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_ch11P23RSAMPAlongrange

// AMPA synapse for P23RS - P6RS

	if ({exists Ex_ch11P23RSAMPAlongrange})
		return
	end

	create		synchan	Ex_ch11P23RSAMPAlongrange
    	setfield	        Ex_ch11P23RSAMPAlongrange \
		Ek			{EGlu} \
		tau1		{ 2.0e-3 } \	// sec
		tau2		{ 2.0e-3 } \ 	// sec
		gmax		{GGlu} // Siemens
end

function make_Ex_ch11P23RSNMDAlongrange

// NMDA synapse for P23RS - P6RS

    if ({exists Ex_ch11P23RSNMDAlongrange})
        return
    end

    create  synchan  Ex_ch11P23RSNMDAlongrange

        setfield     Ex_ch11P23RSNMDAlongrange     \
        Ek           {EGlu}         \
        tau2         { 0.67e-3 }    \ // sec
        tau1         { 130.0e-3 }   \ // sec
        gmax         {GGlu}           // Siemens

    create Mg_block Ex_ch11P23RSNMDAlongrange/block
        setfield         Ex_ch11P23RSNMDAlongrange/block \
        CMg              {CMg}            \
        KMg_A            {1.0/eta}        \
        KMg_B            {1.0/gamma}      

    addmsg Ex_ch11P23RSNMDAlongrange Ex_ch11P23RSNMDA/block CHANNEL Gk Ek

    addmsg Ex_ch11P23RSNMDAlongrange/block . CHANNEL Gk Ek

    addmsg . Ex_ch11P23RSNMDAlongrange/block VOLTAGE Vm

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

    // addmsg . Ex_ch11P23RSNMDAlongrange VOLTAGE Vm

end

function make_Ex_ch11P5IBAMPAlongrange

// AMPA synapse for P5IB - P6RS

	if ({exists Ex_ch11P5IBAMPAlongrange})
		return
	end

	create		synchan	Ex_ch11P5IBAMPAlongrange
    	setfield	        Ex_ch11P5IBAMPAlongrange \
		Ek			{EGlu} \
		tau1		{ 2.0e-3 } \	// sec
		tau2		{ 2.0e-3 } \ 	// sec
		gmax		{GGlu} // Siemens
end

function make_Ex_ch11P5IBNMDAlongrange

// NMDA synapse for P5IB - P6RS

    if ({exists Ex_ch11P5IBNMDAlongrange})
        return
    end

    create  synchan  Ex_ch11P5IBNMDAlongrange

        setfield     Ex_ch11P5IBNMDAlongrange     \
        Ek           {EGlu}         \
        tau2         { 0.67e-3 }    \ // sec
        tau1         { 130.0e-3 }   \ // sec
        gmax         {GGlu}           // Siemens

    create Mg_block Ex_ch11P5IBNMDAlongrange/block
        setfield         Ex_ch11P5IBNMDAlongrange/block \
        CMg              {CMg}            \
        KMg_A            {1.0/eta}        \
        KMg_B            {1.0/gamma}      

    addmsg Ex_ch11P5IBNMDAlongrange Ex_ch11P5IBNMDA/block CHANNEL Gk Ek

    addmsg Ex_ch11P5IBNMDAlongrange/block . CHANNEL Gk Ek

    addmsg . Ex_ch11P5IBNMDAlongrange/block VOLTAGE Vm

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

    // addmsg . Ex_ch11P5IBNMDAlongrange VOLTAGE Vm

end

function make_Inh_ch11B5FSGABAalongrange

//GABA_A synapse for B5FS - P6RS

	if ({exists Inh_ch11B5FSGABAalongrange})
		return
	end

	create		synchan	Inh_ch11B5FSGABAalongrange
    	setfield	        Inh_ch11B5FSGABAalongrange \
	Ek			{ EGABA } \
	tau1		{ 6.0e-3 } \	// sec
    tau2        { 1.0e-12 } \    // sec
	gmax		{GGABA}		// Siemens
end

function make_Ex_ch11P6RSAMPAlongrange

// AMPA synapse for P6RS - P6RS

	if ({exists Ex_ch11P6RSAMPAlongrange})
		return
	end

	create		synchan	Ex_ch11P6RSAMPAlongrange
    	setfield	        Ex_ch11P6RSAMPAlongrange \
		Ek			{EGlu} \
		tau1		{ 2.0e-3 } \	// sec
		tau2		{ 2.0e-3 } \ 	// sec
		gmax		{GGlu} // Siemens
end

function make_Ex_ch11P6RSNMDAlongrange

// NMDA synapse for P6RS - P6RS

    if ({exists Ex_ch11P6RSNMDAlongrange})
        return
    end

    create  synchan  Ex_ch11P6RSNMDAlongrange

        setfield     Ex_ch11P6RSNMDAlongrange     \
        Ek           {EGlu}         \
        tau2         { 0.67e-3 }    \ // sec
        tau1         { 130.0e-3 }   \ // sec
        gmax         {GGlu}           // Siemens

    create Mg_block Ex_ch11P6RSNMDAlongrange/block
        setfield         Ex_ch11P6RSNMDAlongrange/block \
        CMg              {CMg}            \
        KMg_A            {1.0/eta}        \
        KMg_B            {1.0/gamma}      

    addmsg Ex_ch11P6RSNMDAlongrange Ex_ch11P6RSNMDA/block CHANNEL Gk Ek

    addmsg Ex_ch11P6RSNMDAlongrange/block . CHANNEL Gk Ek

    addmsg . Ex_ch11P6RSNMDAlongrange/block VOLTAGE Vm

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

    // addmsg . Ex_ch11P6RSNMDAlongrange VOLTAGE Vm

end

function make_Inh_ch11C23FSGABAalongrange

//GABA_A synapse for C23FS - P6RS

	if ({exists Inh_ch11C23FSGABAalongrange})
		return
	end

	create		synchan	Inh_ch11C23FSGABAalongrange
    	setfield	        Inh_ch11C23FSGABAalongrange \
	Ek			{ EGABA } \
	tau1		{ 6.0e-3 } \	// sec
    tau2        { 1.0e-12 } \    // sec
	gmax		{GGABA}		// Siemens
end

function make_Inh_ch11C5FSGABAalongrange

//GABA_A synapse for C5FS - P6RS

	if ({exists Inh_ch11C5FSGABAalongrange})
		return
	end

	create		synchan	Inh_ch11C5FSGABAalongrange
    	setfield	        Inh_ch11C5FSGABAalongrange \
	Ek			{ EGABA } \
	tau1		{ 6.0e-3 } \	// sec
    tau2        { 1.0e-12 } \    // sec
	gmax		{GGABA}		// Siemens
end

function make_Ex_ch11ST4RSAMPAlongrange

// AMPA synapse for ST4RS - P6RS

	if ({exists Ex_ch11ST4RSAMPAlongrange})
		return
	end

	create		synchan	Ex_ch11ST4RSAMPAlongrange
    	setfield	        Ex_ch11ST4RSAMPAlongrange \
		Ek			{EGlu} \
		tau1		{ 2.0e-3 } \	// sec
		tau2		{ 2.0e-3 } \ 	// sec
		gmax		{GGlu} // Siemens
end

function make_Ex_ch11ST4RSNMDAlongrange

// NMDA synapse for ST4RS - P6RS

    if ({exists Ex_ch11ST4RSNMDAlongrange})
        return
    end

    create  synchan  Ex_ch11ST4RSNMDAlongrange

        setfield     Ex_ch11ST4RSNMDAlongrange     \
        Ek           {EGlu}         \
        tau2         { 0.67e-3 }    \ // sec
        tau1         { 130.0e-3 }   \ // sec
        gmax         {GGlu}           // Siemens

    create Mg_block Ex_ch11ST4RSNMDAlongrange/block
        setfield         Ex_ch11ST4RSNMDAlongrange/block \
        CMg              {CMg}            \
        KMg_A            {1.0/eta}        \
        KMg_B            {1.0/gamma}      

    addmsg Ex_ch11ST4RSNMDAlongrange Ex_ch11ST4RSNMDA/block CHANNEL Gk Ek

    addmsg Ex_ch11ST4RSNMDAlongrange/block . CHANNEL Gk Ek

    addmsg . Ex_ch11ST4RSNMDAlongrange/block VOLTAGE Vm

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

    // addmsg . Ex_ch11ST4RSNMDAlongrange VOLTAGE Vm

end

function make_Inh_ch11I23LTSGABAalongrange

//GABA_A synapse for I23LTS - P6RS

	if ({exists Inh_ch11I23LTSGABAalongrange})
		return
	end

	create		synchan	Inh_ch11I23LTSGABAalongrange
    	setfield	        Inh_ch11I23LTSGABAalongrange \
	Ek			{ EGABA } \
	tau1		{ 20.0e-3 } \	// sec
    tau2        { 1.0e-12 } \    // sec
	gmax		{GGABA}		// Siemens
end

function make_Inh_ch11I5LTSGABAalongrange

//GABA_A synapse for I5LTS - P6RS

	if ({exists Inh_ch11I5LTSGABAalongrange})
		return
	end

	create		synchan	Inh_ch11I5LTSGABAalongrange
    	setfield	        Inh_ch11I5LTSGABAalongrange \
	Ek			{ EGABA } \
	tau1		{ 20.0e-3 } \	// sec
    tau2        { 1.0e-12 } \    // sec
	gmax		{GGABA}		// Siemens
end

function make_Ex_ch11TCRAMPAlongrange

// AMPA synapse for TCR - P6RS

	if ({exists Ex_ch11TCRAMPAlongrange})
		return
	end

	create		synchan	Ex_ch11TCRAMPAlongrange
    	setfield	        Ex_ch11TCRAMPAlongrange \
		Ek			{EGlu} \
		tau1		{ 2.0e-3 } \	// sec
		tau2		{ 2.0e-3 } \ 	// sec
		gmax		{GGlu} // Siemens
end

function make_Ex_ch11TCRNMDAlongrange

// NMDA synapse for TCR - P6RS

    if ({exists Ex_ch11TCRNMDAlongrange})
        return
    end

    create  synchan  Ex_ch11TCRNMDAlongrange

        setfield     Ex_ch11TCRNMDAlongrange     \
        Ek           {EGlu}         \
        tau2         { 0.67e-3 }    \ // sec
        tau1         { 130.0e-3 }   \ // sec
        gmax         {GGlu}           // Siemens

    create Mg_block Ex_ch11TCRNMDAlongrange/block
        setfield         Ex_ch11TCRNMDAlongrange/block \
        CMg              {CMg}            \
        KMg_A            {1.0/eta}        \
        KMg_B            {1.0/gamma}      

    addmsg Ex_ch11TCRNMDAlongrange Ex_ch11TCRNMDA/block CHANNEL Gk Ek

    addmsg Ex_ch11TCRNMDAlongrange/block . CHANNEL Gk Ek

    addmsg . Ex_ch11TCRNMDAlongrange/block VOLTAGE Vm

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

    // addmsg . Ex_ch11TCRNMDAlongrange VOLTAGE Vm

end

function make_Ex_ch11TCRAMPAlongrange

// AMPA synapse for TCR - P6RS

	if ({exists Ex_ch11TCRAMPAlongrange})
		return
	end

	create		synchan	Ex_ch11TCRAMPAlongrange
    	setfield	        Ex_ch11TCRAMPAlongrange \
		Ek			{EGlu} \
		tau1		{ 2.0e-3 } \	// sec
		tau2		{ 2.0e-3 } \ 	// sec
		gmax		{GGlu} // Siemens
end

function make_Ex_ch11TCRNMDAlongrange

// NMDA synapse for TCR - P6RS

    if ({exists Ex_ch11TCRNMDAlongrange})
        return
    end

    create  synchan  Ex_ch11TCRNMDAlongrange

        setfield     Ex_ch11TCRNMDAlongrange     \
        Ek           {EGlu}         \
        tau2         { 0.67e-3 }    \ // sec
        tau1         { 130.0e-3 }   \ // sec
        gmax         {GGlu}           // Siemens

    create Mg_block Ex_ch11TCRNMDAlongrange/block
        setfield         Ex_ch11TCRNMDAlongrange/block \
        CMg              {CMg}            \
        KMg_A            {1.0/eta}        \
        KMg_B            {1.0/gamma}      

    addmsg Ex_ch11TCRNMDAlongrange Ex_ch11TCRNMDA/block CHANNEL Gk Ek

    addmsg Ex_ch11TCRNMDAlongrange/block . CHANNEL Gk Ek

    addmsg . Ex_ch11TCRNMDAlongrange/block VOLTAGE Vm

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

    // addmsg . Ex_ch11TCRNMDAlongrange VOLTAGE Vm

end

function make_Ex_ch11P23FRBAMPAlongrange

// AMPA synapse for P23FRB - P6RS

	if ({exists Ex_ch11P23FRBAMPAlongrange})
		return
	end

	create		synchan	Ex_ch11P23FRBAMPAlongrange
    	setfield	        Ex_ch11P23FRBAMPAlongrange \
		Ek			{EGlu} \
		tau1		{ 2.0e-3 } \	// sec
		tau2		{ 2.0e-3 } \ 	// sec
		gmax		{GGlu} // Siemens
end

function make_Ex_ch11P23FRBNMDAlongrange

// NMDA synapse for P23FRB - P6RS

    if ({exists Ex_ch11P23FRBNMDAlongrange})
        return
    end

    create  synchan  Ex_ch11P23FRBNMDAlongrange

        setfield     Ex_ch11P23FRBNMDAlongrange     \
        Ek           {EGlu}         \
        tau2         { 0.67e-3 }    \ // sec
        tau1         { 130.0e-3 }   \ // sec
        gmax         {GGlu}           // Siemens

    create Mg_block Ex_ch11P23FRBNMDAlongrange/block
        setfield         Ex_ch11P23FRBNMDAlongrange/block \
        CMg              {CMg}            \
        KMg_A            {1.0/eta}        \
        KMg_B            {1.0/gamma}      

    addmsg Ex_ch11P23FRBNMDAlongrange Ex_ch11P23FRBNMDA/block CHANNEL Gk Ek

    addmsg Ex_ch11P23FRBNMDAlongrange/block . CHANNEL Gk Ek

    addmsg . Ex_ch11P23FRBNMDAlongrange/block VOLTAGE Vm

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

    // addmsg . Ex_ch11P23FRBNMDAlongrange VOLTAGE Vm

end

function make_Ex_ch11P5RSAMPAlongrange

// AMPA synapse for P5RS - P6RS

	if ({exists Ex_ch11P5RSAMPAlongrange})
		return
	end

	create		synchan	Ex_ch11P5RSAMPAlongrange
    	setfield	        Ex_ch11P5RSAMPAlongrange \
		Ek			{EGlu} \
		tau1		{ 2.0e-3 } \	// sec
		tau2		{ 2.0e-3 } \ 	// sec
		gmax		{GGlu} // Siemens
end

function make_Ex_ch11P5RSNMDAlongrange

// NMDA synapse for P5RS - P6RS

    if ({exists Ex_ch11P5RSNMDAlongrange})
        return
    end

    create  synchan  Ex_ch11P5RSNMDAlongrange

        setfield     Ex_ch11P5RSNMDAlongrange     \
        Ek           {EGlu}         \
        tau2         { 0.67e-3 }    \ // sec
        tau1         { 130.0e-3 }   \ // sec
        gmax         {GGlu}           // Siemens

    create Mg_block Ex_ch11P5RSNMDAlongrange/block
        setfield         Ex_ch11P5RSNMDAlongrange/block \
        CMg              {CMg}            \
        KMg_A            {1.0/eta}        \
        KMg_B            {1.0/gamma}      

    addmsg Ex_ch11P5RSNMDAlongrange Ex_ch11P5RSNMDA/block CHANNEL Gk Ek

    addmsg Ex_ch11P5RSNMDAlongrange/block . CHANNEL Gk Ek

    addmsg . Ex_ch11P5RSNMDAlongrange/block VOLTAGE Vm

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

    // addmsg . Ex_ch11P5RSNMDAlongrange VOLTAGE Vm

end

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