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:
   KCa3_ChannelML_new (Type: Channel mechanism, Model: ChannelML based process)

   with parameters: 
   /channelml/@units = Physiological Units 
   /channelml/notes = A channel from Bhalla, U.S.and Bower, J.M. Exploring parameter space in detailed single neuron models:     simulations of the mitral and granule cells ... 
   /channelml/channel_type/@name = KCa3_ChannelML_new 
   /channelml/channel_type/@density = yes 
   /channelml/channel_type/status/@value = in_progress 
   /channelml/channel_type/status/issue = This ChannelML file is intended to replicate the GENESIS functionality of a tabchannel version of Kca_mit_usb  
   /channelml/channel_type/status/contributor/name = Simon O'Connor 
   /channelml/channel_type/notes = Calcium dependent K channel 
   /channelml/channel_type/publication/fullTitle = Bhalla, U.S.and Bower, J.M. Exploring parameter space in detailed single neuron models:     simulations of the mitral and granule cells of the olfacto ... 
   /channelml/channel_type/publication/pubmedRef = http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=7688798&dopt=Abstract 
   /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/@cond_law = ohmic 
   /channelml/channel_type/current_voltage_relation/@ion = k 
   /channelml/channel_type/current_voltage_relation/@default_gmax = 3.6 
   /channelml/channel_type/current_voltage_relation/@default_erev = -80 
   /channelml/channel_type/current_voltage_relation/conc_dependence/@name = Calcium 
   /channelml/channel_type/current_voltage_relation/conc_dependence/@ion = ca 
   /channelml/channel_type/current_voltage_relation/conc_dependence/@charge = 2 
   /channelml/channel_type/current_voltage_relation/conc_dependence/@variable_name = ca_conc 
   /channelml/channel_type/current_voltage_relation/conc_dependence/@min_conc = 0 
   /channelml/channel_type/current_voltage_relation/conc_dependence/@max_conc = 1e-8 
   /channelml/channel_type/current_voltage_relation/gate[1]/@name = m 
   /channelml/channel_type/current_voltage_relation/gate[1]/@instances = 1 
   /channelml/channel_type/current_voltage_relation/gate[1]/closed_state/@id = m0 
   /channelml/channel_type/current_voltage_relation/gate[1]/open_state/@id = m 
   /channelml/channel_type/current_voltage_relation/gate[1]/open_state/@fraction = 1 
   /channelml/channel_type/current_voltage_relation/gate[1]/transition[1]/@name = alpha 
   /channelml/channel_type/current_voltage_relation/gate[1]/transition[1]/@from = m0 
   /channelml/channel_type/current_voltage_relation/gate[1]/transition[1]/@to = m 
   /channelml/channel_type/current_voltage_relation/gate[1]/transition[1]/@expr_form = generic 
   /channelml/channel_type/current_voltage_relation/gate[1]/transition[1]/@expr = (exp ((v-65)/27)) 
   /channelml/channel_type/current_voltage_relation/gate[1]/transition[2]/@name = beta 
   /channelml/channel_type/current_voltage_relation/gate[1]/transition[2]/@from = m 
   /channelml/channel_type/current_voltage_relation/gate[1]/transition[2]/@to = m0 
   /channelml/channel_type/current_voltage_relation/gate[1]/transition[2]/@expr_form = generic 
   /channelml/channel_type/current_voltage_relation/gate[1]/transition[2]/@expr = 0.008 
   /channelml/channel_type/current_voltage_relation/gate[2]/@name = z 
   /channelml/channel_type/current_voltage_relation/gate[2]/@instances = 1 
   /channelml/channel_type/current_voltage_relation/gate[2]/closed_state/@id = z0 
   /channelml/channel_type/current_voltage_relation/gate[2]/open_state/@id = z 
   /channelml/channel_type/current_voltage_relation/gate[2]/open_state/@fraction = 1 
   /channelml/channel_type/current_voltage_relation/gate[2]/transition[1]/@name = alpha 
   /channelml/channel_type/current_voltage_relation/gate[2]/transition[1]/@from = z0 
   /channelml/channel_type/current_voltage_relation/gate[2]/transition[1]/@to = z 
   /channelml/channel_type/current_voltage_relation/gate[2]/transition[1]/@expr_form = generic 
   /channelml/channel_type/current_voltage_relation/gate[2]/transition[1]/@expr = (500.0*(0.015 - (ca_conc*1e6)))/( (exp ((0.015 - (ca_conc*1e6))/0.0013)) -1) 
   /channelml/channel_type/current_voltage_relation/gate[2]/transition[2]/@name = beta 
   /channelml/channel_type/current_voltage_relation/gate[2]/transition[2]/@from = z 
   /channelml/channel_type/current_voltage_relation/gate[2]/transition[2]/@to = z0 
   /channelml/channel_type/current_voltage_relation/gate[2]/transition[2]/@expr_form = generic 
   /channelml/channel_type/current_voltage_relation/gate[2]/transition[2]/@expr = 0.0021 
   /channelml/channel_type/impl_prefs/table_settings/@max_v = 50 
   /channelml/channel_type/impl_prefs/table_settings/@min_v = -100 
   /channelml/channel_type/impl_prefs/table_settings/@table_divisions = 300 

// File from which this was generated: /home/Simon/nC_projects/Rat_Mitral_Cell_Gap_Network_copy4/cellMechanisms/KCa3_ChannelML_new/KCa_Chan.xml

// XSL file with mapping to simulator: /home/Simon/nC_projects/Rat_Mitral_Cell_Gap_Network_copy4/cellMechanisms/KCa3_ChannelML_new/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
    A channel from Bhalla, U.S.and Bower, J.M. Exploring parameter space in detailed single neuron models:
    simulations of the mitral and granule cells of the olfactory bulb
ENDCOMMENT

TITLE Channel: KCa3_ChannelML_new

COMMENT
    Calcium dependent K channel
ENDCOMMENT


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


    
NEURON {
      

    SUFFIX KCa3_ChannelML_new
    USEION k READ ek WRITE ik VALENCE 1  ? reversal potential of ion is read, outgoing current is written
           
        
    USEION ca READ cai VALENCE 2 ? internal concentration of ion is read

    
    RANGE gmax, gion
    
    RANGE minf, mtau
    
    RANGE zinf, ztau
    
}

PARAMETER { 
      

    gmax = 0.0036 (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)
          

    ? The internal concentration of ion: ca is used in the rate equations...
    cai (mM)   
    
    
    gion (S/cm2)
    minf
    mtau (ms)
    zinf
    ztau (ms)
    
}

BREAKPOINT { SOLVE states METHOD derivimplicit     

    gion = gmax*((1*m)^1)*((1*z)^1)      

    ik = gion*(v - ek)
            

}



INITIAL {
    
    ek = -80
        
    settables(v,cai)
    m = minf
           
    z = zinf
           
    
    
}
    
STATE {
    m
    z
    
}

DERIVATIVE states {
    settables(v,cai)
    m' = (minf - m)/mtau
    z' = (zinf - z)/ztau
    
}

PROCEDURE settables(v(mV), cai(mM)) {  
    
    ? Note: not all of these may be used, depending on the form of rate equations
    LOCAL  alpha, beta, tau, inf, gamma, zeta, ca_conc, temp_adj_m, A_alpha_m, B_alpha_m, Vhalf_alpha_m, A_beta_m, B_beta_m, Vhalf_beta_m, temp_adj_z, A_alpha_z, B_alpha_z, Vhalf_alpha_z, A_beta_z, B_beta_z, Vhalf_beta_z
    
    
    UNITSOFF
    temp_adj_m = 1
    temp_adj_z = 1
    
    ? Gate depends on the concentration of ca
    ca_conc = cai ? In NEURON, the variable for the concentration  of ca is cai
    
            
                
           

        
    ?      ***  Adding rate equations for gate: m  ***
         
    ? Found a generic form of the rate equation for alpha, using expression: (exp ((v-65)/27))
    
    ? Equations can depend on concentration. NEURON uses 'SI Units' internally for concentration, 
    ? but the ChannelML file is in Physiological Units...
    ca_conc = ca_conc / 1000000
    alpha = (exp ((v-65)/27))
        
    ? Resetting concentration...
    ca_conc = ca_conc * 1000000
    
     
    ? Found a generic form of the rate equation for beta, using expression: 0.008
    
    ? Equations can depend on concentration. NEURON uses 'SI Units' internally for concentration, 
    ? but the ChannelML file is in Physiological Units...
    ca_conc = ca_conc / 1000000
    beta = 0.008
        
    ? Resetting concentration...
    ca_conc = ca_conc * 1000000
    
    mtau = 1/(temp_adj_m*(alpha + beta))
    minf = alpha/(alpha + beta)
          
       
    
    ?     *** Finished rate equations for gate: m ***
    

    
            
                
           

        
    ?      ***  Adding rate equations for gate: z  ***
         
    ? Found a generic form of the rate equation for alpha, using expression: (500.0*(0.015 - (ca_conc*1e6)))/( (exp ((0.015 - (ca_conc*1e6))/0.0013)) -1)
    
    ? Equations can depend on concentration. NEURON uses 'SI Units' internally for concentration, 
    ? but the ChannelML file is in Physiological Units...
    ca_conc = ca_conc / 1000000
    alpha = (500.0*(0.015 - (ca_conc*1e6)))/( (exp ((0.015 - (ca_conc*1e6))/0.0013)) -1)
        
    ? Resetting concentration...
    ca_conc = ca_conc * 1000000
    
     
    ? Found a generic form of the rate equation for beta, using expression: 0.0021
    
    ? Equations can depend on concentration. NEURON uses 'SI Units' internally for concentration, 
    ? but the ChannelML file is in Physiological Units...
    ca_conc = ca_conc / 1000000
    beta = 0.0021
        
    ? Resetting concentration...
    ca_conc = ca_conc * 1000000
    
    ztau = 1/(temp_adj_z*(alpha + beta))
    zinf = alpha/(alpha + beta)
          
       
    
    ?     *** Finished rate equations for gate: z ***
    

         

}


UNITSON



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