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;
// netparams.g - defining Network cell spacings and numbers

// ayu: General (non-neuron type specific) configuration has been moved to
// Neocortex.g

//float SEPX = 25e-6
//float SEPY = 25e-6

// If this is set to an odd number, some cell types with reduced count
// proportions (i.e. everything except P23RS[abcd]) can end up with slightly
// uneven numbers compared to each other. For example, at 5x5 B23FS will end up
// with 13 in each minicolumn, and B5FS ends up with 12. To be more precise,
// this will happen if N[XY] is not evenly divisible by 2 and 4.
//float NX = 4
//float NY = 4

float	P23RSa_SEPX = SEPX
float	P23RSa_SEPY = SEPY
float	P23RSa_NX = NX
float	P23RSa_NY = NY

float	P23RSb_SEPX = SEPX
float	P23RSb_SEPY = SEPY
float	P23RSb_NX = NX
float	P23RSb_NY = NY

float	P23RSc_SEPX = SEPX
float	P23RSc_SEPY = SEPY
float	P23RSc_NX = NX
float	P23RSc_NY = NY

float	P23RSd_SEPX = SEPX
float	P23RSd_SEPY = SEPY
float	P23RSd_NX = NX
float	P23RSd_NY = NY

float	B23FS_SEPX = SEPX
float	B23FS_SEPY = SEPY
float	B23FS_NX = NX
float	B23FS_NY = NY

float	P5IBa_SEPX = SEPX
float	P5IBa_SEPY = SEPY
float	P5IBa_NX = NX
float	P5IBa_NY = NY

float	P5IBb_SEPX = SEPX
float	P5IBb_SEPY = SEPY
float	P5IBb_NX = NX
float	P5IBb_NY = NY

float	P5IBc_SEPX = SEPX
float	P5IBc_SEPY = SEPY
float	P5IBc_NX = NX
float	P5IBc_NY = NY

float	P5IBd_SEPX = SEPX
float	P5IBd_SEPY = SEPY
float	P5IBd_NX = NX
float	P5IBd_NY = NY

float	B5FS_SEPX = SEPX
float	B5FS_SEPY = SEPY
float	B5FS_NX = NX
float	B5FS_NY = NY

float	P6RSa_SEPX = SEPX
float	P6RSa_SEPY = SEPY
float	P6RSa_NX = NX
float	P6RSa_NY = NY

float	P6RSb_SEPX = SEPX
float	P6RSb_SEPY = SEPY
float	P6RSb_NX = NX
float	P6RSb_NY = NY

float	P6RSc_SEPX = SEPX
float	P6RSc_SEPY = SEPY
float	P6RSc_NX = NX
float	P6RSc_NY = NY

float	P6RSd_SEPX = SEPX
float	P6RSd_SEPY = SEPY
float	P6RSd_NX = NX
float	P6RSd_NY = NY

float	C23FS_SEPX = SEPX
float	C23FS_SEPY = SEPY
float	C23FS_NX = NX
float	C23FS_NY = NY

float	C5FS_SEPX = SEPX
float	C5FS_SEPY = SEPY
float	C5FS_NX = NX
float	C5FS_NY = NY

float	ST4RS_SEPX = SEPX
float	ST4RS_SEPY = SEPY
float	ST4RS_NX = NX
float	ST4RS_NY = NY

float	I23LTS_SEPX = SEPX
float	I23LTS_SEPY = SEPY
float	I23LTS_NX = NX
float	I23LTS_NY = NY

float	I5LTS_SEPX = SEPX
float	I5LTS_SEPY = SEPY
float	I5LTS_NX = NX
float	I5LTS_NY = NY

float	TCR_SEPX = SEPX
float	TCR_SEPY = SEPY
float	TCR_NX = NX
float	TCR_NY = NY

float	nRT_SEPX = SEPX
float	nRT_SEPY = SEPY
float	nRT_NX = NX
float	nRT_NY = NY

if ({columntype == 0 })

     float	P23FRBa_SEPX = SEPX
     float	P23FRBa_SEPY = SEPY
     float	P23FRBa_NX = NX
     float	P23FRBa_NY = NY

end

if ({columntype == 1 })

     float	P23FRBa_SEPX = {SEPX}*2
     float	P23FRBa_SEPY = {SEPY}*2
     float	P23FRBa_NX = {NX}/2
     float	P23FRBa_NY = {NY}/2

end

float	P5RSa_SEPX = SEPX
float	P5RSa_SEPY = SEPY
float	P5RSa_NX = NX
float	P5RSa_NY = NY

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