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

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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 [Samuel.Neymotin at nki.rfmh.org]; 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;
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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
                            
[fixed]
morph.Vrest = -90.220509483 -90.220509483 -90.220509483 True
h.v_init = -70.0432010302 -70.0432010302 -70.0432010302 True
morph.kdmc_gbar = 0.000916263431341 0.000916263431341 0.000916263431341 True
morph.cap = 0.700445928608 0.700445928608 0.7004459286080 True
morph.spinecapfactor = 1.48057846279 1.48057846279 1.48057846279 True
morph.rall = 137.494564931 137.494564931 137.494564931 TruePTcell
morph.rm = 38457.4393085 38457.4393085 38457.4393085 True
morph.h_gbar = 6.6129403774e-05 6.6129403774e-05 6.6129403774e-05 True
[params]
# each param is assignment string (comma-separated variable names), min, max, original, bounded
morph.kdmc_gbar = 0.000725698962891 0.00114999553934 0.000916263431341 False 
morph.kBK_gpeak = 4.63449910469e-05 7.41871806763e-05 6e-05 False 
morph.cal_gcalbar = 3.9402995e-06 6.06015e-06 5e-06 False 
morph.can_gcanbar = 3.9601e-06 6.27546347488e-06 5e-06 False 
morph.kap_gbar = 0.04 0.0689923565988 0.05 False 
morph.kdr_gbar = 0.00494043336051 0.0086984469343 0.007 False 
morph.nax_gbar = 0.0116673995259 0.024 0.02 False 
morph.kBK_caVhminShift = 44.7725194146 54.1455684051 50.0 False 
morph.cadad_taur = 1.0 100.0 1.0 False 
morph.cadad_depth = 0.0864623739218 0.113341526033 0.1 False 
[run]
#cellimport is the py file that has code for creating a cell
cellimport = morph
#cellfunc is function that returns a cell
cellfunc = Cell
# this cellfuncargs argument specifies morphology
cellfuncargs = 'BS0284.ASC'
#postassign called after params assigned to the global variables to set in cell
postassign = cell.reconfig()
#locations to record voltage from. first location recorded from is used in voltage optimization
recordV = cell.soma[0](0.5)
#recordSpike is location where spikes are recorded from
#morph.py syntax
recordSpike = cell.soma[0](0.5)
usecvode = True
tstop = 3000.0
baset = 1000.0
stimdel = 500.0
stimdur = 1000.0
[data]
#experimental voltage traces - in entirety
evolts = data/BS0284_tracedata_10KHz.npy
# stimulus amplitudes
lstimamp = data/BS0284_lstimamp.npy
# sampling rate
sampr = 10000

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