Dendritic Impedance in Neocortical L5 PT neurons (Kelley et al. 2021)

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Accession:266851
We simulated chirp current stimulation in the apical dendrites of 5 biophysically-detailed multi-compartment models of neocortical pyramidal tract neurons and found that a combination of HCN channels and TASK-like channels produced the best fit to experimental measurements of dendritic impedance. We then explored how HCN and TASK-like channels can shape the dendritic impedance as well as the voltage response to synaptic currents.
Reference:
1 . Kelley C, Dura-Bernal S, Neymotin SA, Antic SD, Carnevale NT, Migliore M, Lytton WW (2021) Effects of Ih and TASK-like shunting current on dendritic impedance in layer 5 pyramidal-tract neurons. J Neurophysiology 125:1501-1516 [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:
Cell Type(s): Neocortex L5/6 pyramidal GLU cell; Neocortex M1 L5B pyramidal pyramidal tract GLU cell;
Channel(s): I h; TASK channel;
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: NEURON; Python; NetPyNE;
Model Concept(s): Impedance;
Implementer(s): Kelley, Craig;
Search NeuronDB for information about:  Neocortex L5/6 pyramidal GLU cell; Neocortex M1 L5B pyramidal pyramidal tract GLU cell; I h; TASK channel;
# load in packages
import sys
import os

# Handle command line arguments
## load cell

from getCells import HayCell
morph_file = sys.argv[-1]
pt_cell = HayCell(morphology_file=morph_file)

## create output directories
out_path = '/home/craig_kelley_downstate_edu/L5PYR_Resonance/Hay/' + morph_file.split('/')[-1].split('.')[0] + '/'
try:
    os.mkdir(out_path)
except:
    pass
try:
    os.mkdir(out_path + 'impedance_measures')
except:
    pass
try:
    os.mkdir(out_path + 'gcp_batch_files')
except:
    pass
try:
    os.mkdir(out_path + 'logs')
except:
    pass
try:
    os.mkdir(out_path + 'errs')
except:
    pass

# main code for generating sbatch files and bash file to submit them
## create bash file
sh_file = open(out_path+'gcp_batch_files/chirp-batch.sh','w')
sh_file.write('#!/bin/bash\n')
## loop for sbatch files
### basal sections
for i, sec in enumerate(pt_cell.basal):
    file_name = str(sec)+'-batch.sbatch'
    file = open(out_path+'gcp_batch_files/'+file_name,'w')
    
    file.write('#!/bin/bash\n')
    job_name = '#SBATCH --job-name=' + str(sec)+ '\n'
    file.write(job_name)
    file.write('#SBATCH -A default\n')
    file.write('#SBATCH -t 12:00:00\n')
    file.write('#SBATCH --nodes=1\n')
    file.write('#SBATCH --ntasks-per-node=1\n')
    log_line = '#SBATCH -o ' + out_path + 'logs/' + str(sec) + '.log\n'
    file.write(log_line)
    err_line = '#SBATCH -e ' + out_path + 'errs/' + str(sec) + '.err\n'
    file.write(err_line)
    if i == 0:
        file.write('#SBATCH --mail-user=craig.kelley@downstate.edu\n')
        file.write('#SBATCH --mail-type=end\n')
    file.write('source /home/craig_kelley_downstate_edu/.bashrc\n')
    file.write('cd /home/craig_kelley_downstate_edu/L5PYR_Resonance/\n')
    run_line = 'ipython chirpMorph.py ' + sys.argv[-1] + ' ' + str(sec) + '\n'
    file.write(run_line)
    file.close()
    
    #### write to bash file calling sbash
    sh_line = 'sbatch ' + file_name + '\n'
    sh_file.write(sh_line)
### apical sections
for i, sec in enumerate(pt_cell.apical):
    file_name = str(sec)+'-batch.sbatch'
    file = open(out_path+'gcp_batch_files/'+file_name,'w')
    
    file.write('#!/bin/bash\n')
    job_name = '#SBATCH --job-name=' + str(sec)+ '\n'
    file.write(job_name)
    file.write('#SBATCH -A default\n')
    file.write('#SBATCH -t 12:00:00\n')
    file.write('#SBATCH --nodes=1\n')
    file.write('#SBATCH --ntasks-per-node=1\n')
    log_line = '#SBATCH -o ' + out_path + 'logs/' + str(sec) + '.log\n'
    file.write(log_line)
    err_line = '#SBATCH -e ' + out_path + 'errs/' + str(sec) + '.err\n'
    file.write(err_line)
    if i == 0:
        file.write('#SBATCH --mail-user=craig.kelley@downstate.edu\n')
        file.write('#SBATCH --mail-type=end\n')
    file.write('source /home/craig_kelley_downstate_edu/.bashrc\n')
    file.write('cd /home/craig_kelley_downstate_edu/L5PYR_Resonance/\n')
    run_line = 'ipython chirpMorph.py ' + sys.argv[-1] + ' ' + str(sec) + '\n'
    file.write(run_line)
    file.close()
    
    #### write to bash file calling sbash
    sh_line = 'sbatch ' + file_name + '\n'
    sh_file.write(sh_line)

sh_file.close()

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