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
// rasterdefspos1.g

//make_Vmgraph P23RSa{probedexP23RS} 1 0
//addmsg /P23RSanet/P23RSa[{probedexP23RS}]/soma /dataP23RSa{probedex}/VmP23RSa{probedex} PLOT Vm *volts *red

//make_raster P23RSa{probedexP23RS} 1 0
//addmsg /P23RSanet/P23RSa[{probedexP23RS}]/soma/spk1 /dataP23RSa{probedex}/spikeP23RSa{probedex} \ 
//PLOTSCALE state *spike *red 0.01 0

addmsg /P23RSanet/P23RSa[{probedexP23RS}]/soma/spk1 /rasterdata{probedex}/Spike{probedex} \ 
PLOTSCALE state *P23RSa{probedexP23RS} *red 1.0 9.0

//make_Vmgraph B23FS{probedexB23FS} 1 1
//addmsg /B23FSnet/B23FS[{probedexB23FS}]/soma /dataB23FS{probedex}/VmB23FS{probedex} PLOT Vm *volts *blue

addmsg /B23FSnet/B23FS[{probedexB23FS}]/soma/spk5 /rasterdata{probedex}/Spike{probedex} \ 
PLOTSCALE state *B23FS{probedexB23FS} *blue 1.0 8.0

//make_Vmgraph P5IBa{probedexP5IB} 1 2
//addmsg /P5IBanet/P5IBa[{probedexP5IB}]/soma /dataP5IBa{probedex}/VmP5IBa{probedex} PLOT Vm *volts *red

addmsg /P5IBanet/P5IBa[{probedexP5IB}]/soma/spk6 /rasterdata{probedex}/Spike{probedex} \ 
PLOTSCALE state *P5IBa{probedexP5IB} *red 1.0 7.0

//make_Vmgraph B5FS{probedexB5FS} 1 3
//addmsg /B5FSnet/B5FS[{probedexB5FS}]/soma /dataB5FS{probedex}/VmB5FS{probedex} PLOT Vm *volts *blue

addmsg /B5FSnet/B5FS[{probedexB5FS}]/soma/spk10 /rasterdata{probedex}/Spike{probedex} \ 
PLOTSCALE state *B5FS{probedexB5FS} *blue 1.0 6.0

//make_Vmgraph I23LTS{probedexI23LTS} 1 4
//addmsg /I23LTSnet/I23LTS[{probedexI23LTS}]/soma /dataI23LTS{probedex}/VmI23LTS{probedex} PLOT Vm *volts *blue

addmsg /I23LTSnet/I23LTS[{probedexI23LTS}]/soma/spk18 /rasterdata{probedex}/Spike{probedex} \ 
PLOTSCALE state *I23LTS{probedexI23LTS} *blue 1.0 5.0

//make_Vmgraph P6RSa{probedexP6RS} 2 0
//addmsg /P6RSanet/P6RSa[{probedexP6RS}]/soma /dataP6RSa{probedex}/VmP6RSa{probedex} PLOT Vm *volts *red

addmsg /P6RSanet/P6RSa[{probedexP6RS}]/soma/spk11 /rasterdata{probedex}/Spike{probedex} \ 
PLOTSCALE state *P6RSa{probedexP6RS} *red 1.0 4.0

//make_Vmgraph C23FS{probedexC23FS} 2 1
//addmsg /C23FSnet/C23FS[{probedexC23FS}]/soma /dataC23FS{probedex}/VmC23FS{probedex} PLOT Vm *volts *blue

addmsg /C23FSnet/C23FS[{probedexC23FS}]/soma/spk15 /rasterdata{probedex}/Spike{probedex} \ 
PLOTSCALE state *C23FS{probedexC23FS} *blue 1.0 3.0

//make_Vmgraph C5FS{probedexC5FS} 2 2
//addmsg /C5FSnet/C5FS[{probedexC5FS}]/soma /dataC5FS{probedex}/VmC5FS{probedex} PLOT Vm *volts *blue

addmsg /C5FSnet/C5FS[{probedexC5FS}]/soma/spk16 /rasterdata{probedex}/Spike{probedex} \ 
PLOTSCALE state *C5FS{probedexC5FS} *blue 1.0 2.0

//make_Vmgraph ST4RS{probedexST4RS} 2 3
//addmsg /ST4RSnet/ST4RS[{probedexST4RS}]/soma /dataST4RS{probedex}/VmST4RS{probedex} PLOT Vm *volts *red

addmsg /ST4RSnet/ST4RS[{probedexST4RS}]/soma/spk17 /rasterdata{probedex}/Spike{probedex} \ 
PLOTSCALE state *ST4RS{probedexST4RS} *red 1.0 1.0

//make_Vmgraph I5LTS{probedexI5LTS} 2 4
//addmsg /I5LTSnet/I5LTS[{probedexI5LTS}]/soma /dataI5LTS{probedex}/VmI5LTS{probedex} PLOT Vm *volts *blue

addmsg /I5LTSnet/I5LTS[{probedexI5LTS}]/soma/spk19 /rasterdata{probedex}/Spike{probedex} \ 
PLOTSCALE state *I5LTS{probedexI5LTS} *blue 1.0 0.0

if ({thalamocortical == 1})

     //make_Vmgraph TCR {probedexTCR} 1 5
     //addmsg /TCRnet/TCR[{probedexTCR}]/soma /dataTCR{probedex}/VmTCR{probedex} PLOT Vm *volts *blue

     addmsg /TCRnet/TCR[{probedexTCR}]/soma/spk20 /rasterdata{probedex}/Spike{probedex} \ 
     PLOTSCALE state *TCR{probedexTCR} *red  1.0 -1.0

     //make_Vmgraph nRT {probedexnRT} 1 5
     //addmsg /nRTnet/nRT[{probedexnRT}]/soma /datanRT{probedex}/VmnRT{probedex} PLOT Vm *volts *blue

     addmsg /nRTnet/nRT[{probedexnRT}]/soma/spk21 /rasterdata{probedex}/Spike{probedex} \ 
     PLOTSCALE state *nRT{probedexnRT} *blue  1.0 -2.0


end

//make_Vmgraph P23FRBa{probedexP23FRB} 1 0
//addmsg /P23FRBanet/P23FRBa[{probedexP23FRB}]/soma /dataP23FRBa{probedex}/VmP23FRBa{probedex} PLOT Vm *volts *red

//make_raster P23FRBa{probedexP23FRB} 1 0
//addmsg /P23FRBanet/P23FRBa[{probedexP23FRB}]/soma/spk22 /dataP23FRBa{probedex}/spikeP23FRBa{probedex} \ 
//PLOTSCALE state *spike *red 0.01 0

addmsg /P23FRBanet/P23FRBa[{probedexP23FRB}]/soma/spk22 /rasterdata{probedex}/Spike{probedex} \ 
PLOTSCALE state *P23FRBa{probedexP23FRB} *red 1.0 -3.0

//make_Vmgraph P5RSa{probedexP5RS} 1 0
//addmsg /P5RSanet/P5RSa[{probedexP5RS}]/soma /dataP5RSa{probedex}/VmP5RSa{probedex} PLOT Vm *volts *red

//make_raster P5RSa{probedexP5RS} 1 0
//addmsg /P5RSanet/P5RSa[{probedexP5RS}]/soma/spk23 /dataP5RSa{probedex}/spikeP5RSa{probedex} \ 
//PLOTSCALE state *spike *red 0.01 0

addmsg /P5RSanet/P5RSa[{probedexP5RS}]/soma/spk23 /rasterdata{probedex}/Spike{probedex} \ 
PLOTSCALE state *P5RSa{probedexP5RS} *red 1.0 -4.0

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