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

/***********************************************************************
**                                                                    **
**  Compartments.g : compartment definition file, neuron builder kit  **
**                                                                    **
**      By E. De Schutter, Nov 1990                                   **
**      Modified June 1990                                            **
**                                                                    **
**	Modified by D. Beeman for GENESIS 2.0,  April 1995            **
************************************************************************/

/* FUNCTIONS TO MAKE DEFAULT LIBRARY COMPARTMENTS */

// NOTE: Previous (GENESIS 1.*) versions assumed that global variables
// for RM, CN, RA and EREST_ACT had been previously declared and set
// This is no longer necessary

function make_cylind_compartment
        // These default compartment parameters can be overridden by readcell
	float RM = 0.33333      // specific membrane resistance (ohms m^2)
	float CM = 0.01         // specific membrane capacitance (farads/m^2)
	float RA = 0.3          // specific axial resistance (ohms m)
	float EREST_ACT = -0.07 // resting membrane potential (volts)
	float	len = 100.0e-6
	float	dia = 2.0e-6
	float PI = 3.14159
	float surface = len * dia * PI

	if (!{exists compartment})
		create	compartment compartment
	end
	setfield compartment \
		Cm		{CM * surface} \		// F
		Ra		{4.0*RA*len / (dia*dia*PI)} \	// ohm
		Em  	{EREST_ACT} \			// V
		Rm		{RM / surface} \ 		// ohm
                dia             {dia} \
		len		{len} \	
		inject		0.0
end

function make_cylind_symcompartment
        // These default compartment parameters can be overridden by readcell
	float RM = 0.33333      // specific membrane resistance (ohms m^2)
	float CM = 0.01         // specific membrane capacitance (farads/m^2)
	float RA = 0.3          // specific axial resistance (ohms m)
	float EREST_ACT = -0.07 // resting membrane potential (volts)
	float	len = 100.0e-6
	float	dia = 2.0e-6
	float PI = 3.14159
	float surface = len * dia * PI

	if (!{exists symcompartment})
		create	symcompartment symcompartment
	end
	setfield symcompartment \
		Cm		{CM * surface} \		// F
		Ra		{4.0*RA*len / (dia*dia*PI)} \	// ohm
		Em  	{EREST_ACT} \			// V
		Rm		{RM / surface} \ 		// ohm
                dia             {dia} \
		len		{len} \	
		inject		0.0

end

/******************************************************************************/
/* These functions are included for compatibility with older neurokit
**  versions, one does not need to call them anymore though! */

function make_sphere_compartment
        // These default compartment parameters can be overridden by readcell
	float RM = 0.33333      // specific membrane resistance (ohms m^2)
	float CM = 0.01         // specific membrane capacitance (farads/m^2)
	float RA = 0.3          // specific axial resistance (ohms m)
	float EREST_ACT = -0.07 // resting membrane potential (volts)
	float	dia = 20.0e-6
	float PI = 3.14159
	float surface = dia * dia * PI

	if (!{exists compartment_sphere})
		create	compartment compartment_sphere
	end
	setfield compartment_sphere \
		Cm		{CM * surface} \	// F
		Ra		{8.0*RA / (dia*PI)} \	// ohm
		Em  	        {EREST_ACT} \			// V
		Rm		{RM / surface} \ 		// ohm
                dia             {dia} \
		len		0.0 \	
		inject		0.0
end

function make_sphere_symcompartment
        // These default compartment parameters can be overridden by readcell
	float RM = 0.33333      // specific membrane resistance (ohms m^2)
	float CM = 0.01         // specific membrane capacitance (farads/m^2)
	float RA = 0.3          // specific axial resistance (ohms m)
	float EREST_ACT = -0.07 // resting membrane potential (volts)
	float	dia = 20.0e-6
	float PI = 3.14159
	float surface = dia * dia * PI

	if (!{exists symcompartment_sphere})
		create	symcompartment symcompartment_sphere
	end
	setfield symcompartment_sphere \
		Cm		{CM * surface} \		// F
		Ra		{8.0*RA / (dia*PI)} \	// ohm
		Em  	        {EREST_ACT} \			// V
		Rm		{RM / surface} \ 		// ohm
                dia             {dia} \
		len		0.0   \	
		inject		0.0
end

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