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_ch16P23RSAMPAlongrange

// AMPA synapse for P23RS - C5FS

	if ({exists Ex_ch16P23RSAMPAlongrange})
		return
	end

	create		synchan	Ex_ch16P23RSAMPAlongrange
    	setfield	        Ex_ch16P23RSAMPAlongrange \
		Ek			{EGlu} \
		tau1		{ 0.8e-3 } \	// sec
		tau2		{ 0.8e-3 } \ 	// sec
		gmax		{GGlu} // Siemens
end

function make_Ex_ch16P23RSNMDAlongrange

// NMDA synapse for P23RS - C5FS

    if ({exists Ex_ch16P23RSNMDAlongrange})
        return
    end

    create  synchan  Ex_ch16P23RSNMDAlongrange

        setfield     Ex_ch16P23RSNMDAlongrange     \
        Ek           {EGlu}         \
        tau1         { 100.0e-3 }    \ // sec
        tau2         { 0.67e-3 }   \ // sec
        gmax         {GGlu}           // Siemens

    create Mg_block Ex_ch16P23RSNMDAlongrange/block
        setfield         Ex_ch16P23RSNMDAlongrange/block \
        CMg              {CMg}            \
        KMg_A            {1.0/eta}        \
        KMg_B            {1.0/gamma}      

    addmsg Ex_ch16P23RSNMDAlongrange Ex_ch16P23RSNMDA/block CHANNEL Gk Ek

    addmsg Ex_ch16P23RSNMDAlongrange/block . CHANNEL Gk Ek

    addmsg . Ex_ch16P23RSNMDAlongrange/block VOLTAGE Vm

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

    // addmsg . Ex_ch1NMDAlongrange VOLTAGE Vm

end

function make_Ex_ch16P5IBAMPAlongrange

// AMPA synapse for P5IB - C5FS

	if ({exists Ex_ch16P5IBAMPAlongrange})
		return
	end

	create		synchan	Ex_ch16P5IBAMPAlongrange
    	setfield	        Ex_ch16P5IBAMPAlongrange \
		Ek			{EGlu} \
		tau1		{ 0.8e-3 } \	// sec
		tau2		{ 0.8e-3 } \ 	// sec
		gmax		{GGlu} // Siemens
end

function make_Ex_ch16P5IBNMDAlongrange

// NMDA synapse for P5IB - C5FS

    if ({exists Ex_ch16P5IBNMDAlongrange})
        return
    end

    create  synchan  Ex_ch16P5IBNMDAlongrange

        setfield     Ex_ch16P5IBNMDAlongrange     \
        Ek           {EGlu}         \
        tau1         { 100.0e-3 }    \ // sec
        tau2         { 0.67e-3 }   \ // sec
        gmax         {GGlu}           // Siemens

    create Mg_block Ex_ch16P5IBNMDAlongrange/block
        setfield         Ex_ch16P5IBNMDAlongrange/block \
        CMg              {CMg}            \
        KMg_A            {1.0/eta}        \
        KMg_B            {1.0/gamma}      

    addmsg Ex_ch16P5IBNMDAlongrange Ex_ch16P5IBNMDA/block CHANNEL Gk Ek

    addmsg Ex_ch16P5IBNMDAlongrange/block . CHANNEL Gk Ek

    addmsg . Ex_ch16P5IBNMDAlongrange/block VOLTAGE Vm

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

    // addmsg . Ex_ch1NMDAlongrange VOLTAGE Vm

end

function make_Inh_ch16B5FSGABAalongrange

//GABA_A synape for B5FS - C5FS

	if ({exists Inh_ch16B5FSGABAalongrange})
		return
	end

	create		synchan	Inh_ch16B5FSGABAalongrange
    	setfield	        Inh_ch16B5FSGABAalongrange \
	Ek			{ EGABA } \
	tau1		{ 3.0e-3 } \	// sec
    tau2        { 1.0e-12 } \    // sec
	gmax		{GGABA}		// Siemens
end

function make_Ex_ch16P6RSAMPAlongrange

// AMPA synapse for P6RS - C5FS

	if ({exists Ex_ch16P6RSAMPAlongrange})
		return
	end

	create		synchan	Ex_ch16P6RSAMPAlongrange
    	setfield	        Ex_ch16P6RSAMPAlongrange \
		Ek			{EGlu} \
		tau1		{ 0.8e-3 } \	// sec
		tau2		{ 0.8e-3 } \ 	// sec
		gmax		{GGlu} // Siemens
end

function make_Ex_ch16P6RSNMDAlongrange

// NMDA synapse for P6RS - C5FS

    if ({exists Ex_ch16P6RSNMDAlongrange})
        return
    end

    create  synchan  Ex_ch16P6RSNMDAlongrange

        setfield     Ex_ch16P6RSNMDAlongrange     \
        Ek           {EGlu}         \
        tau1         { 100.0e-3 }    \ // sec
        tau2         { 0.67e-3 }   \ // sec
        gmax         {GGlu}           // Siemens

    create Mg_block Ex_ch16P6RSNMDAlongrange/block
        setfield         Ex_ch16P6RSNMDAlongrange/block \
        CMg              {CMg}            \
        KMg_A            {1.0/eta}        \
        KMg_B            {1.0/gamma}      

    addmsg Ex_ch16P6RSNMDAlongrange Ex_ch16P6RSNMDA/block CHANNEL Gk Ek

    addmsg Ex_ch16P6RSNMDAlongrange/block . CHANNEL Gk Ek

    addmsg . Ex_ch16P6RSNMDAlongrange/block VOLTAGE Vm

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

    // addmsg . Ex_ch1NMDAlongrange VOLTAGE Vm

end

function make_Ex_ch16ST4RSAMPAlongrange

// AMPA synapse for ST4RS - C5FS

	if ({exists Ex_ch16ST4RSAMPAlongrange})
		return
	end

	create		synchan	Ex_ch16ST4RSAMPAlongrange
    	setfield	        Ex_ch16ST4RSAMPAlongrange \
		Ek			{EGlu} \
		tau1		{ 0.8e-3 } \	// sec
		tau2		{ 0.8e-3 } \ 	// sec
		gmax		{GGlu} // Siemens
end

function make_Ex_ch16ST4RSNMDAlongrange

// NMDA synapse for ST4RS - C5FS

    if ({exists Ex_ch16ST4RSNMDAlongrange})
        return
    end

    create  synchan  Ex_ch16ST4RSNMDAlongrange

        setfield     Ex_ch16ST4RSNMDAlongrange     \
        Ek           {EGlu}         \
        tau1         { 100.0e-3 }    \ // sec
        tau2         { 0.67e-3 }   \ // sec
        gmax         {GGlu}           // Siemens

    create Mg_block Ex_ch16ST4RSNMDAlongrange/block
        setfield         Ex_ch16ST4RSNMDAlongrange/block \
        CMg              {CMg}            \
        KMg_A            {1.0/eta}        \
        KMg_B            {1.0/gamma}      

    addmsg Ex_ch16ST4RSNMDAlongrange Ex_ch16ST4RSNMDA/block CHANNEL Gk Ek

    addmsg Ex_ch16ST4RSNMDAlongrange/block . CHANNEL Gk Ek

    addmsg . Ex_ch16ST4RSNMDAlongrange/block VOLTAGE Vm

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

    // addmsg . Ex_ch1NMDAlongrange VOLTAGE Vm

end

function make_Inh_ch16I23LTSGABAalongrange

//GABA_A synape for I23LTS - C5FS

	if ({exists Inh_ch16I23LTSGABAalongrange})
		return
	end

	create		synchan	Inh_ch16I23LTSGABAalongrange
    	setfield	        Inh_ch16I23LTSGABAalongrange \
	Ek			{ EGABA } \
	tau1		{ 20.0e-3 } \	// sec
    tau2        { 1.0e-12 } \    // sec
	gmax		{GGABA}		// Siemens
end

function make_Inh_ch16I5LTSGABAalongrange

//GABA_A synape for I5LTS - C5FS

	if ({exists Inh_ch16I5LTSGABAalongrange})
		return
	end

	create		synchan	Inh_ch16I5LTSGABAalongrange
    	setfield	        Inh_ch16I5LTSGABAalongrange \
	Ek			{ EGABA } \
	tau1		{ 20.0e-3 } \	// sec
    tau2        { 1.0e-12 } \    // sec
	gmax		{GGABA}		// Siemens
end

function make_Ex_ch16TCRAMPAlongrange

// AMPA synapse for TCR - C5FS

	if ({exists Ex_ch16TCRAMPAlongrange})
		return
	end

	create		synchan	Ex_ch16TCRAMPAlongrange
    	setfield	        Ex_ch16TCRAMPAlongrange \
		Ek			{EGlu} \
		tau1		{ 1.0e-3 } \	// sec
		tau2		{ 1.0e-3 } \ 	// sec
		gmax		{GGlu} // Siemens
end

function make_Ex_ch16TCRNMDAlongrange

// NMDA synapse for TCR - C5FS

    if ({exists Ex_ch16TCRNMDAlongrange})
        return
    end

    create  synchan  Ex_ch16TCRNMDAlongrange

        setfield     Ex_ch16TCRNMDAlongrange     \
        Ek           {EGlu}         \
        tau2         { 0.67e-3 }    \ // sec
        tau1         { 100.0e-3 }   \ // sec
        gmax         {GGlu}           // Siemens

    create Mg_block Ex_ch16TCRNMDAlongrange/block
        setfield         Ex_ch16TCRNMDAlongrange/block \
        CMg              {CMg}            \
        KMg_A            {1.0/eta}        \
        KMg_B            {1.0/gamma}      

    addmsg Ex_ch16TCRNMDAlongrange Ex_ch16TCRNMDA/block CHANNEL Gk Ek

    addmsg Ex_ch16TCRNMDAlongrange/block . CHANNEL Gk Ek

    addmsg . Ex_ch16TCRNMDAlongrange/block VOLTAGE Vm

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

    // addmsg . Ex_ch16TCRNMDAlongrange VOLTAGE Vm

end

function make_Ex_ch16TCRAMPAlongrange

// AMPA synapse for TCR - C5FS

	if ({exists Ex_ch16TCRAMPAlongrange})
		return
	end

	create		synchan	Ex_ch16TCRAMPAlongrange
    	setfield	        Ex_ch16TCRAMPAlongrange \
		Ek			{EGlu} \
		tau1		{ 1.0e-3 } \	// sec
		tau2		{ 1.0e-3 } \ 	// sec
		gmax		{GGlu} // Siemens
end

function make_Ex_ch16TCRNMDAlongrange

// NMDA synapse for TCR - C5FS

    if ({exists Ex_ch16TCRNMDAlongrange})
        return
    end

    create  synchan  Ex_ch16TCRNMDAlongrange

        setfield     Ex_ch16TCRNMDAlongrange     \
        Ek           {EGlu}         \
        tau1         { 100.0e-3 }    \ // sec
        tau2         { 0.67e-3 }   \ // sec
        gmax         {GGlu}           // Siemens

    create Mg_block Ex_ch16TCRNMDAlongrange/block
        setfield         Ex_ch16TCRNMDAlongrange/block \
        CMg              {CMg}            \
        KMg_A            {1.0/eta}        \
        KMg_B            {1.0/gamma}      

    addmsg Ex_ch16TCRNMDAlongrange Ex_ch16TCRNMDA/block CHANNEL Gk Ek

    addmsg Ex_ch16TCRNMDAlongrange/block . CHANNEL Gk Ek

    addmsg . Ex_ch16TCRNMDAlongrange/block VOLTAGE Vm

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

    // addmsg . Ex_ch1NMDAlongrange VOLTAGE Vm

end

function make_Ex_ch16P23FRBAMPAlongrange

// AMPA synapse for P23FRB - C5FS

	if ({exists Ex_ch16P23FRBAMPAlongrange})
		return
	end

	create		synchan	Ex_ch16P23FRBAMPAlongrange
    	setfield	        Ex_ch16P23FRBAMPAlongrange \
		Ek			{EGlu} \
		tau1		{ 0.8e-3 } \	// sec
		tau2		{ 0.8e-3 } \ 	// sec
		gmax		{GGlu} // Siemens
end

function make_Ex_ch16P23FRBNMDAlongrange

// NMDA synapse for P23FRB - C5FS

    if ({exists Ex_ch16P23FRBNMDAlongrange})
        return
    end

    create  synchan  Ex_ch16P23FRBNMDAlongrange

        setfield     Ex_ch16P23FRBNMDAlongrange     \
        Ek           {EGlu}         \
        tau1         { 100.0e-3 }    \ // sec
        tau2         { 0.67e-3 }   \ // sec
        gmax         {GGlu}           // Siemens

    create Mg_block Ex_ch16P23FRBNMDAlongrange/block
        setfield         Ex_ch16P23FRBNMDAlongrange/block \
        CMg              {CMg}            \
        KMg_A            {1.0/eta}        \
        KMg_B            {1.0/gamma}      

    addmsg Ex_ch16P23FRBNMDAlongrange Ex_ch16P23FRBNMDA/block CHANNEL Gk Ek

    addmsg Ex_ch16P23FRBNMDAlongrange/block . CHANNEL Gk Ek

    addmsg . Ex_ch16P23FRBNMDAlongrange/block VOLTAGE Vm

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

    // addmsg . Ex_ch1NMDAlongrange VOLTAGE Vm

end

function make_Ex_ch16P5RSAMPAlongrange

// AMPA synapse for P5RS - C5FS

	if ({exists Ex_ch16P5RSAMPAlongrange})
		return
	end

	create		synchan	Ex_ch16P5RSAMPAlongrange
    	setfield	        Ex_ch16P5RSAMPAlongrange \
		Ek			{EGlu} \
		tau1		{ 0.8e-3 } \	// sec
		tau2		{ 0.8e-3 } \ 	// sec
		gmax		{GGlu} // Siemens
end

function make_Ex_ch16P5RSNMDAlongrange

// NMDA synapse for P5RS - C5FS

    if ({exists Ex_ch16P5RSNMDAlongrange})
        return
    end

    create  synchan  Ex_ch16P5RSNMDAlongrange

        setfield     Ex_ch16P5RSNMDAlongrange     \
        Ek           {EGlu}         \
        tau1         { 100.0e-3 }    \ // sec
        tau2         { 0.67e-3 }   \ // sec
        gmax         {GGlu}           // Siemens

    create Mg_block Ex_ch16P5RSNMDAlongrange/block
        setfield         Ex_ch16P5RSNMDAlongrange/block \
        CMg              {CMg}            \
        KMg_A            {1.0/eta}        \
        KMg_B            {1.0/gamma}      

    addmsg Ex_ch16P5RSNMDAlongrange Ex_ch16P5RSNMDA/block CHANNEL Gk Ek

    addmsg Ex_ch16P5RSNMDAlongrange/block . CHANNEL Gk Ek

    addmsg . Ex_ch16P5RSNMDAlongrange/block VOLTAGE Vm

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

    // addmsg . Ex_ch1NMDAlongrange VOLTAGE Vm

end

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