A multilayer cortical model to study seizure propagation across microdomains (Basu et al. 2015)

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Accession:206238
A realistic neural network was used to simulate a region of neocortex to obtain extracellular LFPs from ‘virtual micro-electrodes’ and produce test data for comparison with multisite microelectrode recordings. A model was implemented in the GENESIS neurosimulator. A simulated region of cortex was represented by layers 2/3, 5/6 (interneurons and pyramidal cells) and layer 4 stelate cells, spaced at 25 µm in each horizontal direction. Pyramidal cells received AMPA and NMDA inputs from neighboring cells at the basal and apical dendrites. The LFP data was generated by simulating 16-site electrode array with the help of ‘efield’ objects arranged at the predetermined positions with respect to the surface of the simulated network. The LFP for the model is derived from a weighted average of the current sources summed over all cellular compartments. Cell models were taken from from Traub et al. (2005) J Neurophysiol 93(4):2194-232.
References:
1 . Basu I, Kudela P, Korzeniewska A, Franaszczuk PJ, Anderson WS (2015) A study of the dynamics of seizure propagation across micro domains in the vicinity of the seizure onset zone. J Neural Eng 12:046016 [PubMed]
2 . Basu I, Kudela P, Anderson WS (2014) Determination of seizure propagation across microdomains using spectral measures of causality. Conf Proc IEEE Eng Med Biol Soc 2014:6349-52 [PubMed]
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 U1 L2/6 pyramidal intratelencephalic GLU cell; Neocortex U1 L5B pyramidal pyramidal tract GLU cell; Thalamus reticular nucleus GABA cell; Neocortex spiking low threshold (LTS) neuron; Neocortex spiking regular (RS) neuron; Neocortex layer 2-3 interneuron; Neocortex layer 5 interneuron;
Channel(s): I Na,p; I Na,t; I K; I A; I M; I h; I K,Ca; I A, slow; I L high threshold; I T low threshold; I Calcium;
Gap Junctions: Gap junctions;
Receptor(s): AMPA; GabaA; NMDA;
Gene(s):
Transmitter(s): Glutamate; Gaba; Amino Acids;
Simulation Environment: GENESIS;
Model Concept(s): Activity Patterns; Epilepsy;
Implementer(s): Anderson, WS ; Kudela, Pawel ;
Search NeuronDB for information about:  Thalamus reticular nucleus GABA cell; Neocortex U1 L5B pyramidal pyramidal tract GLU cell; Neocortex U1 L2/6 pyramidal intratelencephalic GLU cell; GabaA; AMPA; NMDA; I Na,p; I Na,t; I L high threshold; I T low threshold; I A; I K; I M; I h; I K,Ca; I Calcium; I A, slow; Amino Acids; Gaba; Glutamate;
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BasuEtAl2015
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ModelDescription.pdf
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P6RSd_P6RSc.g
P6RSd_P6RSd.g
P6RSd_P6RSd_Gap.g
P6RSd_raninput.g
P6RSd_ST4RS.g
P6RSd_synapsedefs.g
P6RSd_TCR.g
P6RSdcell3Dpk.p
P6RSdchanpk.g
P6RSdprotodefs.g
P6RSsyncond.g
pgenesis_command
protodefs.g
protospikeB23FS.g
protospikeB5FS.g
protospikeC23FS.g
protospikeC5FS.g
protospikeI23LTS.g
protospikeI5LTS.g
protospikenRT.g
protospikeP23FRBa.g
protospikeP23RSa.g
protospikeP23RSb.g
protospikeP23RSc.g
protospikeP23RSd.g
protospikeP5IBa.g
protospikeP5IBb.g
protospikeP5IBc.g
protospikeP5IBd.g
protospikeP5RSa.g
protospikeP6RSa.g
protospikeP6RSb.g
protospikeP6RSc.g
protospikeP6RSd.g
protospikeST4RS.g
protospikeTCR.g
randominputdefs.g
spikedefs.g
ST4RS.g
ST4RS_B23FS.g
ST4RS_B5FS.g
ST4RS_C23FS.g
ST4RS_C5FS.g
ST4RS_I23LTS.g
ST4RS_I5LTS.g
ST4RS_P23FRBa.g
ST4RS_P23RSa.g
ST4RS_P23RSb.g
ST4RS_P23RSc.g
ST4RS_P23RSd.g
ST4RS_P5IBa.g
ST4RS_P5IBb.g
ST4RS_P5IBc.g
ST4RS_P5IBd.g
ST4RS_P5RSa.g
ST4RS_P6RSa.g
ST4RS_P6RSb.g
ST4RS_P6RSc.g
ST4RS_P6RSd.g
ST4RS_raninput.g
ST4RS_ST4RS.g
ST4RS_ST4RS_Gap.g
ST4RS_synapsedefs.g
ST4RScell3Dpk.p
ST4RSchanpk.g
ST4RSprotodefs.g
ST4RSsyncond.g
synapticdelays.g *
synapticprobsTraub.g
synchansB23FS.g *
synchansB5FS.g *
synchansC23FS.g *
synchansC5FS.g *
synchansI23LTS.g *
synchansI5LTS.g *
synchansnRT.g *
synchansP23FRBa.g *
synchansP23RSa.g *
synchansP23RSb.g *
synchansP23RSc.g *
synchansP23RSd.g *
synchansP5IBa.g *
synchansP5IBb.g *
synchansP5IBc.g *
synchansP5IBd.g *
synchansP5RSa.g *
synchansP6RSa.g *
synchansP6RSb.g *
synchansP6RSc.g *
synchansP6RSd.g *
synchansSPIKEs.g *
synchansSPIKEs_base.g
synchansST4RS.g
synchansTCR.g *
syncond.g
syncond2.g
TCR.g
TCR_B23FS.g
TCR_B5FS.g
TCR_C23FS.g
TCR_C5FS.g
TCR_nRT.g
TCR_P23FRBa.g
TCR_P23RSa.g
TCR_P23RSb.g
TCR_P23RSc.g
TCR_P23RSd.g
TCR_P5IBa.g
TCR_P5IBb.g
TCR_P5IBc.g
TCR_P5IBd.g
TCR_P5RSa.g
TCR_P6RSa.g
TCR_P6RSb.g
TCR_P6RSc.g
TCR_P6RSd.g
TCR_raninput.g
TCR_ST4RS.g
TCR_synapsedefs.g
TCRcellpk.p
TCRchanpk.g
TCRprotodefs.g
TCRsyncond.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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