2814
    8.7000  -57.7084
    8.8000  -56.9859
    8.9000  -56.0000
    9.0000  -54.4764
    9.1000  -51.5116
    9.2000  -41.0403
    9.3000   39.6563
    9.4000   35.6148
    9.5000    5.0177
    9.6000  -14.2628
    9.7000  -33.9388
    9.8000  -77.4499
    9.9000  -83.5135
   10.0000  -79.2992
   10.1000  -74.4784
   10.2000  -70.4935
   10.3000  -67.9548
   10.4000  -66.8649
   10.5000  -66.4768
   10.6000  -66.4086
   10.7000  -66.4045
   10.8000  -66.3271
   10.9000  -66.1437
   11.0000  -65.8686
   11.1000  -65.5269
   11.2000  -65.1472
   11.3000  -64.7511
   11.4000  -64.3562
   11.5000  -63.9697
   11.6000  -63.6032
   11.7000  -63.2544
   11.8000  -62.9288
   11.9000  -62.6264
   12.0000  -62.3448
   12.1000  -62.0823
   12.2000  -61.8391
   12.3000  -61.6116
   12.4000  -61.3985
   12.5000  -61.1985
   12.6000  -61.0116
   12.7000  -60.8495
   12.8000  -60.6744
   12.9000  -60.5203
   13.0000  -60.3798
   13.1000  -60.2323
   13.2000  -60.1074
   13.3000  -59.9649
   13.4000  -59.8619
   13.5000  -59.7204
   13.6000  -59.6268
   13.7000  -59.4911
   13.8000  -59.3935
   13.9000  -59.2832
   14.0000  -59.1702
   14.1000  -59.0640
   14.2000  -58.9513
   14.3000  -58.8580
   14.4000  -58.7206
   14.5000  -58.6241
   14.6000  -58.4714
   14.7000  -58.3650
   14.8000  -58.1917
   14.9000  -58.0356
   15.0000  -57.8583
   15.1000  -57.6394
   15.2000  -57.3886
   15.3000  -57.0852
   15.4000  -56.6949
   15.5000  -56.1913
   15.6000  -55.4876
   15.7000  -54.4132
   15.8000  -52.4991
   15.9000  -47.7198
   16.0000  -22.3535
   16.1000   45.3273
   16.2000   17.9953
   16.3000   -6.3817
   16.4000  -25.3085
   16.5000  -59.4232
   16.6000  -81.4237
   16.7000  -80.5754
   16.8000  -75.5319
   16.9000  -71.4379
   17.0000  -68.2197
   17.1000  -66.6026
   17.2000  -66.0558
   17.3000  -65.9824
   17.4000  -66.0820
   17.5000  -66.1552
   17.6000  -66.1201
   17.7000  -65.9561
   17.8000  -65.6999
   17.9000  -65.3813
   18.0000  -65.0282
   18.1000  -64.6647
   18.2000  -64.3079
   18.3000  -63.9655
   18.4000  -63.6473
   18.5000  -63.3556
   18.6000  -63.0905
   18.7000  -62.8538
   18.8000  -62.6415
   18.9000  -62.4518
   19.0000  -62.2951
   19.1000  -62.1582
   19.2000  -62.0379
   19.3000  -61.9477
   19.4000  -61.8812
   19.5000  -61.8065
   19.6000  -61.7591
   19.7000  -61.7371
   19.8000  -61.7324
   19.9000  -61.7393
   20.0000  -61.7541
   20.1000  -61.7749
   20.2000  -61.8040
   20.3000  -61.8366
   20.4000  -61.8779
   20.5000  -61.9633
   20.6000  -62.0332
   20.7000  -62.0950
   20.8000  -62.1733
   20.9000  -62.2652
   21.0000  -62.3383
   21.1000  -62.4190
   21.2000  -62.5161
   21.3000  -62.5916
   21.4000  -62.6701
   21.5000  -62.7641
   21.6000  -62.8391
   21.7000  -62.9108
   21.8000  -62.9966
   21.9000  -63.0691
   22.0000  -63.1284
   22.1000  -63.2048
   22.2000  -63.2744
   22.3000  -63.3341
   22.4000  -63.3848
   22.5000  -63.4509
   22.6000  -63.5062
   22.7000  -63.5587
   22.8000  -63.6030
   22.9000  -63.6484
   23.0000  -63.7009
   23.1000  -63.7411
   23.2000  -63.7819
   23.3000  -63.8188
   23.4000  -63.8513
   23.5000  -63.8799
   23.6000  -63.9267
   23.7000  -63.9605
   23.8000  -63.9870
   23.9000  -64.0166
   24.0000  -64.0438
   24.1000  -64.0665
   24.2000  -64.0882
   24.3000  -64.1078
   24.4000  -64.1246
   24.5000  -64.1604
   24.6000  -64.1880
   24.7000  -64.2090
   24.8000  -64.2259
   24.9000  -64.2399
   25.0000  -64.2587
   25.1000  -64.2778
   25.2000  -64.2937
   25.3000  -64.3069
   25.4000  -64.3178
   25.5000  -64.3278
   25.6000  -64.3386
   25.7000  -64.3489
   25.8000  -64.3584
   25.9000  -64.3668
   26.0000  -64.3742
   26.1000  -64.3995
   26.2000  -64.4203
   26.3000  -64.4353
   26.4000  -64.4471
   26.5000  -64.4567
   26.6000  -64.4645
   26.7000  -64.4709
   26.8000  -64.4762
   26.9000  -64.4807
   27.0000  -64.4845
   27.1000  -64.4878
   27.2000  -64.4907
   27.3000  -64.4951
   27.4000  -64.5061
   27.5000  -64.5162
   27.6000  -64.5242
   27.7000  -64.5305
   27.8000  -64.5355
   27.9000  -64.5395
   28.0000  -64.5427
   28.1000  -64.5453
   28.2000  -64.5475
   28.3000  -64.5493
   28.4000  -64.5508
   28.5000  -64.5521
   28.6000  -64.5532
   28.7000  -64.5541
   28.8000  -64.5548
   28.9000  -64.5554
   29.0000  -64.5559
   29.1000  -64.5563
   29.2000  -64.5566
   29.3000  -64.5568
   29.4000  -64.5569
   29.5000  -64.5568
   29.6000  -64.5567
   29.7000  -64.5566
   29.8000  -64.5563
   29.9000  -64.5560
   30.0000  -64.5556
   30.1000  -64.5551
   30.2000  -64.5545
   30.3000  -64.5539
   30.4000  -64.5532
   30.5000  -64.5524
   30.6000  -64.5515
   30.7000  -64.5506
   30.8000  -64.5496
   30.9000  -64.5485
   31.0000  -64.5473
   31.1000  -64.5461
   31.2000  -64.5448
   31.3000  -64.5434
   31.4000  -64.5419
   31.5000  -64.5404
   31.6000  -64.5389
   31.7000  -64.5373
   31.8000  -64.5356
   31.9000  -64.5338
   32.0000  -64.5321
   32.1000  -64.5302
   32.2000  -64.5283
   32.3000  -64.5263
   32.4000  -64.5243
   32.5000  -64.5223
   32.6000  -64.5201
   32.7000  -64.5180
   32.8000  -64.5158
   32.9000  -64.5135
   33.0000  -64.5112
   33.1000  -64.5088
   33.2000  -64.5064
   33.3000  -64.5040
   33.4000  -64.5015
   33.5000  -64.4989
   33.6000  -64.4963
   33.7000  -64.4935
   33.8000  -64.4886
   33.9000  -64.4768
   34.0000  -64.4660
   34.1000  -64.4572
   34.2000  -64.4499
   34.3000  -64.4438
   34.4000  -64.4385
   34.5000  -64.4340
   34.6000  -64.4299
   34.7000  -64.4261
   34.8000  -64.4226
   34.9000  -64.4193
   35.0000  -64.4161
   35.1000  -64.4132
   35.2000  -64.4104
   35.3000  -64.4077
   35.4000  -64.4045
   35.5000  -64.4011
   35.6000  -64.3979
   35.7000  -64.3949
   35.8000  -64.3919
   35.9000  -64.3891
   36.0000  -64.3863
   36.1000  -64.3835
   36.2000  -64.3808
   36.3000  -64.3782
   36.4000  -64.3756
   36.5000  -64.3560
   36.6000  -64.3372
   36.7000  -64.3223
   36.8000  -64.3093
   36.9000  -64.2988
   37.0000  -64.2902
   37.1000  -64.2832
   37.2000  -64.2773
   37.3000  -64.2722
   37.4000  -64.2677
   37.5000  -64.2636
   37.6000  -64.2599
   37.7000  -64.2564
   37.8000  -64.2530
   37.9000  -64.2498
   38.0000  -64.2466
   38.1000  -64.2435
   38.2000  -64.2403
   38.3000  -64.2337
   38.4000  -64.2208
   38.5000  -64.2094
   38.6000  -64.2001
   38.7000  -64.1925
   38.8000  -64.1860
   38.9000  -64.1805
   39.0000  -64.1757
   39.1000  -64.1713
   39.2000  -64.1673
   39.3000  -64.1636
   39.4000  -64.1601
   39.5000  -64.1569
   39.6000  -64.1539
   39.7000  -64.1506
   39.8000  -64.1470
   39.9000  -64.1435
   40.0000  -64.1402
   40.1000  -64.1370
   40.2000  -64.1340
   40.3000  -64.1310
   40.4000  -64.1282
   40.5000  -64.1254
   40.6000  -64.1029
   40.7000  -64.0839
   40.8000  -64.0694
   40.9000  -64.0561
   41.0000  -64.0450
   41.1000  -64.0361
   41.2000  -64.0288
   41.3000  -64.0227
   41.4000  -64.0175
   41.5000  -64.0130
   41.6000  -64.0090
   41.7000  -64.0054
   41.8000  -64.0020
   41.9000  -63.9987
   42.0000  -63.9956
   42.1000  -63.9926
   42.2000  -63.9897
   42.3000  -63.9868
   42.4000  -63.9810
   42.5000  -63.9678
   42.6000  -63.9559
   42.7000  -63.9462
   42.8000  -63.9383
   42.9000  -63.9318
   43.0000  -63.9263
   43.1000  -63.9215
   43.2000  -63.9173
   43.3000  -63.9136
   43.4000  -63.9101
   43.5000  -63.9068
   43.6000  -63.9037
   43.7000  -63.9008
   43.8000  -63.8981
   43.9000  -63.8955
   44.0000  -63.8931
   44.1000  -63.8906
   44.2000  -63.8874
   44.3000  -63.8843
   44.4000  -63.8814
   44.5000  -63.8786
   44.6000  -63.8759
   44.7000  -63.8578
   44.8000  -63.8359
   44.9000  -63.8213
   45.0000  -63.8097
   45.1000  -63.7980
   45.2000  -63.7879
   45.3000  -63.7796
   45.4000  -63.7730
   45.5000  -63.7675
   45.6000  -63.7628
   45.7000  -63.7588
   45.8000  -63.7553
   45.9000  -63.7521
   46.0000  -63.7492
   46.1000  -63.7465
   46.2000  -63.7439
   46.3000  -63.7414
   46.4000  -63.7389
   46.5000  -63.7365
   46.6000  -63.7341
   46.7000  -63.7317
   46.8000  -63.7259
   46.9000  -63.7128
   47.0000  -63.7011
   47.1000  -63.6916
   47.2000  -63.6838
   47.3000  -63.6772
   47.4000  -63.6717
   47.5000  -63.6670
   47.6000  -63.6630
   47.7000  -63.6594
   47.8000  -63.6562
   47.9000  -63.6532
   48.0000  -63.6505
   48.1000  -63.6479
   48.2000  -63.6454
   48.3000  -63.6430
   48.4000  -63.6407
   48.5000  -63.6383
   48.6000  -63.6361
   48.7000  -63.6340
   48.8000  -63.6321
   48.9000  -63.6303
   49.0000  -63.6286
   49.1000  -63.6269
   49.2000  -63.6250
   49.3000  -63.5982
   49.4000  -63.5783
   49.5000  -63.5644
   49.6000  -63.5540
   49.7000  -63.5456
   49.8000  -63.5362
   49.9000  -63.5276

Loading data, please wait...