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

 Download zip file   Auto-launch 
Help downloading and running models
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: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 GLU cell; Olfactory bulb main interneuron periglomerular GABA cell; Olfactory bulb main interneuron granule MC GABA 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 GLU cell; Olfactory bulb main interneuron periglomerular GABA cell; Olfactory bulb main interneuron granule MC GABA cell;
Files displayed below are from the implementation
/
ShortEtAl2016
run_17
tdt2mat_data
num_of_columns.hoc *
parameters.hoc
                            
breathing_period=400
light_period= 399.75 // 300 is a short run, 398 regular
breath_peak_rate = 200
light1_peak_rate = 640
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
gc_on=4

///////////////////////////////////////////////////
//turn the ET cells back off for this special case:
// don't turn off pg lateral connections
// nc[19][0].weight = 0 // turns off pg2 axon to m1 priden connection
// nc[25][0].weight = 0 // turns off pg1 axon to m2 priden connection
if (1) { //turn ET cells off (1) or on (0)
  for weight_index = 26, 33 {
    nc[weight_index][0].weight = 0
  }
}
//////////////////////////////////////////////////
// add some extra pg recordings
objref pg1_to_m1tuft_events, pg1_axon_to_m2_events, pg2_axon_to_m1priden_events
pg1_to_m1tuft_events = new Vector()
pg1_axon_to_m2_events = new Vector()
pg2_axon_to_m1priden_events = new Vector()

nc[18][0].record(pg1_to_m1tuft_events)
nc[25][0].record(pg1_axon_to_m2_events)
nc[19][0].record(pg2_axon_to_m1priden_events)

// curiously this script seems to be executing in run_X folders
load_file("../tdt2mat_data.hoc") // had to postpone this after the new pg objects declarations above
chdir("..")

do_everything()
quit()
// net_type gc_net

Loading data, please wait...