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;
//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

// ayu: This is the only one of four make_* functions that actually gets used
// by Neocortex.g.
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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