Olfactory bulb mitral cell gap junction NN model: burst firing and synchrony (O`Connor et al. 2012)

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Accession:146030
In a network of 6 mitral cells connected by gap junction in the apical dendrite tuft, continuous current injections of 0.06 nA are injected into 20 locations in the apical tufts of two of the mitral cells. The current injections into one of the cells starts 10 ms after the other to generate asynchronous firing in the cells (Migliore et al. 2005 protocol). Firing of the cells is asynchronous for the first 120 ms. However after the burst firing phase is completed the firing in all cells becomes synchronous.
Reference:
1 . O'Connor S, Angelo K, Jacob TJC (2012) Burst firing versus synchrony in a gap junction connected olfactory bulb mitral cell network model. 6:75. Frontiers in Computational Neuroscience 6:75:1-18
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network;
Brain Region(s)/Organism: Olfactory bulb;
Cell Type(s): Olfactory bulb main mitral GLU cell;
Channel(s): I Na,t; I L high threshold; I A; I K; I K,Ca;
Gap Junctions: Gap junctions;
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: NEURON;
Model Concept(s): Bursting; Oscillations; Synchronization; Active Dendrites; Influence of Dendritic Geometry; Calcium dynamics; Olfaction;
Implementer(s):
Search NeuronDB for information about:  Olfactory bulb main mitral GLU cell; I Na,t; I L high threshold; I A; I K; I K,Ca;
/
oconnoretal2012
README
AMPA.mod
Ca_mit_conc_ChannelML.mod
CurrentClampExt.mod
KA_ChannelML.mod
KCa3_ChannelML_new.mod
Kdr_ChannelML.mod
LCa3_mit_usb_ChannelML.mod
LeakConductance.mod
NaxSH0_ChannelML.mod
NaxSH10_ChannelML.mod
SynForRndSpike.mod
Cell1.hoc
Cell2.hoc
Cell3.hoc
Cell4.hoc
Cell5.hoc
Cell6.hoc
cellCheck.hoc
CellPositions.dat
ElectricalInputs.dat
gap.hoc
init.hoc
mosinit.hoc *
nCtools.hoc
NetworkConnections.dat
regenerateMods
simulation.props
                            
COMMENT

   **************************************************
   File generated by: neuroConstruct v1.3.8 
   **************************************************

   This file holds the implementation in NEURON of the Cell Mechanism:
   Kdr_ChannelML (Type: Channel mechanism, Model: Template based ChannelML file)

   with parameters: 
   /channelml/@units = Physiological Units 
   /channelml/notes = ChannelML file containing a single Channel description 
   /channelml/ion/@name = k 
   /channelml/ion/@default_erev = -77.0 
   /channelml/ion/@charge = 1 
   /channelml/channel_type/@name = Kdr_ChannelML 
   /channelml/channel_type/@density = yes 
   /channelml/channel_type/status/@value = in_progress 
   /channelml/channel_type/status/comment = Equations adapted from paper for modern convention of external potential being zero 
   /channelml/channel_type/status/contributor/name = Padraig Gleeson 
   /channelml/channel_type/notes = Mitral cell K DR channel 
   /channelml/channel_type/neuronDBref/modelName = K channels 
   /channelml/channel_type/neuronDBref/uri = http://senselab.med.yale.edu/senselab/NeuronDB/channelGene2.htm#table3 
   /channelml/channel_type/current_voltage_relation/ohmic/@ion = k 
   /channelml/channel_type/current_voltage_relation/ohmic/conductance/@default_gmax = 36 
   /channelml/channel_type/current_voltage_relation/ohmic/conductance/rate_adjustments/q10_settings/@q10_factor = 3 
   /channelml/channel_type/current_voltage_relation/ohmic/conductance/rate_adjustments/q10_settings/@experimental_temp = 24 
   /channelml/channel_type/current_voltage_relation/ohmic/conductance/gate/@power = 1 
   /channelml/channel_type/current_voltage_relation/ohmic/conductance/gate/state/@name = m 
   /channelml/channel_type/current_voltage_relation/ohmic/conductance/gate/state/@fraction = 1 
   /channelml/channel_type/hh_gate/@state = m 
   /channelml/channel_type/hh_gate/transition/voltage_gate/alpha/parameterised_hh/@type = exponential 
   /channelml/channel_type/hh_gate/transition/voltage_gate/alpha/parameterised_hh/@expr = A*exp(k*(v-d)) 
   /channelml/channel_type/hh_gate/transition/voltage_gate/alpha/parameterised_hh/parameter[1]/@name = A 
   /channelml/channel_type/hh_gate/transition/voltage_gate/alpha/parameterised_hh/parameter[1]/@value = 1 
   /channelml/channel_type/hh_gate/transition/voltage_gate/alpha/parameterised_hh/parameter[2]/@name = k 
   /channelml/channel_type/hh_gate/transition/voltage_gate/alpha/parameterised_hh/parameter[2]/@value = 0.055 
   /channelml/channel_type/hh_gate/transition/voltage_gate/alpha/parameterised_hh/parameter[3]/@name = d 
   /channelml/channel_type/hh_gate/transition/voltage_gate/alpha/parameterised_hh/parameter[3]/@value = -50 
   /channelml/channel_type/hh_gate/transition/voltage_gate/beta/parameterised_hh/@type = exponential 
   /channelml/channel_type/hh_gate/transition/voltage_gate/beta/parameterised_hh/@expr = A*exp(k*(v-d)) 
   /channelml/channel_type/hh_gate/transition/voltage_gate/beta/parameterised_hh/parameter[1]/@name = A 
   /channelml/channel_type/hh_gate/transition/voltage_gate/beta/parameterised_hh/parameter[1]/@value = 1 
   /channelml/channel_type/hh_gate/transition/voltage_gate/beta/parameterised_hh/parameter[2]/@name = k 
   /channelml/channel_type/hh_gate/transition/voltage_gate/beta/parameterised_hh/parameter[2]/@value = 0.0275 
   /channelml/channel_type/hh_gate/transition/voltage_gate/beta/parameterised_hh/parameter[3]/@name = d 
   /channelml/channel_type/hh_gate/transition/voltage_gate/beta/parameterised_hh/parameter[3]/@value = -50 
   /channelml/channel_type/hh_gate/transition/voltage_gate/tau/generic_equation_hh/@expr = beta/(0.0035 *( 1 +alpha)) 
   /channelml/channel_type/hh_gate/transition/voltage_gate/inf/parameterised_hh/@type = sigmoid 
   /channelml/channel_type/hh_gate/transition/voltage_gate/inf/parameterised_hh/@expr = A/(1 + exp(k*(v-d))) 
   /channelml/channel_type/hh_gate/transition/voltage_gate/inf/parameterised_hh/parameter[1]/@name = A 
   /channelml/channel_type/hh_gate/transition/voltage_gate/inf/parameterised_hh/parameter[1]/@value = 1 
   /channelml/channel_type/hh_gate/transition/voltage_gate/inf/parameterised_hh/parameter[2]/@name = k 
   /channelml/channel_type/hh_gate/transition/voltage_gate/inf/parameterised_hh/parameter[2]/@value = -0.1 
   /channelml/channel_type/hh_gate/transition/voltage_gate/inf/parameterised_hh/parameter[3]/@name = d 
   /channelml/channel_type/hh_gate/transition/voltage_gate/inf/parameterised_hh/parameter[3]/@value = 21 
   /channelml/channel_type/impl_prefs/table_settings/@max_v = 100 
   /channelml/channel_type/impl_prefs/table_settings/@min_v = -100 
   /channelml/channel_type/impl_prefs/table_settings/@table_divisions = 400 

// File from which this was generated: /home/Simon/nC_projects/Rat_Mitral_Cell_Gap_Network_copy4/cellMechanisms/Kdr_ChannelML/KChannel.xml

// XSL file with mapping to simulator: /home/Simon/nC_projects/Rat_Mitral_Cell_Gap_Network_copy4/cellMechanisms/Kdr_ChannelML/ChannelML_v1.8.0_NEURONmod.xsl

ENDCOMMENT


?  This is a NEURON mod file generated from a ChannelML file

?  Unit system of original ChannelML file: Physiological Units

COMMENT
    ChannelML file containing a single Channel description
ENDCOMMENT

TITLE Channel: Kdr_ChannelML

COMMENT
    Mitral cell K DR channel
ENDCOMMENT


UNITS {
    (mA) = (milliamp)
    (mV) = (millivolt)
    (S) = (siemens)
    (um) = (micrometer)
    (molar) = (1/liter)
    (mM) = (millimolar)
    (l) = (liter)
}


    
NEURON {
      

    SUFFIX Kdr_ChannelML
    USEION k READ ek WRITE ik VALENCE 1 ? reversal potential of ion is read, outgoing current is written
            
    RANGE gmax, gion
    
    RANGE minf, mtau
}

PARAMETER { 
      

    gmax = 0.036 (S/cm2) ? default value, should be overwritten when conductance placed on cell
    
}



ASSIGNED {
      

    v (mV)
    
    celsius (degC)
    
    ? Reversal potential of k
    ek (mV)
    ? The outward flow of ion: k calculated by rate equations...
    ik (mA/cm2)
            
    
    gion (S/cm2)
    minf
    mtau (ms)
    
}

BREAKPOINT { 
                        
    SOLVE states METHOD cnexp
         

    gion = gmax*((1*m)^1)
    ik = gion*(v - ek)
                

}



INITIAL {
    ek = -77.0
        
    rates(v)
    m = minf
                
        
    
    
}
    
STATE {
    m
    
}

DERIVATIVE states {
    rates(v)
    m' = (minf - m)/mtau
    
}

PROCEDURE rates(v(mV)) {  
    
    ? Note: not all of these may be used, depending on the form of rate equations
    LOCAL  alpha, beta, tau, inf, gamma, zeta, temp_adj_m, A_alpha_m, k_alpha_m, d_alpha_m, A_beta_m, k_beta_m, d_beta_m, A_tau_m, k_tau_m, d_tau_m, A_inf_m, k_inf_m, d_inf_m
        
    TABLE minf, mtau
 DEPEND celsius
 FROM -100 TO 100 WITH 400
    
    
    UNITSOFF
    
    ? There is a Q10 factor which will alter the tau of the gates 
                 

    temp_adj_m = 3^((celsius - 24)/10)
        
    ?      ***  Adding rate equations for gate: m  ***
        
    ? Found a parameterised form of rate equation for alpha, using expression: A*exp(k*(v-d))
    A_alpha_m = 1
    k_alpha_m = 0.055
    d_alpha_m = -50
     
    
    alpha = A_alpha_m * exp((v - d_alpha_m) * k_alpha_m)
    
    
    ? Found a parameterised form of rate equation for beta, using expression: A*exp(k*(v-d))
    A_beta_m = 1
    k_beta_m = 0.0275
    d_beta_m = -50
     
    
    beta = A_beta_m * exp((v - d_beta_m) * k_beta_m)
    
         

    ? Found a generic form of the rate equation for tau, using expression: beta/(0.0035 *( 1 +alpha))
                    tau = beta/(0.0035 *( 1 +alpha))
        
    mtau = tau/temp_adj_m
    
    ? Found a parameterised form of rate equation for inf, using expression: A / (1 + exp(k*(v-d)))
    A_inf_m = 1
    k_inf_m = -0.1
    d_inf_m = 21
     
    
    inf = A_inf_m / (exp((v - d_inf_m) * k_inf_m) + 1)
    
    minf = inf
          
       
    
    ?     *** Finished rate equations for gate: m ***
    
             

}


UNITSON



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