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Large scale neocortical model for PGENESIS (Crone et al 2019)

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Accession:260267
This is model code for a large scale neocortical model based on Traub et al. (2005), modified to run on PGENESIS on supercomputing resources. "In this paper (Crone et al 2019), we evaluate the computational performance of the GEneral NEural SImulation System (GENESIS) for large scale simulations of neural networks. While many benchmark studies have been performed for large scale simulations with leaky integrate-and-fire neurons or neuronal models with only a few compartments, this work focuses on higher fidelity neuronal models represented by 50–74 compartments per neuron. ..."
Reference:
1 . Crone JC, Vindiola MM, Yu AB, Boothe DL, Beeman D, Oie KS, Franaszczuk PJ (2019) Enabling Large-Scale Simulations With the GENESIS Neuronal Simulator Frontiers in Neuroinformatics 13:69
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network;
Brain Region(s)/Organism: Neocortex;
Cell Type(s): Neocortex L2/3 pyramidal GLU cell; Neocortex L5/6 pyramidal GLU cell; Thalamus reticular nucleus GABA cell; Neocortex fast spiking (FS) interneuron; Neocortex layer 2-3 interneuron; Neocortex layer 5 interneuron; Neocortex spiking low threshold (LTS) neuron; Neocortex spiny stellate cell;
Channel(s): I Sodium; I Potassium; I Calcium;
Gap Junctions:
Receptor(s): AMPA; NMDA; GabaA;
Gene(s):
Transmitter(s): Glutamate; Gaba;
Simulation Environment: PGENESIS; GENESIS;
Model Concept(s): Oscillations; Methods; Detailed Neuronal Models; Extracellular Fields;
Implementer(s): Crone, J ; Vindiola, MM ; Yu, AB ; Boothe, DL ; Beeman, Dave; Oie, KS ; Franaszczuk, PJ ; Anderson, WS ; Kudela, Pawel ; Traub, Roger D [rtraub at us.ibm.com];
Search NeuronDB for information about:  Thalamus reticular nucleus GABA cell; Neocortex L5/6 pyramidal GLU cell; Neocortex L2/3 pyramidal GLU cell; GabaA; AMPA; NMDA; I Sodium; I Calcium; I Potassium; Gaba; Glutamate;
/
Crone_et_al_Neocortex_Model_Frontiers_in_Neuroinformatics
config_neuron
synchans
synchansB23FS.g *
synchansB23FSlongrange.g
synchansB5FS.g *
synchansB5FSlongrange.g
synchansC23FS.g *
synchansC23FSlongrange.g
synchansC5FS.g *
synchansC5FSlongrange.g
synchansI23LTS.g *
synchansI23LTSlongrange.g
synchansI5LTS.g *
synchansI5LTSlongrange.g
synchansnRT.g *
synchansnRTlongrange.g
synchansP23FRBa.g *
synchansP23FRBalongrange.g
synchansP23RSa.g *
synchansP23RSalongrange.g
synchansP23RSb.g *
synchansP23RSblongrange.g
synchansP23RSc.g *
synchansP23RSclongrange.g
synchansP23RSd.g *
synchansP23RSdlongrange.g
synchansP5IBa.g *
synchansP5IBalongrange.g
synchansP5IBb.g *
synchansP5IBblongrange.g
synchansP5IBc.g *
synchansP5IBclongrange.g
synchansP5IBd.g *
synchansP5IBdlongrange.g
synchansP5RSa.g *
synchansP5RSalongrange.g
synchansP6RSa.g *
synchansP6RSalongrange.g
synchansP6RSb.g *
synchansP6RSblongrange.g
synchansP6RSc.g *
synchansP6RSclongrange.g
synchansP6RSd.g *
synchansP6RSdlongrange.g
synchansST4RS.g
synchansST4RSlongrange.g
synchansTCR.g *
synchansTCRlongrange.g
                            
//genesis

/* FILE INFORMATION
** "Generic" excitatory (glutamate) and inhibitory (GABA) synaptically
**  activated channels  (based on mitsyn.g by Upi Bhalla)
**
** The channels have an alpha_function type conductance change for
** each synaptic event.
**
** Modified by D. Beeman for GENESIS 2.0 syntax and synchan object - 5/19/94
*/

// CONSTANTS
float EGlu = 0.0
float EGABA = -0.075
float SOMA_A = 1e-9
float GGlu = SOMA_A * 50 
// Actual conductance set by channel field in .p file
float GGABA = SOMA_A * 50

// CONSTANTS for NMDA Channel
float CMg = 1.5     // [Mg] in mM
float eta = 0.33    // per mM
float gamma = 60    // per Volt

//===================================================================
//                     SYNAPTIC CHANNELS   (Values guessed at)
//===================================================================

function make_Ex_ch21P6RSAMPA

// AMPA synapse for P6RS - nRT

	if ({exists Ex_ch21P6RSAMPA})
		return
	end

	create		synchan	Ex_ch21P6RSAMPA
    	setfield	        Ex_ch21P6RSAMPA \
		Ek			{EGlu} \
		tau1		{ 1.0e-3 } \	// sec
		tau2		{ 1.0e-3 } \ 	// sec
		gmax		{GGlu} // Siemens
end

function make_Ex_ch21P6RSNMDA

// NMDA synapse for P6RS - nRT

    if ({exists Ex_ch21P6RSNMDA})
        return
    end

    create  synchan  Ex_ch21P6RSNMDA

        setfield     Ex_ch21P6RSNMDA     \
        Ek           {EGlu}         \
        tau1         { 100.0e-3 }    \ // sec
        tau2         { 0.67e-3 }   \ // sec
        gmax         {GGlu}           // Siemens

    create Mg_block Ex_ch21P6RSNMDA/block
        setfield         Ex_ch21P6RSNMDA/block \
        CMg              {CMg}            \
        KMg_A            {1.0/eta}        \
        KMg_B            {1.0/gamma}      

    addmsg Ex_ch21P6RSNMDA Ex_ch21P6RSNMDA/block CHANNEL Gk Ek

    addmsg Ex_ch21P6RSNMDA/block . CHANNEL Gk Ek

    addmsg . Ex_ch21P6RSNMDA/block VOLTAGE Vm

    // Even though we don't use the channel current, CHECK expects this message.

    // addmsg . Ex_ch1NMDA VOLTAGE Vm

end

function make_Ex_ch21TCRAMPA

// AMPA synapse for TCR - nRT

	if ({exists Ex_ch21TCRAMPA})
		return
	end

	create		synchan	Ex_ch21TCRAMPA
    	setfield	        Ex_ch21TCRAMPA \
		Ek			{EGlu} \
		tau1		{ 2.0e-3 } \	// sec
		tau2		{ 2.0e-3 } \ 	// sec
		gmax		{GGlu} // Siemens
end

function make_Ex_ch21TCRNMDA

// NMDA synapse for TCR - nRT

    if ({exists Ex_ch21TCRNMDA})
        return
    end

    create  synchan  Ex_ch21TCRNMDA

        setfield     Ex_ch21TCRNMDA     \
        Ek           {EGlu}         \
        tau2         { 0.67e-3 }    \ // sec
        tau1         { 150.0e-3 }   \ // sec
        gmax         {GGlu}           // Siemens

    create Mg_block Ex_ch21TCRNMDA/block
        setfield         Ex_ch21TCRNMDA/block \
        CMg              {CMg}            \
        KMg_A            {1.0/eta}        \
        KMg_B            {1.0/gamma}      

    addmsg Ex_ch21TCRNMDA Ex_ch21TCRNMDA/block CHANNEL Gk Ek

    addmsg Ex_ch21TCRNMDA/block . CHANNEL Gk Ek

    addmsg . Ex_ch21TCRNMDA/block VOLTAGE Vm

    // Even though we don't use the channel current, CHECK expects this message.

    // addmsg . Ex_ch21TCRNMDA VOLTAGE Vm

end

function make_Inh_ch21nRTGABAa

//GABA_A synapse for nRT - nRT

	if ({exists Inh_ch21nRTGABAa})
		return
	end

	create		synchan	Inh_ch21nRTGABAa
    	setfield	        Inh_ch21nRTGABAa \
	Ek			{ EGABA } \
	tau1		{ 9.0e-3 } \	// sec
    tau2        { 44.5e-3 } \    // sec
	gmax		{GGABA}		// Siemens
end


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