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

create xform /Neoxout [312,380,500,547]
ce /Neoxout

// Creating a view to look at the selected cellular activity pattern.

float P23RSa_xscale  = 0.7
float P23RSa_yscale  = 0.8
float P23RSa_xoffset = 3 * P23RSa_SEPX
float P23RSa_yoffset = P23RSa_SEPY/2

create xlabel /Neoxout/"Activity Pattern" [25%,2%,45%,30]

create xdraw /Neoxout/draw3 [10%,10%,80%,80%] 
setfield     /Neoxout/draw3  \
    xmin     -0.000559    \
    xmax      0.000457    \
    ymin     -0.00044435  \
    ymax      0.00044465  \
    zmin     -0.0807691   \
    zmax      0.08077     \
    vx       -0.211083    \
    vy       -0.779934    \
    vz        0.589192    \
    transform ortho3d     

// create labels for the xview widgets corresponding to the P23RSa cells

create xshape /Neoxout/draw3/horiz_label -text P23RSa  -tx -0.00005 -ty -0.0001

// Creating the cell display array.

create xview /Neoxout/draw3/P23RSa 
setfield     /Neoxout/draw3/P23RSa          \
             tx {-P23RSa_xoffset}           \  
             ty { P23RSa_yoffset}           \
	     value_min[0] -0.090        \
	     value_max[0]  0.060        \
             sizescale {P23RSa_SEPX * 30.0} \
	     morph_val 0                \
         path /P23RSanet/P23RSa[]/soma \
	     field Vm                   

// Creating a set of toggles to choose the P23RSa cell compartment to be
// displayed in the Activity view.  These will all have to be altered
// to use addmsg, or else the above scheme will have to be altered to 
// use path.  

useclock /Neoxout/draw3/P23RSa 1

xshow /Neoxout

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