Computer models of corticospinal neurons replicate in vitro dynamics (Neymotin et al. 2017)

 Download zip file 
Help downloading and running models
Accession:195615
"Corticospinal neurons (SPI), thick-tufted pyramidal neurons in motor cortex layer 5B that project caudally via the medullary pyramids, display distinct class-specific electrophysiological properties in vitro: strong sag with hyperpolarization, lack of adaptation, and a nearly linear frequency-current (FI) relationship. We used our electrophysiological data to produce a pair of large archives of SPI neuron computer models in two model classes: 1. Detailed models with full reconstruction; 2. Simplified models with 6 compartments. We used a PRAXIS and an evolutionary multiobjective optimization (EMO) in sequence to determine ion channel conductances. ..."
Reference:
1 . Neymotin SA, Suter BA, Dura-Bernal S, Shepherd GM, Migliore M, Lytton WW (2017) Optimizing computer models of corticospinal neurons to replicate in vitro dynamics. J Neurophysiol 117:148-162 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Neuron or other electrically excitable cell;
Brain Region(s)/Organism: Neocortex;
Cell Type(s): Neocortex M1 L5B pyramidal pyramidal tract GLU cell; Neocortex primary motor area pyramidal layer 5 corticospinal cell;
Channel(s): I A; I h; I_KD; I K,Ca; I L high threshold; I Na,t; I N; Ca pump; Kir;
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: NEURON; Python;
Model Concept(s): Parameter Fitting; Activity Patterns; Active Dendrites; Detailed Neuronal Models; Simplified Models;
Implementer(s): Suter, Benjamin ; Neymotin, Sam [samn at neurosim.downstate.edu]; Dura-Bernal, Salvador [salvadordura at gmail.com]; Forzano, Ernie ;
Search NeuronDB for information about:  Neocortex M1 L5B pyramidal pyramidal tract GLU cell; I Na,t; I L high threshold; I N; I A; I h; I K,Ca; I_KD; Ca pump; Kir;
/
spidemo
data
readme.html
cadad.mod
cal2.mod
can_mig.mod
h_kole.mod
kap_BS.mod
kBK.mod
kdmc_BS.mod
kdr_BS.mod
misc.mod *
nax_BS.mod
savedist.mod
vecst.mod *
archfig.py
axonMorph.py
BS0284.ASC
BS0409.ASC
conf.py
Fig6.py
figure_1.png
misc.h
morph.py
mosinit.py
PTcell.BS0284.cfg *
PTcell.BS0409.cfg
PTcell.cfg *
sim.py
SPI6.cfg
SPI6.py
utils.py
                            
axonPts = [[1, 215.897, -818.461, -101.683],
[215.53, -827.75, -89.78, 1.86],
[215.37, -829.59, -89.78, 1.76],
[215.29, -832.57, -89.78, 1.76],
[214.68, -834.73, -88.82, 1.54],
[213.48, -836.17, -88.82, 1.44],
[213.02, -837.74, -88.82, 1.33],
[213.08, -839.33, -88.82, 1.25],
[213.24, -841.07, -90.73, 1.17],
[213.32, -844.07, -90.73, 1.17],
[213.32, -845.99, -90.73, 1.14],
[213.45, -847.54, -90.73, 1.09],
[213.64, -849.43, -90.73, 1.09],
[213.64, -851.21, -90.73, 1.09],
[213.5, -853.82, -91.69, 1.04],
[213.13, -856.99, -91.69, 1.07],
[212.94, -858.66, -91.69, 1.04],
[212.57, -861.35, -91.69, 0.93],
[212.49, -864.71, -92.64, 0.93],
[212.09, -873.33, -93.6, 0.96],
[211.61, -876.64, -93.6, 0.96],
[211.53, -877.81, -96.46, 1.25],
[211.11, -878.98, -96.46, 1.04],
[210.68, -880.76, -96.46, 1.04],
[210.44, -882.31, -96.46, 0.91],
[210.42, -883.45, -96.46, 0.75],
[209.59, -885.96, -97.42, 0.8],
[208.68, -889.31, -97.42, 0.8],
[207.73, -891.71, -96.46, 0.85],
[207.3, -892.88, -96.46, 0.91],
[206.87, -894.87, -97.42, 0.88],
[206.47, -897.19, -97.42, 0.93],
[206.18, -898.34, -97.42, 1.04],
[205.73, -899.83, -97.42, 0.99],
[204.74, -901.5, -98.37, 0.88],
[203.92, -903.9, -100.28, 0.88],
[203.79, -905.13, -99.33, 1.07],
[203.55, -906.54, -99.33, 0.91],
[202.83, -909.44, -99.33, 0.85],
[202.69, -912.29, -99.33, 0.85],
[202.56, -915.14, -99.33, 0.85],
[202.56, -916.92, -101.24, 0.85],
[202.48, -918.92, -101.24, 0.85],
[202.69, -920.38, -101.24, 0.93],
[202.24, -922.01, -102.19, 1.04],
[202.06, -923.55, -103.15, 0.8],
[201.9, -926.56, -103.15, 1.12],
[200.86, -928.4, -104.1, 1.22],
[200.67, -929.78, -104.1, 1.12],
[200.03, -932.31, -104.1, 0.91],
[198.59, -936.12, -105.06, 0.85],
[197.16, -939.6, -106.01, 0.85],
[196.57, -942.64, -105.06, 0.85],
[196.46, -944.64, -106.01, 0.83],
[197.05, -946.53, -105.06, 0.83],
[196.73, -949, -105.06, 0.83],
[196.94, -952.28, -106.01, 0.83],
[196.12, -954.49, -106.01, 0.83],
[195.69, -956.78, -106.01, 0.83],
[195.21, -959.28, -106.01, 0.83],
[194.33, -961.22, -106.01, 0.83],
[193.64, -964.87, -105.06, 0.83],
[193.32, -966.47, -105.06, 1.25],
[193.19, -968.01, -104.1, 1.17],
[193.14, -969.96, -105.06, 0.75],
[193.43, -971.47, -105.06, 0.75],
[193.24, -973.95, -103.15, 0.75],
[192.95, -975.28, -103.15, 0.85],
[193.16, -976.85, -103.15, 0.93],
[193.46, -979.83, -103.15, 0.88],
[193.38, -981.91, -101.24, 0.88],
[193.46, -984.81, -101.24, 0.88],
[193.32, -987.21, -101.24, 0.88],
[193.16, -989.77, -103.15, 0.88],
[193.06, -990.88, -103.15, 1.01],
[192.87, -992.19, -103.15, 1.01],
[192.6, -993.41, -102.19, 0.88],
[192.36, -994.8, -102.19, 0.88],
[191.56, -996.66, -103.15, 0.96],
[191.43, -997.65, -103.15, 1.12],
[190.9, -998.5, -103.15, 0.99],
[190.5, -999.56, -105.06, 0.83],
[189.83, -1000.84, -104.1, 0.83],
[189.12, -1002.71, -105.06, 0.83],
[188.96, -1004.52, -105.06, 0.83],
[189.28, -1005.87, -105.06, 1.07],
[189.43, -1007.68, -105.06, 1.07],
[189.73, -1010.08, -105.06, 0.96],
[189.94, -1013.54, -105.06, 0.96],
[189.97, -1015.41, -105.06, 0.85],
[189.78, -1017.8, -105.06, 0.85],
[189.73, -1020.3, -105.06, 0.85],
[189.46, -1024.67, -105.06, 0.85],
[189.67, -1029.28, -104.1, 0.85],
[189.65, -1032.37, -102.19, 0.96],
[189.54, -1035.61, -102.19, 1.01],
[189.7, -1036.97, -102.19, 1.22],
[189.73, -1038.25, -101.24, 1.17],
[189.91, -1039.05, -101.24, 0.93],
[189.94, -1041.15, -101.24, 0.93],
[190.82, -1043.5, -101.24, 0.93],
[191.56, -1049.38, -101.24, 0.93],
[191.22, -1052.71, -101.24, 0.93],
[191.09, -1055.32, -101.24, 0.93],
[190.5, -1060, -102.19, 0.93],
[189.91, -1061.84, -103.15, 1.17],
[189.67, -1063.2, -103.15, 1.09],
[189.65, -1065.22, -103.15, 0.93],
[189.94, -1067.83, -105.06, 0.93],
[191.22, -1072.68, -106.97, 0.93],
[191.3, -1075.55, -106.97, 0.93],
[191.51, -1077.74, -108.88, 1.49],
[191.56, -1078.83, -108.88, 1.38],
[191.43, -1080, -108.88, 1.01],
[190.98, -1084.6, -108.88, 0.99],
[190.93, -1086.95, -108.88, 0.83],
[190.63, -1088.73, -108.88, 1.09],
[190.39, -1090.73, -110.79, 0.96],
[190.26, -1093.07, -110.79, 0.96],
[190.31, -1094.64, -109.83, 0.88],
[190.74, -1095.97, -109.83, 0.96],
[190.79, -1098.05, -109.83, 1.09],
[191.11, -1099.51, -108.88, 1.01],
[191.56, -1100.71, -108.88, 0.91],
[191.35, -1103.06, -108.88, 0.91],
[192.18, -1106.12, -108.88, 0.91],
[192.18, -1109.39, -107.92, 0.99],
[192.44, -1111.1, -107.92, 0.83],
[192.44, -1113.84, -107.92, 0.91],
[191.86, -1116.79, -107.92, 0.91],
[191.56, -1119, -107.92, 0.91],
[191.41, -1121, -107.92, 0.91],
[190.63, -1122.78, -107.92, 0.91],
[189.65, -1126.25, -107.92, 0.91],
[189.09, -1128.03, -107.92, 0.91],
[188.58, -1130.64, -107.92, 0.91],
[188.24, -1132.42, -107.92, 0.91],
[188.24, -1134.42, -107.92, 0.91],
[187.76, -1136.44, -106.01, 0.99],
[186.99, -1137.8, -104.1, 0.99],
[186.61, -1139.69, -104.1, 0.99],
[186.24, -1140.89, -104.1, 0.99],
[185.57, -1141.9, -104.1, 0.99],
[185.49, -1143.5, -104.1, 0.99],
[182.14, -1149.01, -103.15, 0.99],
[181.39, -1150.18, -103.15, 0.99],
[180.44, -1151.81, -103.15, 0.93],
[179.1, -1153.4, -103.15, 0.88],
[178.47, -1154.92, -103.15, 0.88],
[177.72, -1156.65, -103.15, 0.88],
[177.75, -1158.94, -103.15, 0.88],
[178.2, -1160.65, -103.15, 0.88],
[178.63, -1161.76, -103.15, 0.88],
[178.52, -1162.93, -103.15, 1.12],
[178.44, -1163.92, -103.15, 0.91],
[178.44, -1166.66, -101.24, 0.83],
[178.41, -1169.56, -101.24, 0.83],
[178.28, -1172.55, -101.24, 0.83],
[177.56, -1173.85, -101.24, 0.83],
[177.27, -1174.86, -101.24, 0.83],
[177.08, -1177.77, -101.24, 0.83],
[176.55, -1179.63, -101.24, 0.83],
[174.21, -1184.82, -102.19, 0.83],
[173.67, -1187.62, -102.19, 0.83],
[172.79, -1190.6, -99.33, 0.83],
[172.21, -1192.46, -99.33, 0.83],
[171.44, -1195.6, -99.33, 0.83],
[171.09, -1198.88, -99.33, 0.83],
[169.15, -1209.93, -100.28, 0.83],
[167.87, -1213.42, -100.28, 0.83], 
[166.43, -1219.59, -103.15, 0.83],
[165.87, -1223.24, -104.1, 0.83],
[165.15, -1226.14, -104.1, 0.83],
[164.41, -1228.83, -104.1, 0.83],
[163.66, -1231.52, -104.1, 0.83],
[163.85, -1233.44, -104.1, 0.83],
[165.07, -1235.04, -104.1, 0.83],
[166.94, -1238.84, -100.28, 0.83],
[168.21, -1240.15, -100.28, 0.83],
[168.75, -1243.69, -94.55, 0.83],
[170.56, -1248.75, -95.51, 0.83],
#shape3d_2() 
[170.11, -1252.98, -88.82, 0.83],
[171.14, -1256.36, -80.23, 0.83],
[171.54, -1258.04, -76.41, 1.89],
[172.24, -1259.9, -72.59, 1.14],
[173.43, -1260.99, -67.81, 1.14],
[174.71, -1261.95, -66.86, 1.28],
[175.91, -1261.95, -63.99, 1.14],
[177.03, -1263.1, -63.04, 1.09],
[179.4, -1263.66, -59.21, 0.91],
[180.86, -1263.79, -59.21, 0.91],
[184.32, -1264.7, -55.39, 0.91],
[188, -1265.49, -51.57, 0.91],
[189.28, -1266.56, -51.57, 0.88],
[192.55, -1266.85, -44.89, 0.88],
[192.92, -1267.68, -42.02, 1.44],
[193.16, -1269.81, -41.07, 2.61],
[193.08, -1270.69, -36.29, 5.54],
[193.03, -1270.74, -24.83, 4.1],
[192.98, -1270.71, -20.06, 2.29]]

Loading data, please wait...