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_ch17P23RSAMPA

// AMPA synapse for P23RS - ST4RS

	if ({exists Ex_ch17P23RSAMPA})
		return
	end

	create		synchan	Ex_ch17P23RSAMPA
    	setfield	        Ex_ch17P23RSAMPA \
		Ek			{EGlu} \
		tau1		{ 2.0e-3 } \	// sec
		tau2		{ 2.0e-3 } \ 	// sec
		gmax		{GGlu} // Siemens
end

function make_Ex_ch17P23RSNMDA

// NMDA synapse for P23RS - ST4RS

    if ({exists Ex_ch17P23RSNMDA})
        return
    end

    create  synchan  Ex_ch17P23RSNMDA

        setfield     Ex_ch17P23RSNMDA     \
        Ek           {EGlu}         \
        tau2         { 0.67e-3 }    \ // sec
        tau1         { 130.0e-3 }   \ // sec
        gmax         {GGlu}           // Siemens

    create Mg_block Ex_ch17P23RSNMDA/block
        setfield         Ex_ch17P23RSNMDA/block \
        CMg              {CMg}            \
        KMg_A            {1.0/eta}        \
        KMg_B            {1.0/gamma}      

    addmsg Ex_ch17P23RSNMDA Ex_ch17P23RSNMDA/block CHANNEL Gk Ek

    addmsg Ex_ch17P23RSNMDA/block . CHANNEL Gk Ek

    addmsg . Ex_ch17P23RSNMDA/block VOLTAGE Vm

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

    // addmsg . Ex_ch17P23RSNMDA VOLTAGE Vm

end

function make_Inh_ch17B23FSGABAa

//GABA_A synapse for B23FS - ST4RS

	if ({exists Inh_ch17B23FSGABAa})
		return
	end

	create		synchan	Inh_ch17B23FSGABAa
    	setfield	        Inh_ch17B23FSGABAa \
	Ek			{ EGABA } \
	tau1		{ 6.0e-3 } \	// sec
    tau2        { 1.0e-12 } \    // sec
	gmax		{GGABA}		// Siemens
end

function make_Ex_ch17P5IBAMPA

// AMPA synapse for P5IB - ST4RS

	if ({exists Ex_ch17P5IBAMPA})
		return
	end

	create		synchan	Ex_ch17P5IBAMPA
    	setfield	        Ex_ch17P5IBAMPA \
		Ek			{EGlu} \
		tau1		{ 2.0e-3 } \	// sec
		tau2		{ 2.0e-3 } \ 	// sec
		gmax		{GGlu} // Siemens
end

function make_Ex_ch17P5IBNMDA

// NMDA synapse for P5IB - ST4RS

    if ({exists Ex_ch17P5IBNMDA})
        return
    end

    create  synchan  Ex_ch17P5IBNMDA

        setfield     Ex_ch17P5IBNMDA     \
        Ek           {EGlu}         \
        tau2         { 0.67e-3 }    \ // sec
        tau1         { 130.0e-3 }   \ // sec
        gmax         {GGlu}           // Siemens

    create Mg_block Ex_ch17P5IBNMDA/block
        setfield         Ex_ch17P5IBNMDA/block \
        CMg              {CMg}            \
        KMg_A            {1.0/eta}        \
        KMg_B            {1.0/gamma}      

    addmsg Ex_ch17P5IBNMDA Ex_ch17P5IBNMDA/block CHANNEL Gk Ek

    addmsg Ex_ch17P5IBNMDA/block . CHANNEL Gk Ek

    addmsg . Ex_ch17P5IBNMDA/block VOLTAGE Vm

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

    // addmsg . Ex_ch17P5IBNMDA VOLTAGE Vm

end

function make_Inh_ch17B5FSGABAa

//GABA_A synapse for B5FS - ST4RS

	if ({exists Inh_ch17B5FSGABAa})
		return
	end

	create		synchan	Inh_ch17B5FSGABAa
    	setfield	        Inh_ch17B5FSGABAa \
	Ek			{ EGABA } \
	tau1		{ 6.0e-3 } \	// sec
    tau2        { 1.0e-12 } \    // sec
	gmax		{GGABA}		// Siemens
end

function make_Ex_ch17P6RSAMPA

// AMPA synapse for P6RS - ST4RS

	if ({exists Ex_ch17P6RSAMPA})
		return
	end

	create		synchan	Ex_ch17P6RSAMPA
    	setfield	        Ex_ch17P6RSAMPA \
		Ek			{EGlu} \
		tau1		{ 2.0e-3 } \	// sec
		tau2		{ 2.0e-3 } \ 	// sec
		gmax		{GGlu} // Siemens
end

function make_Ex_ch17P6RSNMDA

// NMDA synapse for P6RS - ST4RS

    if ({exists Ex_ch17P6RSNMDA})
        return
    end

    create  synchan  Ex_ch17P6RSNMDA

        setfield     Ex_ch17P6RSNMDA     \
        Ek           {EGlu}         \
        tau2         { 0.67e-3 }    \ // sec
        tau1         { 130.0e-3 }   \ // sec
        gmax         {GGlu}           // Siemens

    create Mg_block Ex_ch17P6RSNMDA/block
        setfield         Ex_ch17P6RSNMDA/block \
        CMg              {CMg}            \
        KMg_A            {1.0/eta}        \
        KMg_B            {1.0/gamma}      

    addmsg Ex_ch17P6RSNMDA Ex_ch17P6RSNMDA/block CHANNEL Gk Ek

    addmsg Ex_ch17P6RSNMDA/block . CHANNEL Gk Ek

    addmsg . Ex_ch17P6RSNMDA/block VOLTAGE Vm

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

    // addmsg . Ex_ch17P6RSNMDA VOLTAGE Vm

end

function make_Inh_ch17C23FSGABAa

//GABA_A synapse for C23FS - ST4RS

	if ({exists Inh_ch17C23FSGABAa})
		return
	end

	create		synchan	Inh_ch17C23FSGABAa
    	setfield	        Inh_ch17C23FSGABAa \
	Ek			{ EGABA } \
	tau1		{ 6.0e-3 } \	// sec
    tau2        { 1.0e-12 } \    // sec
	gmax		{GGABA}		// Siemens
end

function make_Inh_ch17C5FSGABAa

//GABA_A synapse for C5FS - ST4RS

	if ({exists Inh_ch17C5FSGABAa})
		return
	end

	create		synchan	Inh_ch17C5FSGABAa
    	setfield	        Inh_ch17C5FSGABAa \
	Ek			{ EGABA } \
	tau1		{ 6.0e-3 } \	// sec
    tau2        { 1.0e-12 } \    // sec
	gmax		{GGABA}		// Siemens
end

function make_Ex_ch17ST4RSAMPA

// AMPA synapse for ST4RS - ST4RS

	if ({exists Ex_ch17ST4RSAMPA})
		return
	end

	create		synchan	Ex_ch17ST4RSAMPA
    	setfield	        Ex_ch17ST4RSAMPA \
		Ek			{EGlu} \
		tau1		{ 2.0e-3 } \	// sec
		tau2		{ 2.0e-3 } \ 	// sec
		gmax		{GGlu} // Siemens
end

function make_Ex_ch17ST4RSNMDA

// NMDA synapse for ST4RS - ST4RS

    if ({exists Ex_ch17ST4RSNMDA})
        return
    end

    create  synchan  Ex_ch17ST4RSNMDA

        setfield     Ex_ch17ST4RSNMDA     \
        Ek           {EGlu}         \
        tau2         { 0.67e-3 }    \ // sec
        tau1         { 130.0e-3 }   \ // sec
        gmax         {GGlu}           // Siemens

    create Mg_block Ex_ch17ST4RSNMDA/block
        setfield         Ex_ch17ST4RSNMDA/block \
        CMg              {CMg}            \
        KMg_A            {1.0/eta}        \
        KMg_B            {1.0/gamma}      

    addmsg Ex_ch17ST4RSNMDA Ex_ch17ST4RSNMDA/block CHANNEL Gk Ek

    addmsg Ex_ch17ST4RSNMDA/block . CHANNEL Gk Ek

    addmsg . Ex_ch17ST4RSNMDA/block VOLTAGE Vm

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

    // addmsg . Ex_ch17ST4RSNMDA VOLTAGE Vm

end

function make_Inh_ch17I23LTSGABAa

//GABA_A synapse for I23LTS - ST4RS

	if ({exists Inh_ch17I23LTSGABAa})
		return
	end

	create		synchan	Inh_ch17I23LTSGABAa
    	setfield	        Inh_ch17I23LTSGABAa \
	Ek			{ EGABA } \
	tau1		{ 20.0e-3 } \	// sec
    tau2        { 1.0e-12 } \    // sec
	gmax		{GGABA}		// Siemens
end

function make_Inh_ch17I5LTSGABAa

//GABA_A synapse for I5LTS - ST4RS

	if ({exists Inh_ch17I5LTSGABAa})
		return
	end

	create		synchan	Inh_ch17I5LTSGABAa
    	setfield	        Inh_ch17I5LTSGABAa \
	Ek			{ EGABA } \
	tau1		{ 20.0e-3 } \	// sec
    tau2        { 1.0e-12 } \    // sec
	gmax		{GGABA}		// Siemens
end

function make_Ex_ch17TCRAMPA

// AMPA synapse for TCR - ST4RS

	if ({exists Ex_ch17TCRAMPA})
		return
	end

	create		synchan	Ex_ch17TCRAMPA
    	setfield	        Ex_ch17TCRAMPA \
		Ek			{EGlu} \
		tau1		{ 2.0e-3 } \	// sec
		tau2		{ 2.0e-3 } \ 	// sec
		gmax		{GGlu} // Siemens
end

function make_Ex_ch17TCRNMDA

// NMDA synapse for TCR - ST4RS

    if ({exists Ex_ch17TCRNMDA})
        return
    end

    create  synchan  Ex_ch17TCRNMDA

        setfield     Ex_ch17TCRNMDA     \
        Ek           {EGlu}         \
        tau2         { 0.67e-3 }    \ // sec
        tau1         { 130.0e-3 }   \ // sec
        gmax         {GGlu}           // Siemens

    create Mg_block Ex_ch17TCRNMDA/block
        setfield         Ex_ch17TCRNMDA/block \
        CMg              {CMg}            \
        KMg_A            {1.0/eta}        \
        KMg_B            {1.0/gamma}      

    addmsg Ex_ch17TCRNMDA Ex_ch17TCRNMDA/block CHANNEL Gk Ek

    addmsg Ex_ch17TCRNMDA/block . CHANNEL Gk Ek

    addmsg . Ex_ch17TCRNMDA/block VOLTAGE Vm

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

    // addmsg . Ex_ch17TCRNMDA VOLTAGE Vm

end

function make_Ex_ch17TCRAMPA

// AMPA synapse for TCR - ST4RS

	if ({exists Ex_ch17TCRAMPA})
		return
	end

	create		synchan	Ex_ch17TCRAMPA
    	setfield	        Ex_ch17TCRAMPA \
		Ek			{EGlu} \
		tau1		{ 2.0e-3 } \	// sec
		tau2		{ 2.0e-3 } \ 	// sec
		gmax		{GGlu} // Siemens
end

function make_Ex_ch17TCRNMDA

// NMDA synapse for TCR - ST4RS

    if ({exists Ex_ch17TCRNMDA})
        return
    end

    create  synchan  Ex_ch17TCRNMDA

        setfield     Ex_ch17TCRNMDA     \
        Ek           {EGlu}         \
        tau2         { 0.67e-3 }    \ // sec
        tau1         { 130.0e-3 }   \ // sec
        gmax         {GGlu}           // Siemens

    create Mg_block Ex_ch17TCRNMDA/block
        setfield         Ex_ch17TCRNMDA/block \
        CMg              {CMg}            \
        KMg_A            {1.0/eta}        \
        KMg_B            {1.0/gamma}      

    addmsg Ex_ch17TCRNMDA Ex_ch17TCRNMDA/block CHANNEL Gk Ek

    addmsg Ex_ch17TCRNMDA/block . CHANNEL Gk Ek

    addmsg . Ex_ch17TCRNMDA/block VOLTAGE Vm

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

    // addmsg . Ex_ch17TCRNMDA VOLTAGE Vm

end

function make_Ex_ch17P23FRBAMPA

// AMPA synapse for P23FRB - ST4RS

	if ({exists Ex_ch17P23FRBAMPA})
		return
	end

	create		synchan	Ex_ch17P23FRBAMPA
    	setfield	        Ex_ch17P23FRBAMPA \
		Ek			{EGlu} \
		tau1		{ 2.0e-3 } \	// sec
		tau2		{ 2.0e-3 } \ 	// sec
		gmax		{GGlu} // Siemens
end

function make_Ex_ch17P23FRBNMDA

// NMDA synapse for P23FRB - ST4RS

    if ({exists Ex_ch17P23FRBNMDA})
        return
    end

    create  synchan  Ex_ch17P23FRBNMDA

        setfield     Ex_ch17P23FRBNMDA     \
        Ek           {EGlu}         \
        tau2         { 0.67e-3 }    \ // sec
        tau1         { 130.0e-3 }   \ // sec
        gmax         {GGlu}           // Siemens

    create Mg_block Ex_ch17P23FRBNMDA/block
        setfield         Ex_ch17P23FRBNMDA/block \
        CMg              {CMg}            \
        KMg_A            {1.0/eta}        \
        KMg_B            {1.0/gamma}      

    addmsg Ex_ch17P23FRBNMDA Ex_ch17P23FRBNMDA/block CHANNEL Gk Ek

    addmsg Ex_ch17P23FRBNMDA/block . CHANNEL Gk Ek

    addmsg . Ex_ch17P23FRBNMDA/block VOLTAGE Vm

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

    // addmsg . Ex_ch17P23FRBNMDA VOLTAGE Vm

end

function make_Ex_ch17P5RSAMPA

// AMPA synapse for P5RS - ST4RS

	if ({exists Ex_ch17P5RSAMPA})
		return
	end

	create		synchan	Ex_ch17P5RSAMPA
    	setfield	        Ex_ch17P5RSAMPA \
		Ek			{EGlu} \
		tau1		{ 2.0e-3 } \	// sec
		tau2		{ 2.0e-3 } \ 	// sec
		gmax		{GGlu} // Siemens
end

function make_Ex_ch17P5RSNMDA

// NMDA synapse for P5RS - ST4RS

    if ({exists Ex_ch17P5RSNMDA})
        return
    end

    create  synchan  Ex_ch17P5RSNMDA

        setfield     Ex_ch17P5RSNMDA     \
        Ek           {EGlu}         \
        tau2         { 0.67e-3 }    \ // sec
        tau1         { 130.0e-3 }   \ // sec
        gmax         {GGlu}           // Siemens

    create Mg_block Ex_ch17P5RSNMDA/block
        setfield         Ex_ch17P5RSNMDA/block \
        CMg              {CMg}            \
        KMg_A            {1.0/eta}        \
        KMg_B            {1.0/gamma}      

    addmsg Ex_ch17P5RSNMDA Ex_ch17P5RSNMDA/block CHANNEL Gk Ek

    addmsg Ex_ch17P5RSNMDA/block . CHANNEL Gk Ek

    addmsg . Ex_ch17P5RSNMDA/block VOLTAGE Vm

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

    // addmsg . Ex_ch17P5RSNMDA VOLTAGE Vm

end

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