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_ch16P23RSAMPA

// AMPA synapse for P23RS - C5FS

	if ({exists Ex_ch16P23RSAMPA})
		return
	end

	create		synchan	Ex_ch16P23RSAMPA
    	setfield	        Ex_ch16P23RSAMPA \
		Ek			{EGlu} \
		tau1		{ 0.8e-3 } \	// sec
		tau2		{ 0.8e-3 } \ 	// sec
		gmax		{GGlu} // Siemens
end

function make_Ex_ch16P23RSNMDA

// NMDA synapse for P23RS - C5FS

    if ({exists Ex_ch16P23RSNMDA})
        return
    end

    create  synchan  Ex_ch16P23RSNMDA

        setfield     Ex_ch16P23RSNMDA     \
        Ek           {EGlu}         \
        tau1         { 100.0e-3 }    \ // sec
        tau2         { 0.67e-3 }   \ // sec
        gmax         {GGlu}           // Siemens

    create Mg_block Ex_ch16P23RSNMDA/block
        setfield         Ex_ch16P23RSNMDA/block \
        CMg              {CMg}            \
        KMg_A            {1.0/eta}        \
        KMg_B            {1.0/gamma}      

    addmsg Ex_ch16P23RSNMDA Ex_ch16P23RSNMDA/block CHANNEL Gk Ek

    addmsg Ex_ch16P23RSNMDA/block . CHANNEL Gk Ek

    addmsg . Ex_ch16P23RSNMDA/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_ch16P5IBAMPA

// AMPA synapse for P5IB - C5FS

	if ({exists Ex_ch16P5IBAMPA})
		return
	end

	create		synchan	Ex_ch16P5IBAMPA
    	setfield	        Ex_ch16P5IBAMPA \
		Ek			{EGlu} \
		tau1		{ 0.8e-3 } \	// sec
		tau2		{ 0.8e-3 } \ 	// sec
		gmax		{GGlu} // Siemens
end

function make_Ex_ch16P5IBNMDA

// NMDA synapse for P5IB - C5FS

    if ({exists Ex_ch16P5IBNMDA})
        return
    end

    create  synchan  Ex_ch16P5IBNMDA

        setfield     Ex_ch16P5IBNMDA     \
        Ek           {EGlu}         \
        tau1         { 100.0e-3 }    \ // sec
        tau2         { 0.67e-3 }   \ // sec
        gmax         {GGlu}           // Siemens

    create Mg_block Ex_ch16P5IBNMDA/block
        setfield         Ex_ch16P5IBNMDA/block \
        CMg              {CMg}            \
        KMg_A            {1.0/eta}        \
        KMg_B            {1.0/gamma}      

    addmsg Ex_ch16P5IBNMDA Ex_ch16P5IBNMDA/block CHANNEL Gk Ek

    addmsg Ex_ch16P5IBNMDA/block . CHANNEL Gk Ek

    addmsg . Ex_ch16P5IBNMDA/block VOLTAGE Vm

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

    // addmsg . Ex_ch1NMDA VOLTAGE Vm

end

function make_Inh_ch16B5FSGABAa

//GABA_A synape for B5FS - C5FS

	if ({exists Inh_ch16B5FSGABAa})
		return
	end

	create		synchan	Inh_ch16B5FSGABAa
    	setfield	        Inh_ch16B5FSGABAa \
	Ek			{ EGABA } \
	tau1		{ 3.0e-3 } \	// sec
    tau2        { 1.0e-12 } \    // sec
	gmax		{GGABA}		// Siemens
end

function make_Ex_ch16P6RSAMPA

// AMPA synapse for P6RS - C5FS

	if ({exists Ex_ch16P6RSAMPA})
		return
	end

	create		synchan	Ex_ch16P6RSAMPA
    	setfield	        Ex_ch16P6RSAMPA \
		Ek			{EGlu} \
		tau1		{ 0.8e-3 } \	// sec
		tau2		{ 0.8e-3 } \ 	// sec
		gmax		{GGlu} // Siemens
end

function make_Ex_ch16P6RSNMDA

// NMDA synapse for P6RS - C5FS

    if ({exists Ex_ch16P6RSNMDA})
        return
    end

    create  synchan  Ex_ch16P6RSNMDA

        setfield     Ex_ch16P6RSNMDA     \
        Ek           {EGlu}         \
        tau1         { 100.0e-3 }    \ // sec
        tau2         { 0.67e-3 }   \ // sec
        gmax         {GGlu}           // Siemens

    create Mg_block Ex_ch16P6RSNMDA/block
        setfield         Ex_ch16P6RSNMDA/block \
        CMg              {CMg}            \
        KMg_A            {1.0/eta}        \
        KMg_B            {1.0/gamma}      

    addmsg Ex_ch16P6RSNMDA Ex_ch16P6RSNMDA/block CHANNEL Gk Ek

    addmsg Ex_ch16P6RSNMDA/block . CHANNEL Gk Ek

    addmsg . Ex_ch16P6RSNMDA/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_ch16ST4RSAMPA

// AMPA synapse for ST4RS - C5FS

	if ({exists Ex_ch16ST4RSAMPA})
		return
	end

	create		synchan	Ex_ch16ST4RSAMPA
    	setfield	        Ex_ch16ST4RSAMPA \
		Ek			{EGlu} \
		tau1		{ 0.8e-3 } \	// sec
		tau2		{ 0.8e-3 } \ 	// sec
		gmax		{GGlu} // Siemens
end

function make_Ex_ch16ST4RSNMDA

// NMDA synapse for ST4RS - C5FS

    if ({exists Ex_ch16ST4RSNMDA})
        return
    end

    create  synchan  Ex_ch16ST4RSNMDA

        setfield     Ex_ch16ST4RSNMDA     \
        Ek           {EGlu}         \
        tau1         { 100.0e-3 }    \ // sec
        tau2         { 0.67e-3 }   \ // sec
        gmax         {GGlu}           // Siemens

    create Mg_block Ex_ch16ST4RSNMDA/block
        setfield         Ex_ch16ST4RSNMDA/block \
        CMg              {CMg}            \
        KMg_A            {1.0/eta}        \
        KMg_B            {1.0/gamma}      

    addmsg Ex_ch16ST4RSNMDA Ex_ch16ST4RSNMDA/block CHANNEL Gk Ek

    addmsg Ex_ch16ST4RSNMDA/block . CHANNEL Gk Ek

    addmsg . Ex_ch16ST4RSNMDA/block VOLTAGE Vm

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

    // addmsg . Ex_ch1NMDA VOLTAGE Vm

end

function make_Inh_ch16I23LTSGABAa

//GABA_A synape for I23LTS - C5FS

	if ({exists Inh_ch16I23LTSGABAa})
		return
	end

	create		synchan	Inh_ch16I23LTSGABAa
    	setfield	        Inh_ch16I23LTSGABAa \
	Ek			{ EGABA } \
	tau1		{ 20.0e-3 } \	// sec
    tau2        { 1.0e-12 } \    // sec
	gmax		{GGABA}		// Siemens
end

function make_Inh_ch16I5LTSGABAa

//GABA_A synape for I5LTS - C5FS

	if ({exists Inh_ch16I5LTSGABAa})
		return
	end

	create		synchan	Inh_ch16I5LTSGABAa
    	setfield	        Inh_ch16I5LTSGABAa \
	Ek			{ EGABA } \
	tau1		{ 20.0e-3 } \	// sec
    tau2        { 1.0e-12 } \    // sec
	gmax		{GGABA}		// Siemens
end

function make_Ex_ch16TCRAMPA

// AMPA synapse for TCR - C5FS

	if ({exists Ex_ch16TCRAMPA})
		return
	end

	create		synchan	Ex_ch16TCRAMPA
    	setfield	        Ex_ch16TCRAMPA \
		Ek			{EGlu} \
		tau1		{ 1.0e-3 } \	// sec
		tau2		{ 1.0e-3 } \ 	// sec
		gmax		{GGlu} // Siemens
end

function make_Ex_ch16TCRNMDA

// NMDA synapse for TCR - C5FS

    if ({exists Ex_ch16TCRNMDA})
        return
    end

    create  synchan  Ex_ch16TCRNMDA

        setfield     Ex_ch16TCRNMDA     \
        Ek           {EGlu}         \
        tau2         { 0.67e-3 }    \ // sec
        tau1         { 100.0e-3 }   \ // sec
        gmax         {GGlu}           // Siemens

    create Mg_block Ex_ch16TCRNMDA/block
        setfield         Ex_ch16TCRNMDA/block \
        CMg              {CMg}            \
        KMg_A            {1.0/eta}        \
        KMg_B            {1.0/gamma}      

    addmsg Ex_ch16TCRNMDA Ex_ch16TCRNMDA/block CHANNEL Gk Ek

    addmsg Ex_ch16TCRNMDA/block . CHANNEL Gk Ek

    addmsg . Ex_ch16TCRNMDA/block VOLTAGE Vm

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

    // addmsg . Ex_ch16TCRNMDA VOLTAGE Vm

end

function make_Ex_ch16TCRAMPA

// AMPA synapse for TCR - C5FS

	if ({exists Ex_ch16TCRAMPA})
		return
	end

	create		synchan	Ex_ch16TCRAMPA
    	setfield	        Ex_ch16TCRAMPA \
		Ek			{EGlu} \
		tau1		{ 1.0e-3 } \	// sec
		tau2		{ 1.0e-3 } \ 	// sec
		gmax		{GGlu} // Siemens
end

function make_Ex_ch16TCRNMDA

// NMDA synapse for TCR - C5FS

    if ({exists Ex_ch16TCRNMDA})
        return
    end

    create  synchan  Ex_ch16TCRNMDA

        setfield     Ex_ch16TCRNMDA     \
        Ek           {EGlu}         \
        tau1         { 100.0e-3 }    \ // sec
        tau2         { 0.67e-3 }   \ // sec
        gmax         {GGlu}           // Siemens

    create Mg_block Ex_ch16TCRNMDA/block
        setfield         Ex_ch16TCRNMDA/block \
        CMg              {CMg}            \
        KMg_A            {1.0/eta}        \
        KMg_B            {1.0/gamma}      

    addmsg Ex_ch16TCRNMDA Ex_ch16TCRNMDA/block CHANNEL Gk Ek

    addmsg Ex_ch16TCRNMDA/block . CHANNEL Gk Ek

    addmsg . Ex_ch16TCRNMDA/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_ch16P23FRBAMPA

// AMPA synapse for P23FRB - C5FS

	if ({exists Ex_ch16P23FRBAMPA})
		return
	end

	create		synchan	Ex_ch16P23FRBAMPA
    	setfield	        Ex_ch16P23FRBAMPA \
		Ek			{EGlu} \
		tau1		{ 0.8e-3 } \	// sec
		tau2		{ 0.8e-3 } \ 	// sec
		gmax		{GGlu} // Siemens
end

function make_Ex_ch16P23FRBNMDA

// NMDA synapse for P23FRB - C5FS

    if ({exists Ex_ch16P23FRBNMDA})
        return
    end

    create  synchan  Ex_ch16P23FRBNMDA

        setfield     Ex_ch16P23FRBNMDA     \
        Ek           {EGlu}         \
        tau1         { 100.0e-3 }    \ // sec
        tau2         { 0.67e-3 }   \ // sec
        gmax         {GGlu}           // Siemens

    create Mg_block Ex_ch16P23FRBNMDA/block
        setfield         Ex_ch16P23FRBNMDA/block \
        CMg              {CMg}            \
        KMg_A            {1.0/eta}        \
        KMg_B            {1.0/gamma}      

    addmsg Ex_ch16P23FRBNMDA Ex_ch16P23FRBNMDA/block CHANNEL Gk Ek

    addmsg Ex_ch16P23FRBNMDA/block . CHANNEL Gk Ek

    addmsg . Ex_ch16P23FRBNMDA/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_ch16P5RSAMPA

// AMPA synapse for P5RS - C5FS

	if ({exists Ex_ch16P5RSAMPA})
		return
	end

	create		synchan	Ex_ch16P5RSAMPA
    	setfield	        Ex_ch16P5RSAMPA \
		Ek			{EGlu} \
		tau1		{ 0.8e-3 } \	// sec
		tau2		{ 0.8e-3 } \ 	// sec
		gmax		{GGlu} // Siemens
end

function make_Ex_ch16P5RSNMDA

// NMDA synapse for P5RS - C5FS

    if ({exists Ex_ch16P5RSNMDA})
        return
    end

    create  synchan  Ex_ch16P5RSNMDA

        setfield     Ex_ch16P5RSNMDA     \
        Ek           {EGlu}         \
        tau1         { 100.0e-3 }    \ // sec
        tau2         { 0.67e-3 }   \ // sec
        gmax         {GGlu}           // Siemens

    create Mg_block Ex_ch16P5RSNMDA/block
        setfield         Ex_ch16P5RSNMDA/block \
        CMg              {CMg}            \
        KMg_A            {1.0/eta}        \
        KMg_B            {1.0/gamma}      

    addmsg Ex_ch16P5RSNMDA Ex_ch16P5RSNMDA/block CHANNEL Gk Ek

    addmsg Ex_ch16P5RSNMDA/block . CHANNEL Gk Ek

    addmsg . Ex_ch16P5RSNMDA/block VOLTAGE Vm

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

    // addmsg . Ex_ch1NMDA VOLTAGE Vm

end

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