Mitral cell activity gating by respiration and inhibition in an olfactory bulb NN (Short et al 2016)

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Accession:183300
To explore interactions between respiration, inhibition, and olfaction, experiments using light to active channel rhodopsin in sensory neurons expressing Olfactory Marker Protein were performed in mice and modeled in silico. This archive contains NEURON models that were run on parallel computers to explore the interactions between varying strengths of respiratory activity and olfactory sensory neuron input and the roles of periglomerular, granule, and external tufted cells in shaping mitral cell responses.
Reference:
1 . Short SM, Morse TM, McTavish TS, Shepherd GM, Verhagen JV (2016) Respiration gates sensory input responses in the Mitral Cell layer of the Olfactory Bulb PLOS ONE 11(12):e0168356 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network; Neuron or other electrically excitable cell;
Brain Region(s)/Organism: Olfactory bulb;
Cell Type(s): Olfactory bulb main mitral cell; Olfactory bulb main interneuron periglomerular cell; Olfactory bulb main interneuron granule MC cell; Olfactory bulb main tufted cell external;
Channel(s):
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: NEURON;
Model Concept(s): Activity Patterns; Sensory processing; Sensory coding; Bursting; Oscillations; Olfaction;
Implementer(s): Morse, Tom [Tom.Morse at Yale.edu];
Search NeuronDB for information about:  Olfactory bulb main mitral cell; Olfactory bulb main interneuron periglomerular cell; Olfactory bulb main interneuron granule MC cell;
Files displayed below are from the implementation
/
ShortEtAl2016
early_theta_version
event_generator
import
py
run_0
run_1
run_10
run_11
run_12
run_13
run_14
run_15
run_16
run_17
run_2
run_3
run_4
run_5
run_6
run_7
run_8
run_9
run_test
saved_sim_makers
spike_output
stimulation
synaptic_activity
tdt2mat_data
tmp
VecStim
readme.html
readme.louise
readme.NSG
readme.specialcase.txt
ampanmda.mod *
cadecay.mod *
cadecay2.mod *
Caint.mod *
Can.mod *
CaPN.mod *
CaT.mod *
fi.mod
GradeAMPA.mod *
GradeGABA.mod *
GradNMDA.mod *
hpg.mod *
Ih.mod *
kamt.mod *
KCa.mod *
kdrmt.mod *
kfasttab.mod *
kM.mod *
KS.mod *
kslowtab.mod *
LCa.mod *
nafast.mod *
NaP.mod *
naxn.mod
Nicotin.mod *
nmdanet.mod *
OdorInput.mod *
thetastim.mod *
ThreshDetect.mod *
vecstim.mod *
batch_run_first_NSG.py
batch_runs.py
batch_runs.py20150708
batch_runs.py20150808gc_error
batch_runs_first_NSG.py
build_net.hoc
build_net_Shep.hoc
build_net_Shep_NSG.hoc
build_net_Shep_NSG20160825.hoc
build_net_SMS.hoc
build_net_theta.hoc
build_net20150312.hoc
build_pg_net.hoc
cell_properties_for_ET_from_standalone.txt
cells_volt_graphs.ses
cells_volt_graphs_pg.ses
create_arrays.py
documentation.txt
et.hoc
et_rig.ses
et_rig2.ses
Et_start.zip
granule.hoc *
graph_fncs.hoc
graph_fncs_pg.hoc
gui_stim.hoc
how_to_run_pre_init_on_mac.txt
inhib_study.eps
inhib_study.ps
init.hoc
init.py
make_lookup_table.sh
makelib.err
makelib.out
mct_cells.hoc
mitral.hoc
mosinit.hoc
nrnivmodl.out
num_of_columns.hoc
PG_def.hoc
pre_init.py
pre_init_first_NSG.py
pre_init_no_changes_in_weights.py
roberts_python_help.txt
run_on_serial.hoc
runcntrl.ses
sample_gc1_v_graph.ses
sample_mitral_pg_space_plots.ses
screenshot.png
screenshot0.png
tdt2mat_data.hoc
temporary_file.tmp
test_matplotlib.hoc
                            
#!/usr/bin/python

"""batch_runs.py will create multiple folders for simple_circuit model
runs with names like run_X where X goes from 1 to the number of jobs.

phase 1 the run_X folders are created and the programs and folders by
recursively copying simple_circuit into them.

phase 2 the num_of_columns.hoc and parameters.hoc files are created in
each run_x folder so that they are all ready to run with their
different assigned values.  A parameters[] list prepares the contents of
each of these files before they are written.

For now the following phases are external to this program:
initiated with
qsub run.pbs
and 
matlab
batch_polar_plots
or
batch_bi_polar_plots

phase 3 the mod files are compiled in each run_x folder and the jobs
are started by running build_net_Shep.hoc in each run_X folder These
jobs automatically save the tank and spike time data used to create
subsequent graphs

phase 4 the matlab tanks are created

phase 5 the tanks are analyzed to create and save matlab polar plot
figures

phase 6 the raster plots of spike activity are created and
saved.
"""


#************************************************************************
print "phase 1"
#************************************************************************
# In phase 1 the run_X folders are created and the programs and folders by recursively copying simple_circuit
# into them.

# the task of create arrays is to create "both" which has both the breathing peak rate
# and the stimulus (light) peak rate in list of (B, S) tuples.  Once this is created
# we can determine the number of jobs by multiplying the length of both by three for
# three different types of network models
execfile("create_arrays.py")
jobs_per_nn=len(both)
num_of_columns_tested=len(add_columns) # add_columns supplied by create_arrays.py
num_of_nn_types=4 # pg, gc, full, noinhib
num_of_jobs=jobs_per_nn*num_of_nn_types*num_of_columns_tested
print "num_of_jobs: "+ str(num_of_jobs)
# absolute_path="/home/tmm46/projects/VerhagenLab/20150611/batch_runs/"
#absolute_path="/home/tmm46/projects/VerhagenLab/20150622/batch_runs/"
#absolute_path="/home/tmm46/projects/VerhagenLab/20150708/batch_runs/"
absolute_path="/home/tmm46/projects/VerhagenLab/20150720/cols_100_300/batch_runs/"

# http://stackoverflow.com/questions/600268/mkdir-p-functionality-in-python

import os, errno

def mkdir_p(path):
    try:
        os.makedirs(path)
    except OSError as exc: # Python >2.5
        if exc.errno == errno.EEXIST and os.path.isdir(path):
            print "the folder ",path," seems to already exist - it will be cleared ********"
            pass
        else: raise

for folder_num in range(num_of_jobs):
  new_folder="run_"+str(folder_num)
  mkdir_p(new_folder)

# now make sure the folders are empty
# http://stackoverflow.com/questions/185936/delete-folder-contents-in-python

import os, shutil
for folder_num in range(num_of_jobs):
  # folder = '/path/to/folder'
  folder="run_"+str(folder_num)
  for the_file in os.listdir(folder):
    file_path = os.path.join(folder, the_file)
    try:
        if os.path.isfile(file_path):
            os.unlink(file_path)
        elif os.path.isdir(file_path): shutil.rmtree(file_path)
    except Exception, e:
        print e

# now copy over the simple_circuit folder
# http://stackoverflow.com/questions/12683834/how-to-copy-directory-recursively-in-python-and-overwrite-all
for folder_num in range(num_of_jobs):
  cmd_string="cp -rf ../simple_circuits/* run_"+str(folder_num)
  os.system(cmd_string)

#************************************************************************
print "phase 2"
#************************************************************************
# In phase 2 the num_of_columns.hoc and parameters.hoc files are created in each run_x folder so that they
# are all ready to run with their different assigned values.

# num_of_columns.hoc setting
# set the total_num_of_columns_master to the value desired to be used for each of all the simulations

# use below if for simple case of two columns total - otherwise rely on columns supplied from create_arrays.py
#total_num_of_columns_master=2
#num_of_additional_columns = total_num_of_columns_master - 1

# note that since the hoc code uses num_of_columns to set the number of columns in addition to the "recorded"
# mitral cell column, the setting of num_of_columns should be to num_of_additional_columns

# instead of using the below code assign num_of_columns[] list to write the 
# num_of_columns.hoc files when the parameters.hoc files are being written,
# that way, it can be coordinated with the network types

#for folder_num in range(num_of_jobs):
#  folder="run_"+str(folder_num)
#  fid=open(folder+"/num_of_columns.hoc","w")
#  fid.write("n = "+str(num_of_additional_columns)+" // n easier to type than num_of_cols\n")
#  fid.close()

# parameters.hoc settings
# includes both setting parameters and running functions that copy parameters to all the columns
# functions:
#   adjust_netcons_from_top() copies all netcons from [X][0] to [X][Y>0]
#   toggle_gc_connection() toggles all columns gc netcons 0/gc_on
#   toggle_pg_connection() toggles all columns pg netcons 0/pg_on
#   where gc_on and pg_on have a default value of 1
#
# parameter dictionary parameters holds all values for simulations
parameters={}
columns={}
# helper lists
# B for breathing rates
# 0 to 620 in increments of 20

num_of_sims = num_of_jobs
num_of_procs = 14 * 4 # 14 nodes at 4 processoers per node
serial_num_of_sims=int(num_of_sims / num_of_procs + 1) # ceiling of division because some procs will 
# be running 1 extra unless exactly an integer result of division
one_sim_time =  (2*60+35) / 4. # it took 2 hours 35 mins to previously run 4 serial jobs
time_to_run = serial_num_of_sims * one_sim_time
# where the 4 serial jobs came from 192 jobs/56 processors = 3.4 jobs/proc
print "this job is predicted to take "+repr(time_to_run)+" mins = "+repr(time_to_run/60)+" hrs"
print "on "+str(num_of_procs)+" processors"

# let 0 through 63 be pg mediated inhibition with nc[15][]=0 and
# 64 through 127 be  pg mediated inhibition with nc[15][]=1 and
# 128 through 191 be gc mediated inhibition
# with jobs_per_nn becomes
# let 0 through jobs_per_nn-1 be pg mediated inhibition with nc[15][]=0 and
# jobs_per_nn through 2*jobs_per_nn-1 be  pg mediated inhibition with nc[15][]=1 and
# 2*jobs_per_nn through 3*jobs_per_nn-1 be gc mediated inhibition


#for folder_num in range(jobs_per_nn):  # pg mediated inhibition with nc[15][]=0
#  parameters[folder_num]="""
#breathing_period=400
#light_period=398 // 300 is a short run, 398 regular
#breath_peak_rate = %d
#light1_peak_rate = %d
#light2_peak_rate = 0
#breath_half_width=20
#light_half_width=20
#for i=0, n-1 {
#  nc[15][i].weight = 0 // turn off breathing input to pg cells
#}
#toggle_gc_connection() // turns off all gc cell connections
#objref pwm
#pwm=new PWManager()
#pwm.hide(3) // close voltage window for faster run
#do_everything()
#quit()
#""" % both[folder_num]

for folder_num in range(num_of_columns_tested): #, 2*jobs_per_nn):  # pg mediated inhibition with nc[15][]=1
  parameters[folder_num]="""
breathing_period=400
light_period=399 // 300 is a short run, 398 regular
breath_peak_rate = %d
light1_peak_rate = %d
light2_peak_rate = 0
breath_half_width=30
light_half_width=30
for i=0, n-1 {
  nc[15][i].weight = 1 // turn off breathing input to pg cells
}
toggle_gc_connection() // turns off all gc cell connections
objref pwm
pwm=new PWManager()
pwm.hide(3) // close voltage window for faster run
do_everything()
quit()
// net_type pg_net
""" % both[folder_num%jobs_per_nn]
  columns[folder_num]="""
n = %s // n easier to type than num_of_cols
""" % tuple(add_columns)[folder_num % num_of_columns_tested]

for folder_num in range( num_of_columns_tested, 2* num_of_columns_tested): # gc mediated
  parameters[folder_num]="""
breathing_period=400
light_period=399 // 300 is a short run, 398 regular
breath_peak_rate = %d
light1_peak_rate = %d
light2_peak_rate = 0
breath_half_width=30
light_half_width=30
// for some reason toggle_pg_connection() was causing an error however
// the below worked
    for i=0, n-1 {
      nc[14][i].weight = 0
      nc[15][i].weight = 0
      nc[16][i].weight = 0
      nc[17][i].weight = 0
      nc[18][i].weight = 0
      nc[19][i].weight = 0
      nc[20][i].weight = 0
      nc[21][i].weight = 0
      nc[22][i].weight = 0
      nc[23][i].weight = 0
      nc[24][i].weight = 0
      nc[25][i].weight = 0
    // xstatebutton automatically sets pg_connection_state=0
    }
// toggle_pg_connection() // turns off all pg cell connections
objref pwm
pwm=new PWManager()
pwm.hide(3) // close voltage window for faster run
do_everything()
quit()
// net_type gc_net
""" % both[folder_num%jobs_per_nn]
  columns[folder_num]="""
n = %s // n easier to type than num_of_cols
""" % tuple(add_columns)[folder_num % num_of_columns_tested]

for folder_num in range(2* num_of_columns_tested, 3* num_of_columns_tested): # gc mediated
  parameters[folder_num]="""
breathing_period=400
light_period=399 // 300 is a short run, 398 regular
breath_peak_rate = %d
light1_peak_rate = %d
light2_peak_rate = 0
breath_half_width=30
light_half_width=30
// for some reason toggle_pg_connection() was causing an error however
// the below worked
    for i=0, n-1 {
      nc[14][i].weight = 0
      nc[15][i].weight = 0
      nc[16][i].weight = 0
      nc[17][i].weight = 0
      nc[18][i].weight = 0
      nc[19][i].weight = 0
      nc[20][i].weight = 0
      nc[21][i].weight = 0
      nc[22][i].weight = 0
      nc[23][i].weight = 0
      nc[24][i].weight = 0
      nc[25][i].weight = 0
    // xstatebutton automatically sets pg_connection_state=0
    }
// toggle_pg_connection() // turns off all pg cell connections
toggle_gc_connection() // turns off all gc cell connections
objref pwm
pwm=new PWManager()
pwm.hide(3) // close voltage window for faster run
do_everything()
quit()
// net_type noinhib_net
""" % both[folder_num%jobs_per_nn]
  columns[folder_num]="""
n = %s // n easier to type than num_of_cols
""" % tuple(add_columns)[folder_num % num_of_columns_tested]

for folder_num in range(3* num_of_columns_tested, 4* num_of_columns_tested): # gc mediated
  parameters[folder_num]="""
breathing_period=400
light_period=399 // 300 is a short run, 398 regular
breath_peak_rate = %d
light1_peak_rate = %d
light2_peak_rate = 0
breath_half_width=30
light_half_width=30
objref pwm
pwm=new PWManager()
pwm.hide(3) // close voltage window for faster run
do_everything()
quit()
// net_type full_net
""" % both[folder_num%jobs_per_nn]
  columns[folder_num]="""
n = %s // n easier to type than num_of_cols
""" % tuple(add_columns)[folder_num % num_of_columns_tested]

for folder_num in range(num_of_jobs):
  folder="run_"+str(folder_num)
  fid=open(folder+"/parameters.hoc","w")
  fid.write(parameters[folder_num])
  fid.close()
  fid=open(folder+"/num_of_columns.hoc","w")
  fid.write(columns[folder_num])
  fid.close()

print"*** the following phases are external to this program:"
#************************************************************************
print "phase 3"
#************************************************************************
# In phase 3 the mod files are compiled in each run_x folder and the
# jobs are started by running build_net_Shep.hoc in each run_X folder
# These jobs automatically save the tank and spike time data used to
# create subsequent graphs
# 
# use simpleque to create a list of nrnivmodl tasks and run them
fid=open(absolute_path+"tasklist","w")
for folder_num in range(num_of_jobs):
  folder=absolute_path+"run_"+str(folder_num)
  fid.write("cd %s; source /home/tmm46/.bash_profile; /home/tmm46/bin/neuron/nrn/x86_64/bin/nrnivmodl; /home/tmm46/bin/neuron/nrn/x86_64/bin/nrngui %s/build_net_Shep.hoc\n" % (folder,folder))
fid.close()

print 'start job by running "qsub run.pbs"'
# 
# Following http://maguro.cs.yale.edu/mediawiki/index.php/SimpleQueue
# I used a command 
# /usr/local/cluster/software/installation/SimpleQueue/sqPBS.py gen 8 tmm46 nrn_task tasklist > run.pbs
# to generate run.pbs however then I edited run.pbs to 1 node and 10 ppn to
# more efficiently use louise (it seems to work for our first case of requiring 10 jobs).
# 
# To run first batch_run.py is run which will create some run_X folders and tasklist.  Then tasklist is run with
# qsub run.pbs
#
#
#************************************************************************
print "phase 4"
#************************************************************************
# In phase 4 the matlab tanks are created
#

#************************************************************************
print "phase 5"
#************************************************************************
# In phase 5 the tanks are analyzed to create and save matlab polar plot figures
#

#************************************************************************
print "phase 6"
#************************************************************************
# In phase 6 the raster plots of spike activity are created and saved.
#

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