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_ch23P23RSAMPA

// AMPA synapse for P23RS - P5RS

	if ({exists Ex_ch23P23RSAMPA})
		return
	end

	create		synchan	Ex_ch23P23RSAMPA
    	setfield	        Ex_ch23P23RSAMPA \
		Ek			{EGlu} \
		tau1		{ 2.0e-3 } \	// sec
		tau2		{ 2.0e-3 } \ 	// sec
		gmax		{GGlu} // Siemens
end

function make_Ex_ch23P23RSNMDA

// NMDA synapse for P23RS - P5RS

    if ({exists Ex_ch23P23RSNMDA})
        return
    end

    create  synchan  Ex_ch23P23RSNMDA

        setfield     Ex_ch23P23RSNMDA     \
        Ek           {EGlu}         \
        tau2         { 0.67e-3 }    \ // sec
        tau1         { 130.0e-3 }   \ // sec
        gmax         {GGlu}           // Siemens

    create Mg_block Ex_ch23P23RSNMDA/block
        setfield         Ex_ch23P23RSNMDA/block \
        CMg              {CMg}            \
        KMg_A            {1.0/eta}        \
        KMg_B            {1.0/gamma}      

    addmsg Ex_ch23P23RSNMDA Ex_ch23P23RSNMDA/block CHANNEL Gk Ek

    addmsg Ex_ch23P23RSNMDA/block . CHANNEL Gk Ek

    addmsg . Ex_ch23P23RSNMDA/block VOLTAGE Vm

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

    // addmsg . Ex_ch23P23RSNMDA VOLTAGE Vm

end


function make_Inh_ch23B23FSGABAa

//GABA_A synapse for B23FS - P5RS

	if ({exists Inh_ch23B23FSGABAa})
		return
	end

	create		synchan	Inh_ch23B23FSGABAa
    	setfield	        Inh_ch23B23FSGABAa \
	Ek			{ EGABA } \
	tau1		{ 6.0e-3 } \	// sec
    tau2        { 1.0e-12 } \    // sec
	gmax		{GGABA}		// Siemens
end

function make_Ex_ch23P5IBAMPA

// AMPA synapse for P5IB - P5RS

	if ({exists Ex_ch23P5IBAMPA})
		return
	end

	create		synchan	Ex_ch23P5IBAMPA
    	setfield	        Ex_ch23P5IBAMPA \
		Ek			{EGlu} \
		tau1		{ 2.0e-3 } \	// sec
		tau2		{ 2.0e-3 } \ 	// sec
		gmax		{GGlu} // Siemens
end

function make_Ex_ch23P5IBNMDA

// NMDA synapse for P5IB - P5RS

    if ({exists Ex_ch23P5IBNMDA})
        return
    end

    create  synchan  Ex_ch23P5IBNMDA

        setfield     Ex_ch23P5IBNMDA     \
        Ek           {EGlu}         \
        tau2         { 0.67e-3 }    \ // sec
        tau1         { 130.0e-3 }   \ // sec
        gmax         {GGlu}           // Siemens

    create Mg_block Ex_ch23P5IBNMDA/block
        setfield         Ex_ch23P5IBNMDA/block \
        CMg              {CMg}            \
        KMg_A            {1.0/eta}        \
        KMg_B            {1.0/gamma}      

    addmsg Ex_ch23P5IBNMDA Ex_ch23P5IBNMDA/block CHANNEL Gk Ek

    addmsg Ex_ch23P5IBNMDA/block . CHANNEL Gk Ek

    addmsg . Ex_ch23P5IBNMDA/block VOLTAGE Vm

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

    // addmsg . Ex_ch23P5IBNMDA VOLTAGE Vm

end

function make_Inh_ch23B5FSGABAa

//GABA_A synapse for B5FS - P5RS

	if ({exists Inh_ch23B5FSGABAa})
		return
	end

	create		synchan	Inh_ch23B5FSGABAa
    	setfield	        Inh_ch23B5FSGABAa \
	Ek			{ EGABA } \
	tau1		{ 6.0e-3 } \	// sec
    tau2        { 1.0e-12 } \    // sec
	gmax		{GGABA}		// Siemens
end

function make_Ex_ch23P6RSAMPA

// AMPA synapse for P6RS - P5RS

	if ({exists Ex_ch23P6RSAMPA})
		return
	end

	create		synchan	Ex_ch23P6RSAMPA
    	setfield	        Ex_ch23P6RSAMPA \
		Ek			{EGlu} \
		tau1		{ 2.0e-3 } \	// sec
		tau2		{ 2.0e-3 } \ 	// sec
		gmax		{GGlu} // Siemens
end

function make_Ex_ch23P6RSNMDA

// NMDA synapse for P6RS - P5RS

    if ({exists Ex_ch23P6RSNMDA})
        return
    end

    create  synchan  Ex_ch23P6RSNMDA

        setfield     Ex_ch23P6RSNMDA     \
        Ek           {EGlu}         \
        tau2         { 0.67e-3 }    \ // sec
        tau1         { 130.0e-3 }   \ // sec
        gmax         {GGlu}           // Siemens

    create Mg_block Ex_ch23P6RSNMDA/block
        setfield         Ex_ch23P6RSNMDA/block \
        CMg              {CMg}            \
        KMg_A            {1.0/eta}        \
        KMg_B            {1.0/gamma}      

    addmsg Ex_ch23P6RSNMDA Ex_ch23P6RSNMDA/block CHANNEL Gk Ek

    addmsg Ex_ch23P6RSNMDA/block . CHANNEL Gk Ek

    addmsg . Ex_ch23P6RSNMDA/block VOLTAGE Vm

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

    // addmsg . Ex_ch23P6RSNMDA VOLTAGE Vm

end

function make_Inh_ch23C23FSGABAa

//GABA_A synapse for C23FS - P5RS

	if ({exists Inh_ch23C23FSGABAa})
		return
	end

	create		synchan	Inh_ch23C23FSGABAa
    	setfield	        Inh_ch23C23FSGABAa \
	Ek			{ EGABA } \
	tau1		{ 6.0e-3 } \	// sec
    tau2        { 1.0e-12 } \    // sec
	gmax		{GGABA}		// Siemens
end

function make_Inh_ch23C5FSGABAa

//GABA_A synapse for C5FS - P5RS

	if ({exists Inh_ch23C5FSGABAa})
		return
	end

	create		synchan	Inh_ch23C5FSGABAa
    	setfield	        Inh_ch23C5FSGABAa \
	Ek			{ EGABA } \
	tau1		{ 6.0e-3 } \	// sec
    tau2        { 1.0e-12 } \    // sec
	gmax		{GGABA}		// Siemens
end

function make_Ex_ch23ST4RSAMPA

// AMPA synapse for ST4RS - P5RS

	if ({exists Ex_ch23ST4RSAMPA})
		return
	end

	create		synchan	Ex_ch23ST4RSAMPA
    	setfield	        Ex_ch23ST4RSAMPA \
		Ek			{EGlu} \
		tau1		{ 2.0e-3 } \	// sec
		tau2		{ 2.0e-3 } \ 	// sec
		gmax		{GGlu} // Siemens
end

function make_Ex_ch23ST4RSNMDA

// NMDA synapse for ST4RS - P5RS

    if ({exists Ex_ch23ST4RSNMDA})
        return
    end

    create  synchan  Ex_ch23ST4RSNMDA

        setfield     Ex_ch23ST4RSNMDA     \
        Ek           {EGlu}         \
        tau2         { 0.67e-3 }    \ // sec
        tau1         { 130.0e-3 }   \ // sec
        gmax         {GGlu}           // Siemens

    create Mg_block Ex_ch23ST4RSNMDA/block
        setfield         Ex_ch23ST4RSNMDA/block \
        CMg              {CMg}            \
        KMg_A            {1.0/eta}        \
        KMg_B            {1.0/gamma}      

    addmsg Ex_ch23ST4RSNMDA Ex_ch23ST4RSNMDA/block CHANNEL Gk Ek

    addmsg Ex_ch23ST4RSNMDA/block . CHANNEL Gk Ek

    addmsg . Ex_ch23ST4RSNMDA/block VOLTAGE Vm

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

    // addmsg . Ex_ch23ST4RSNMDA VOLTAGE Vm

end

function make_Inh_ch23I23LTSGABAa

//GABA_A synapse for I23LTS - P5RS

	if ({exists Inh_ch23I23LTSGABAa})
		return
	end

	create		synchan	Inh_ch23I23LTSGABAa
    	setfield	        Inh_ch23I23LTSGABAa \
	Ek			{ EGABA } \
	tau1		{ 20.0e-3 } \	// sec
    tau2        { 1.0e-12 } \    // sec
	gmax		{GGABA}		// Siemens
end

function make_Inh_ch23I5LTSGABAa

//GABA_A synapse for I5LTS - P5RS

	if ({exists Inh_ch23I5LTSGABAa})
		return
	end

	create		synchan	Inh_ch23I5LTSGABAa
    	setfield	        Inh_ch23I5LTSGABAa \
	Ek			{ EGABA } \
	tau1		{ 20.0e-3 } \	// sec
    tau2        { 1.0e-12 } \    // sec
	gmax		{GGABA}		// Siemens
end

function make_Ex_ch23TCRAMPA

// AMPA synapse for TCR - P5RS

	if ({exists Ex_ch23TCRAMPA})
		return
	end

	create		synchan	Ex_ch23TCRAMPA
    	setfield	        Ex_ch23TCRAMPA \
		Ek			{EGlu} \
		tau1		{ 2.0e-3 } \	// sec
		tau2		{ 2.0e-3 } \ 	// sec
		gmax		{GGlu} // Siemens
end

function make_Ex_ch23TCRNMDA

// NMDA synapse for TCR - P5RS

    if ({exists Ex_ch23TCRNMDA})
        return
    end

    create  synchan  Ex_ch23TCRNMDA

        setfield     Ex_ch23TCRNMDA     \
        Ek           {EGlu}         \
        tau2         { 0.67e-3 }    \ // sec
        tau1         { 130.0e-3 }   \ // sec
        gmax         {GGlu}           // Siemens

    create Mg_block Ex_ch23TCRNMDA/block
        setfield         Ex_ch23TCRNMDA/block \
        CMg              {CMg}            \
        KMg_A            {1.0/eta}        \
        KMg_B            {1.0/gamma}      

    addmsg Ex_ch23TCRNMDA Ex_ch23TCRNMDA/block CHANNEL Gk Ek

    addmsg Ex_ch23TCRNMDA/block . CHANNEL Gk Ek

    addmsg . Ex_ch23TCRNMDA/block VOLTAGE Vm

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

    // addmsg . Ex_ch23TCRNMDA VOLTAGE Vm

end

function make_Ex_ch23TCRAMPA

// AMPA synapse for TCR - P5RS

	if ({exists Ex_ch23TCRAMPA})
		return
	end

	create		synchan	Ex_ch23TCRAMPA
    	setfield	        Ex_ch23TCRAMPA \
		Ek			{EGlu} \
		tau1		{ 2.0e-3 } \	// sec
		tau2		{ 2.0e-3 } \ 	// sec
		gmax		{GGlu} // Siemens
end

function make_Ex_ch23TCRNMDA

// NMDA synapse for TCR - P5RS

    if ({exists Ex_ch23TCRNMDA})
        return
    end

    create  synchan  Ex_ch23TCRNMDA

        setfield     Ex_ch23TCRNMDA     \
        Ek           {EGlu}         \
        tau2         { 0.67e-3 }    \ // sec
        tau1         { 130.0e-3 }   \ // sec
        gmax         {GGlu}           // Siemens

    create Mg_block Ex_ch23TCRNMDA/block
        setfield         Ex_ch23TCRNMDA/block \
        CMg              {CMg}            \
        KMg_A            {1.0/eta}        \
        KMg_B            {1.0/gamma}      

    addmsg Ex_ch23TCRNMDA Ex_ch23TCRNMDA/block CHANNEL Gk Ek

    addmsg Ex_ch23TCRNMDA/block . CHANNEL Gk Ek

    addmsg . Ex_ch23TCRNMDA/block VOLTAGE Vm

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

    // addmsg . Ex_ch23TCRNMDA VOLTAGE Vm

end

function make_Ex_ch23P23FRBAMPA

// AMPA synapse for P23FRB - P5RS

	if ({exists Ex_ch23P23FRBAMPA})
		return
	end

	create		synchan	Ex_ch23P23FRBAMPA
    	setfield	        Ex_ch23P23FRBAMPA \
		Ek			{EGlu} \
		tau1		{ 2.0e-3 } \	// sec
		tau2		{ 2.0e-3 } \ 	// sec
		gmax		{GGlu} // Siemens
end

function make_Ex_ch23P23FRBNMDA

// NMDA synapse for P23FRB - P5RS

    if ({exists Ex_ch23P23FRBNMDA})
        return
    end

    create  synchan  Ex_ch23P23FRBNMDA

        setfield     Ex_ch23P23FRBNMDA     \
        Ek           {EGlu}         \
        tau2         { 0.67e-3 }    \ // sec
        tau1         { 130.0e-3 }   \ // sec
        gmax         {GGlu}           // Siemens

    create Mg_block Ex_ch23P23FRBNMDA/block
        setfield         Ex_ch23P23FRBNMDA/block \
        CMg              {CMg}            \
        KMg_A            {1.0/eta}        \
        KMg_B            {1.0/gamma}      

    addmsg Ex_ch23P23FRBNMDA Ex_ch23P23FRBNMDA/block CHANNEL Gk Ek

    addmsg Ex_ch23P23FRBNMDA/block . CHANNEL Gk Ek

    addmsg . Ex_ch23P23FRBNMDA/block VOLTAGE Vm

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

    // addmsg . Ex_ch23P23FRBNMDA VOLTAGE Vm

end

function make_Ex_ch23P5RSAMPA

// AMPA synapse for P5RS - P5RS

	if ({exists Ex_ch23P5RSAMPA})
		return
	end

	create		synchan	Ex_ch23P5RSAMPA
    	setfield	        Ex_ch23P5RSAMPA \
		Ek			{EGlu} \
		tau1		{ 2.0e-3 } \	// sec
		tau2		{ 2.0e-3 } \ 	// sec
		gmax		{GGlu} // Siemens
end

function make_Ex_ch23P5RSNMDA

// NMDA synapse for P5RS - P5RS

    if ({exists Ex_ch23P5RSNMDA})
        return
    end

    create  synchan  Ex_ch23P5RSNMDA

        setfield     Ex_ch23P5RSNMDA     \
        Ek           {EGlu}         \
        tau2         { 0.67e-3 }    \ // sec
        tau1         { 130.0e-3 }   \ // sec
        gmax         {GGlu}           // Siemens

    create Mg_block Ex_ch23P5RSNMDA/block
        setfield         Ex_ch23P5RSNMDA/block \
        CMg              {CMg}            \
        KMg_A            {1.0/eta}        \
        KMg_B            {1.0/gamma}      

    addmsg Ex_ch23P5RSNMDA Ex_ch23P5RSNMDA/block CHANNEL Gk Ek

    addmsg Ex_ch23P5RSNMDA/block . CHANNEL Gk Ek

    addmsg . Ex_ch23P5RSNMDA/block VOLTAGE Vm

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

    // addmsg . Ex_ch23P5RSNMDA VOLTAGE Vm

end

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