2D model of olfactory bulb gamma oscillations (Li and Cleland 2017)

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Accession:232097
This is a biophysical model of the olfactory bulb (OB) that contains three types of neurons: mitral cells, granule cells and periglomerular cells. The model is used to study the cellular and synaptic mechanisms of OB gamma oscillations. We concluded that OB gamma oscillations can be best modeled by the coupled oscillator architecture termed pyramidal resonance inhibition network gamma (PRING).
Reference:
1 . Li G, Cleland TA (2017) A coupled-oscillator model of olfactory bulb gamma oscillations. PLoS Comput Biol 13:e1005760 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network;
Brain Region(s)/Organism:
Cell Type(s): Olfactory bulb main mitral GLU cell; Olfactory bulb main interneuron granule MC GABA cell; Olfactory bulb main interneuron periglomerular GABA cell;
Channel(s):
Gap Junctions:
Receptor(s): AMPA; NMDA; GabaA;
Gene(s):
Transmitter(s):
Simulation Environment: NEURON;
Model Concept(s): Olfaction;
Implementer(s): Li, Guoshi [guoshi_li at med.unc.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; GabaA; AMPA; NMDA;
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OBGAMMA
celldata
connection
data0
input
README
cadecay.mod *
cadecay2.mod *
Caint.mod *
Can.mod *
CaPN.mod *
CaT.mod *
GradeAMPA.mod *
GradeGABA.mod *
GradNMDA.mod *
hpg.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 *
SineInput.mod
Background.hoc
Cal_Synch.hoc
Connect.hoc
Figure.hoc
GC_def.hoc
GC_save.hoc *
GC_Stim.hoc
Input.hoc
mathslib.hoc
MC_def.hoc
MC_save.hoc
MC_Stim.hoc
mosinit.hoc
OBNet.hoc
Parameter.hoc
PG_def.hoc
PG_save.hoc *
PG_Stim.hoc
SaveData.hoc
tabchannels.dat *
tabchannels.hoc
                            
// Save simulation data to a folder (data0)

DT  = 0.2       // Record data with a resolution of 0.2 ms
DTT = 0.02      // Record data with a resolution of 0.02 ms

sum = 0

objref f1
f1 = new File()

strdef filepath, filepath1, string, filename, WD

objref time, input, Vmean, Vmean2 
objref Gpm[nmitx][nmity]
objref Ggm[nMit][nGran], Ggm_Total[nMit]
objref Vms[nmitx][nmity], Vmd[nmitx][nmity], Vmt[nmitx][nmity]
objref Vgs[ngranx][ngrany], Vgb[ngranx][ngrany]
objref Vps[npgx][npgy], Vpb[npgx][npgy] 

objref Tt
objref Vmc22[5]


filepath1 = "RSP2/"  // used to store random background inputs; not used currently

Tt = new Vector()
time   = new Vector()
input  = new Vector()


// Record time	
Tt.record(&t, DTT)  
time.record(&t, DT)

// Record input timecourse
input.record(&MCinput[0][0].i, DT)


//====================================================
//                  Record Voltage
//====================================================	
 for i = 0, 4 {
     Vmc22[i] = new Vector()
 }
   
  Vmc22[0].record(&mit[2][2].soma.v(0.5),  DTT)
  Vmc22[1].record(&mit[2][2].dend.v(0.16), DTT)
  Vmc22[2].record(&mit[2][2].dend.v(0.35), DTT)
  Vmc22[3].record(&mit[2][2].dend.v(0.47), DTT) 
  Vmc22[4].record(&mit[2][2].dend.v(0.99),  DTT) 
  

// Record Mit Soma Voltage
 for i=0, nmitx-1 {
    for j=0, nmity-1 {
     Vms[i][j] = new Vector()
     Vms[i][j].record(&mit[i][j].soma.v(0.5), DT)
  }
 }


// Record Mit Dend Voltage
 for i=0, nmitx-1 {
   for j=0, nmity-1 {
    Vmd[i][j] = new Vector()
    Vmd[i][j].record(&mit[i][j].dend.v(1.0), DT)
  }
 }
 
 // Record Mit tuft Voltage
 for i=0, nmitx-1 {
   for j=0, nmity-1 {
    Vmt[i][j] = new Vector()
    Vmt[i][j].record(&mit[i][j].tuft.v(0.5), DT)
  }
 }
 
 
// Record PG Soma Voltage
 for i=0, npgx-1 {
  for j=0, npgy-1 {  
    Vps[i][j] = new Vector()
    Vps[i][j].record(&pg[i][j].soma.v(0.5), DT)
  }
 }
  
// Record PG Spine Voltage
 for i=0, npgx-1 {
  for j=0, npgy-1 {  
    Vpb[i][j] = new Vector()
    Vpb[i][j].record(&pg[i][j].gemmbody.v(0.5), DT)
  }
 }  
 
 
// Record GC Soma Voltage
 for i=0, nmitx-1 {
  for j=0, nmity-1 {  
    Vgs[i][j] = new Vector()
    Vgs[i][j].record(&gran[i][j].soma.v(0.5), DT)
  }
 }
 
// Record Gran Spine Voltage
 for i=0, ngranx-1 {
  for j=0, ngrany-1 {  
    Vgb[i][j] = new Vector()
    Vgb[i][j].record(&gran[i][j].gemmbody.v(0.5), DT)
  }
 }
 
 
//====================================================
//                Record Conductance
//====================================================

// Record PG->MC conductance
 for i=0, nmitx-1 {
    for j=0, nmity-1 {
       Gpm[i][j] = new Vector()
       Gpm[i][j].record(&p2m[i][j].g, DT)
	  }
 }
 
// Record GC->MC conductance
   for i=0, nMit-1 {
    for j=0, GMS[i]-1 {
        Ggm[i][j] = new Vector()
        Ggm[i][j].record(&g2m[i][j].g, DT)  
    }
  }


 
//====================================================
//                 Save Data
//====================================================

proc save_data() {
   WD = getcwd()
   
   sprint(filepath, "data%d",$1)
   print filepath
   print "\n"
   
   FL=chdir(filepath)
   
   if (FL==-1) {
    sprint(string, "system(\"mkdir %s\")", filepath)
    //chdir("getcwd()")
    chdir(WD)
	execute(string)
    } else {
    chdir(WD)
   }
   
   

 //====================================================
 
    size1  = Vms[0][0].size()
    Vmean  = new Vector(size1, 0)
	
  // Calculate mean voltage   
    for i=0, nmitx-1 {
       for j=0, nmity-1 {
	    Vmean = Vmean.c.add(Vms[i][j]) 
     } 
    }
	
    size2  = Vgb[0][0].size()
    Vmean2 = new Vector(size2, 0)
  
    for i=0, ngranx-1 {
       for j=0, ngrany-1 {
	    Vmean2 = Vmean2.c.add(Vgb[i][j]) 
      } 
	}

 // Calculate the total GC GABAa conductance to each MC   
    size = Ggm[0][0].size()
	
    for i=0, nMit-1 {
        Ggm_Total[i] = new Vector(size, 0)
       for j=0, GMS[i]-1 {  
        Ggm_Total[i] = Ggm_Total[i].c.add(Ggm[i][j])
      }
    } 

  
// ====================================================
//              Save Input
// ====================================================  
    sprint(filename, "%s/OSN", filepath)
	f1.wopen(filename)
	input.printf(f1)
	f1.close()

	
    sprint(filename, "%s/Odor", filepath)
    f1.wopen(filename)
    for i = 0, nmitx-1 { 
       for j = 0, nmity-1 {    
          f1.printf("%5.4f ", odor[i][j])
          f1.printf("\n")
       } 
     }
 
    f1.close()  
// ====================================================
//             Save Simulation Time
// ====================================================
    sprint(filename, "%s/tt", filepath)
    f1.wopen(filename)
    time.printf(f1)
    f1.close()

    sprint(filename, "%s/Tt", filepath)
    f1.wopen(filename)
    Tt.printf(f1)
    f1.close()

//====================================================
//               Save Conductance
//====================================================		
   
// Save PG-->MC conductance

  for i=0, nmitx-1 {
    for j=0, nmity-1 {
     sprint(filename, "%s/Gpm%d%d",filepath, i,j)
     f1.wopen(filename)
     Gpm[i][j].printf(f1)
     f1.close()	
    } 
  }	
	
	
 // Save GC-->MC conductance

    for i=0, nMit-1 {
     sprint(filename, "%s/Ggm%d",filepath, i)
     f1.wopen(filename)
     Ggm_Total[i].printf(f1)
     f1.close()	
    } 
	
   
//====================================================
//                 Save Voltage
//====================================================		
 // Save voltage of lateral DEND of MC22 at various points
  for i = 0, 4 {
    sprint(filename, "%s/Vmc22_%d",filepath, i)
    f1.wopen(filename)
    Vmc22[i].printf(f1)
    f1.close()	
   }  


 // Save mean MC voltage	
    Vmean = Vmean.div(nMit)
	sprint(filename, "%s/Vam", filepath)
    f1.wopen(filename)
    Vmean.printf(f1)
    f1.close()	
	
	Vmean2 = Vmean2.div(nGran)
	sprint(filename, "%s/Vag", filepath)
    f1.wopen(filename)
    Vmean2.printf(f1)
    f1.close()	
		
  // Save voltage of mitral cells
  // Soma 
  for i=0, nmitx-1 {
    for j=0, nmity-1 {
     sprint(filename, "%s/Vms_%d_%d",filepath, i,j)
     f1.wopen(filename)
     Vms[i][j].printf(f1)
     f1.close()	
    } 
  }
 

  // Dendrite
  for i=0, nmitx-1 {
    for j=0, nmity-1 {
    sprint(filename, "%s/Vmd_%d_%d",filepath, i,j)
    f1.wopen(filename)
    Vmd[i][j].printf(f1)
    f1.close()	
   }  
  }   

  
// Save PG voltages
  // Soma
  /*
  for i=0, npgx-1 {
    for j=0, npgy-1 {
    sprint(filename, "%s/Vps%d%d",filepath, i,j)
    f1.wopen(filename)
    Vps[i][j].printf(f1)
    f1.close()	
   } 
  }   
  */
  
  // Spine
  for i=0, npgx-1 {
    for j=0, npgy-1 {
    sprint(filename, "%s/Vpb_%d_%d",filepath, i,j)
    f1.wopen(filename)
    Vpb[i][j].printf(f1)
    f1.close()	
   } 
  }     
  
  
// Save GC voltages
// Soma
  /*
  for i=0, nmitx-1 {
    for j=0, nmity-1 {
    sprint(filename, "%s/Vgs%d%d",filepath, i,j)
    f1.wopen(filename)
    Vgs[i][j].printf(f1)
    f1.close()	
   } 
  } 
  */
  
 // Spine
  for i=0, ngranx-1 {
    for j=0, ngrany-1 {
    sprint(filename, "%s/Vgb_%d_%d",filepath, i,j)
    f1.wopen(filename)
    Vgb[i][j].printf(f1)
    f1.close()	
   } 
  }  
  
  
//====================================================
//               Save Spike Time
//====================================================	
 // Save MC somatic spike time	
  for i=0, nmitx-1 {
    for j=0, nmity-1 {
    sprint(filename, "%s/Ms_%d_%d",filepath, i,j)
	f1.wopen(filename)
	mit[i][j].spiketimes.printf(f1)
	f1.close()
    }		  
  }
  
 // Save MC dendritic spike time	
  for i=0, nmitx-1 {
    for j=0, nmity-1 {	
    sprint(filename, "%s/Md_%d_%d",filepath, i,j)
	f1.wopen(filename)
	mit[i][j].dendspike.printf(f1)
	f1.close()
   }
  }   
 
 
  // Save GC somatic spike time	
  for i=0, ngranx-1 {
     for j=0, ngrany-1 {
      sprint(filename, "%s/Gs_%d_%d",filepath, i,j)
	  f1.wopen(filename)
	  gran[i][j].spiketimes.printf(f1)
	  f1.close()
   }
  }
  
  // Save GC dendritic spike time	
  for i=0, ngranx-1 {
     for j=0, ngrany-1 {
      sprint(filename, "%s/Gd_%d_%d",filepath, i,j)
	  f1.wopen(filename)
	  gran[i][j].dendspike.printf(f1)
	  f1.close()
   }
  }  

  // Save PG somatic spike time	
  for i=0, npgx-1 {
     for j=0, npgy-1 {
      sprint(filename, "%s/Ps_%d_%d",filepath, i,j)
	  f1.wopen(filename)
	  pg[i][j].spiketimes.printf(f1)
	  f1.close()
   }
  }
  
 // Save PG dendritic spike time	
  for i=0, npgx-1 {
     for j=0, npgy-1 {
      sprint(filename, "%s/Pd_%d_%d",filepath, i,j)
	  f1.wopen(filename)
	  pg[i][j].dendspike.printf(f1)
	  f1.close()
   }
  } 
  
//===============================================
// Save random spontaneous spikes
/*
   for i = 0, nmitx-1 {
     for j = 0, nmity-1 {
       sprint(filename, "%ssp%d%d",filepath1, i, j)
	   f1.wopen(filename)
	   RSP[i][j].printf(f1)
	   f1.close()
    }		
   } 
 */ 
  
}



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