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 = -0.081
float SOMA_A = 1e-9
float GGlu = SOMA_A * 50
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_ch12P23RSAMPA

// AMPA synapse for P23RS - P6RS

	if ({exists Ex_ch12P23RSAMPA})
		return
	end

	create		synchan	Ex_ch12P23RSAMPA
    	setfield	        Ex_ch12P23RSAMPA \
		Ek			{EGlu} \
		tau1		{ 2.0e-3 } \	// sec
		tau2		{ 2.0e-3 } \ 	// sec
		gmax		{GGlu} // Siemens
end

function make_Ex_ch12P23RSNMDA

// NMDA synapse for P23RS - P6RS

    if ({exists Ex_ch12P23RSNMDA})
        return
    end

    create  synchan  Ex_ch12P23RSNMDA

        setfield     Ex_ch12P23RSNMDA     \
        Ek           {EGlu}         \
        tau2         { 0.67e-3 }    \ // sec
        tau1         { 130.0e-3 }   \ // sec
        gmax         {GGlu}           // Siemens

    create Mg_block Ex_ch12P23RSNMDA/block
        setfield         Ex_ch12P23RSNMDA/block \
        CMg              {CMg}            \
        KMg_A            {1.0/eta}        \
        KMg_B            {1.0/gamma}      

    addmsg Ex_ch12P23RSNMDA Ex_ch12P23RSNMDA/block CHANNEL Gk Ek

    addmsg Ex_ch12P23RSNMDA/block . CHANNEL Gk Ek

    addmsg . Ex_ch12P23RSNMDA/block VOLTAGE Vm

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

    // addmsg . Ex_ch12P23RSNMDA VOLTAGE Vm

end

function make_Ex_ch12P5IBAMPA

// AMPA synapse for P5IB - P6RS

	if ({exists Ex_ch12P5IBAMPA})
		return
	end

	create		synchan	Ex_ch12P5IBAMPA
    	setfield	        Ex_ch12P5IBAMPA \
		Ek			{EGlu} \
		tau1		{ 2.0e-3 } \	// sec
		tau2		{ 2.0e-3 } \ 	// sec
		gmax		{GGlu} // Siemens
end

function make_Ex_ch12P5IBNMDA

// NMDA synapse for P5IB - P6RS

    if ({exists Ex_ch12P5IBNMDA})
        return
    end

    create  synchan  Ex_ch12P5IBNMDA

        setfield     Ex_ch12P5IBNMDA     \
        Ek           {EGlu}         \
        tau2         { 0.67e-3 }    \ // sec
        tau1         { 130.0e-3 }   \ // sec
        gmax         {GGlu}           // Siemens

    create Mg_block Ex_ch12P5IBNMDA/block
        setfield         Ex_ch12P5IBNMDA/block \
        CMg              {CMg}            \
        KMg_A            {1.0/eta}        \
        KMg_B            {1.0/gamma}      

    addmsg Ex_ch12P5IBNMDA Ex_ch12P5IBNMDA/block CHANNEL Gk Ek

    addmsg Ex_ch12P5IBNMDA/block . CHANNEL Gk Ek

    addmsg . Ex_ch12P5IBNMDA/block VOLTAGE Vm

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

    // addmsg . Ex_ch12P5IBNMDA VOLTAGE Vm

end

function make_Inh_ch12B5FSGABAa

//GABA_A synapse for B5FS - P6RS

	if ({exists Inh_ch12B5FSGABAa})
		return
	end

	create		synchan	Inh_ch12B5FSGABAa
    	setfield	        Inh_ch12B5FSGABAa \
	Ek			{ EGABA } \
	tau1		{ 6.0e-3 } \	// sec
    tau2        { 1.0e-12 } \    // sec
	gmax		{GGABA}		// Siemens
end

function make_Ex_ch12P6RSAMPA

// AMPA synapse for P6RS - P6RS

	if ({exists Ex_ch12P6RSAMPA})
		return
	end

	create		synchan	Ex_ch12P6RSAMPA
    	setfield	        Ex_ch12P6RSAMPA \
		Ek			{EGlu} \
		tau1		{ 2.0e-3 } \	// sec
		tau2		{ 2.0e-3 } \ 	// sec
		gmax		{GGlu} // Siemens
end

function make_Ex_ch12P6RSNMDA

// NMDA synapse for P6RS - P6RS

    if ({exists Ex_ch12P6RSNMDA})
        return
    end

    create  synchan  Ex_ch12P6RSNMDA

        setfield     Ex_ch12P6RSNMDA     \
        Ek           {EGlu}         \
        tau2         { 0.67e-3 }    \ // sec
        tau1         { 130.0e-3 }   \ // sec
        gmax         {GGlu}           // Siemens

    create Mg_block Ex_ch12P6RSNMDA/block
        setfield         Ex_ch12P6RSNMDA/block \
        CMg              {CMg}            \
        KMg_A            {1.0/eta}        \
        KMg_B            {1.0/gamma}      

    addmsg Ex_ch12P6RSNMDA Ex_ch12P6RSNMDA/block CHANNEL Gk Ek

    addmsg Ex_ch12P6RSNMDA/block . CHANNEL Gk Ek

    addmsg . Ex_ch12P6RSNMDA/block VOLTAGE Vm

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

    // addmsg . Ex_ch12P6RSNMDA VOLTAGE Vm

end

function make_Inh_ch12C23FSGABAa

//GABA_A synapse for C23FS - P6RS

	if ({exists Inh_ch12C23FSGABAa})
		return
	end

	create		synchan	Inh_ch12C23FSGABAa
    	setfield	        Inh_ch12C23FSGABAa \
	Ek			{ EGABA } \
	tau1		{ 6.0e-3 } \	// sec
    tau2        { 1.0e-12 } \    // sec
	gmax		{GGABA}		// Siemens
end

function make_Inh_ch12C5FSGABAa

//GABA_A synapse for C5FS - P6RS

	if ({exists Inh_ch12C5FSGABAa})
		return
	end

	create		synchan	Inh_ch12C5FSGABAa
    	setfield	        Inh_ch12C5FSGABAa \
	Ek			{ EGABA } \
	tau1		{ 6.0e-3 } \	// sec
    tau2        { 1.0e-12 } \    // sec
	gmax		{GGABA}		// Siemens
end

function make_Ex_ch12ST4RSAMPA

// AMPA synapse for ST4RS - P6RS

	if ({exists Ex_ch12ST4RSAMPA})
		return
	end

	create		synchan	Ex_ch12ST4RSAMPA
    	setfield	        Ex_ch12ST4RSAMPA \
		Ek			{EGlu} \
		tau1		{ 2.0e-3 } \	// sec
		tau2		{ 2.0e-3 } \ 	// sec
		gmax		{GGlu} // Siemens
end

function make_Ex_ch12ST4RSNMDA

// NMDA synapse for ST4RS - P6RS

    if ({exists Ex_ch12ST4RSNMDA})
        return
    end

    create  synchan  Ex_ch12ST4RSNMDA

        setfield     Ex_ch12ST4RSNMDA     \
        Ek           {EGlu}         \
        tau2         { 0.67e-3 }    \ // sec
        tau1         { 130.0e-3 }   \ // sec
        gmax         {GGlu}           // Siemens

    create Mg_block Ex_ch12ST4RSNMDA/block
        setfield         Ex_ch12ST4RSNMDA/block \
        CMg              {CMg}            \
        KMg_A            {1.0/eta}        \
        KMg_B            {1.0/gamma}      

    addmsg Ex_ch12ST4RSNMDA Ex_ch12ST4RSNMDA/block CHANNEL Gk Ek

    addmsg Ex_ch12ST4RSNMDA/block . CHANNEL Gk Ek

    addmsg . Ex_ch12ST4RSNMDA/block VOLTAGE Vm

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

    // addmsg . Ex_ch12ST4RSNMDA VOLTAGE Vm

end

function make_Inh_ch12I23LTSGABAa

//GABA_A synapse for I23LTS - P6RS

	if ({exists Inh_ch12I23LTSGABAa})
		return
	end

	create		synchan	Inh_ch12I23LTSGABAa
    	setfield	        Inh_ch12I23LTSGABAa \
	Ek			{ EGABA } \
	tau1		{ 20.0e-3 } \	// sec
    tau2        { 1.0e-12 } \    // sec
	gmax		{GGABA}		// Siemens
end

function make_Inh_ch12I5LTSGABAa

//GABA_A synapse for I5LTS - P6RS

	if ({exists Inh_ch12I5LTSGABAa})
		return
	end

	create		synchan	Inh_ch12I5LTSGABAa
    	setfield	        Inh_ch12I5LTSGABAa \
	Ek			{ EGABA } \
	tau1		{ 20.0e-3 } \	// sec
    tau2        { 1.0e-12 } \    // sec
	gmax		{GGABA}		// Siemens
end

function make_Ex_ch12TCRAMPA

// AMPA synapse for TCR - P6RS

	if ({exists Ex_ch12TCRAMPA})
		return
	end

	create		synchan	Ex_ch12TCRAMPA
    	setfield	        Ex_ch12TCRAMPA \
		Ek			{EGlu} \
		tau1		{ 2.0e-3 } \	// sec
		tau2		{ 2.0e-3 } \ 	// sec
		gmax		{GGlu} // Siemens
end

function make_Ex_ch12TCRNMDA

// NMDA synapse for TCR - P6RS

    if ({exists Ex_ch12TCRNMDA})
        return
    end

    create  synchan  Ex_ch12TCRNMDA

        setfield     Ex_ch12TCRNMDA     \
        Ek           {EGlu}         \
        tau2         { 0.67e-3 }    \ // sec
        tau1         { 130.0e-3 }   \ // sec
        gmax         {GGlu}           // Siemens

    create Mg_block Ex_ch12TCRNMDA/block
        setfield         Ex_ch12TCRNMDA/block \
        CMg              {CMg}            \
        KMg_A            {1.0/eta}        \
        KMg_B            {1.0/gamma}      

    addmsg Ex_ch12TCRNMDA Ex_ch12TCRNMDA/block CHANNEL Gk Ek

    addmsg Ex_ch12TCRNMDA/block . CHANNEL Gk Ek

    addmsg . Ex_ch12TCRNMDA/block VOLTAGE Vm

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

    // addmsg . Ex_ch12TCRNMDA VOLTAGE Vm

end

function make_Ex_ch12TCRAMPA

// AMPA synapse for TCR - P6RS

	if ({exists Ex_ch12TCRAMPA})
		return
	end

	create		synchan	Ex_ch12TCRAMPA
    	setfield	        Ex_ch12TCRAMPA \
		Ek			{EGlu} \
		tau1		{ 2.0e-3 } \	// sec
		tau2		{ 2.0e-3 } \ 	// sec
		gmax		{GGlu} // Siemens
end

function make_Ex_ch12TCRNMDA

// NMDA synapse for TCR - P6RS

    if ({exists Ex_ch12TCRNMDA})
        return
    end

    create  synchan  Ex_ch12TCRNMDA

        setfield     Ex_ch12TCRNMDA     \
        Ek           {EGlu}         \
        tau2         { 0.67e-3 }    \ // sec
        tau1         { 130.0e-3 }   \ // sec
        gmax         {GGlu}           // Siemens

    create Mg_block Ex_ch12TCRNMDA/block
        setfield         Ex_ch12TCRNMDA/block \
        CMg              {CMg}            \
        KMg_A            {1.0/eta}        \
        KMg_B            {1.0/gamma}      

    addmsg Ex_ch12TCRNMDA Ex_ch12TCRNMDA/block CHANNEL Gk Ek

    addmsg Ex_ch12TCRNMDA/block . CHANNEL Gk Ek

    addmsg . Ex_ch12TCRNMDA/block VOLTAGE Vm

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

    // addmsg . Ex_ch12TCRNMDA VOLTAGE Vm

end

function make_Ex_ch12P23FRBAMPA

// AMPA synapse for P23FRB - P6RS

	if ({exists Ex_ch12P23FRBAMPA})
		return
	end

	create		synchan	Ex_ch12P23FRBAMPA
    	setfield	        Ex_ch12P23FRBAMPA \
		Ek			{EGlu} \
		tau1		{ 2.0e-3 } \	// sec
		tau2		{ 2.0e-3 } \ 	// sec
		gmax		{GGlu} // Siemens
end

function make_Ex_ch12P23FRBNMDA

// NMDA synapse for P23FRB - P6RS

    if ({exists Ex_ch12P23FRBNMDA})
        return
    end

    create  synchan  Ex_ch12P23FRBNMDA

        setfield     Ex_ch12P23FRBNMDA     \
        Ek           {EGlu}         \
        tau2         { 0.67e-3 }    \ // sec
        tau1         { 130.0e-3 }   \ // sec
        gmax         {GGlu}           // Siemens

    create Mg_block Ex_ch12P23FRBNMDA/block
        setfield         Ex_ch12P23FRBNMDA/block \
        CMg              {CMg}            \
        KMg_A            {1.0/eta}        \
        KMg_B            {1.0/gamma}      

    addmsg Ex_ch12P23FRBNMDA Ex_ch12P23FRBNMDA/block CHANNEL Gk Ek

    addmsg Ex_ch12P23FRBNMDA/block . CHANNEL Gk Ek

    addmsg . Ex_ch12P23FRBNMDA/block VOLTAGE Vm

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

    // addmsg . Ex_ch12P23FRBNMDA VOLTAGE Vm

end

function make_Ex_ch12P5RSAMPA

// AMPA synapse for P5RS - P6RS

	if ({exists Ex_ch12P5RSAMPA})
		return
	end

	create		synchan	Ex_ch12P5RSAMPA
    	setfield	        Ex_ch12P5RSAMPA \
		Ek			{EGlu} \
		tau1		{ 2.0e-3 } \	// sec
		tau2		{ 2.0e-3 } \ 	// sec
		gmax		{GGlu} // Siemens
end

function make_Ex_ch12P5RSNMDA

// NMDA synapse for P5RS - P6RS

    if ({exists Ex_ch12P5RSNMDA})
        return
    end

    create  synchan  Ex_ch12P5RSNMDA

        setfield     Ex_ch12P5RSNMDA     \
        Ek           {EGlu}         \
        tau2         { 0.67e-3 }    \ // sec
        tau1         { 130.0e-3 }   \ // sec
        gmax         {GGlu}           // Siemens

    create Mg_block Ex_ch12P5RSNMDA/block
        setfield         Ex_ch12P5RSNMDA/block \
        CMg              {CMg}            \
        KMg_A            {1.0/eta}        \
        KMg_B            {1.0/gamma}      

    addmsg Ex_ch12P5RSNMDA Ex_ch12P5RSNMDA/block CHANNEL Gk Ek

    addmsg Ex_ch12P5RSNMDA/block . CHANNEL Gk Ek

    addmsg . Ex_ch12P5RSNMDA/block VOLTAGE Vm

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

    // addmsg . Ex_ch12P5RSNMDA VOLTAGE Vm

end

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