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;
// spikedefs.g - defining SPIKE elements for all somae

// See second half for long range spikes

ce /P23RSa/soma
make_spk1
addmsg /P23RSa/soma /P23RSa/soma/spk1 INPUT Vm
ce /

ce /P23RSb/soma
make_spk2
addmsg /P23RSb/soma /P23RSb/soma/spk2 INPUT Vm
ce /

ce /P23RSc/soma
make_spk3
addmsg /P23RSc/soma /P23RSc/soma/spk3 INPUT Vm
ce /

ce /P23RSd/soma
make_spk4
addmsg /P23RSd/soma /P23RSd/soma/spk4 INPUT Vm
ce /

ce /B23FS/soma
make_spk5
addmsg /B23FS/soma /B23FS/soma/spk5 INPUT Vm
ce /

ce /P5IBa/soma
make_spk6
addmsg /P5IBa/soma /P5IBa/soma/spk6 INPUT Vm
ce /

ce /P5IBb/soma
make_spk7
addmsg /P5IBb/soma /P5IBb/soma/spk7 INPUT Vm
ce /

ce /P5IBc/soma
make_spk8
addmsg /P5IBc/soma /P5IBc/soma/spk8 INPUT Vm
ce /

ce /P5IBd/soma
make_spk9
addmsg /P5IBd/soma /P5IBd/soma/spk9 INPUT Vm
ce /

ce /B5FS/soma
make_spk10
addmsg /B5FS/soma /B5FS/soma/spk10 INPUT Vm
ce /

ce /P6RSa/soma
make_spk11
addmsg /P6RSa/soma /P6RSa/soma/spk11 INPUT Vm
ce /

ce /P6RSb/soma
make_spk12
addmsg /P6RSb/soma /P6RSb/soma/spk12 INPUT Vm
ce /

if ({columntype == 0})

     ce /P6RSc/soma
     make_spk13
     addmsg /P6RSc/soma /P6RSc/soma/spk13 INPUT Vm
     ce /

     ce /P6RSd/soma
     make_spk14
     addmsg /P6RSd/soma /P6RSd/soma/spk14 INPUT Vm
     ce /

end

ce /C23FS/soma
make_spk15
addmsg /C23FS/soma /C23FS/soma/spk15 INPUT Vm
ce /

ce /C5FS/soma
make_spk16
addmsg /C5FS/soma /C5FS/soma/spk16 INPUT Vm
ce /

ce /ST4RS/soma
make_spk17
addmsg /ST4RS/soma /ST4RS/soma/spk17 INPUT Vm
ce /

ce /I23LTS/soma
make_spk18
addmsg /I23LTS/soma /I23LTS/soma/spk18 INPUT Vm
ce /

ce /I5LTS/soma
make_spk19
addmsg /I5LTS/soma /I5LTS/soma/spk19 INPUT Vm
ce /

if ({thalamocortical == 1})

     ce /TCR/soma
     make_spk20
     addmsg /TCR/soma /TCR/soma/spk20 INPUT Vm
     ce /

     ce /nRT/soma
     make_spk21
     addmsg /nRT/soma /nRT/soma/spk21 INPUT Vm
     ce /

end

ce /P23FRBa/soma
make_spk22
addmsg /P23FRBa/soma /P23FRBa/soma/spk22 INPUT Vm
ce /

ce /P5RSa/soma
make_spk23
addmsg /P5RSa/soma /P5RSa/soma/spk23 INPUT Vm
ce /


//////////////////////////////////////////////////
// Long range spikes
if ({Nregions>1})

    ce /P23RSa/soma
    make_spk1longrange
    addmsg /P23RSa/soma /P23RSa/soma/spk1longrange INPUT Vm
    ce /

    ce /P23RSb/soma
    make_spk2longrange
    addmsg /P23RSb/soma /P23RSb/soma/spk2longrange INPUT Vm
    ce /

    ce /P23RSc/soma
    make_spk3longrange
    addmsg /P23RSc/soma /P23RSc/soma/spk3longrange INPUT Vm
    ce /

    ce /P23RSd/soma
    make_spk4longrange
    addmsg /P23RSd/soma /P23RSd/soma/spk4longrange INPUT Vm
    ce /

    // ce /B23FS/soma
    // make_spk5longrange
    // addmsg /B23FS/soma /B23FS/soma/spk5longrange INPUT Vm
    // ce /

    ce /P5IBa/soma
    make_spk6longrange
    addmsg /P5IBa/soma /P5IBa/soma/spk6longrange INPUT Vm
    ce /

    ce /P5IBb/soma
    make_spk7longrange
    addmsg /P5IBb/soma /P5IBb/soma/spk7longrange INPUT Vm
    ce /

    ce /P5IBc/soma
    make_spk8longrange
    addmsg /P5IBc/soma /P5IBc/soma/spk8longrange INPUT Vm
    ce /

    ce /P5IBd/soma
    make_spk9longrange
    addmsg /P5IBd/soma /P5IBd/soma/spk9longrange INPUT Vm
    ce /

    // ce /B5FS/soma
    // make_spk10longrange
    // addmsg /B5FS/soma /B5FS/soma/spk10longrange INPUT Vm
    // ce /

    ce /P6RSa/soma
    make_spk11longrange
    addmsg /P6RSa/soma /P6RSa/soma/spk11longrange INPUT Vm
    ce /

    ce /P6RSb/soma
    make_spk12longrange
    addmsg /P6RSb/soma /P6RSb/soma/spk12longrange INPUT Vm
    ce /
 
// if ({columntype == 0})
// 
//      ce /P6RSc/soma
//      make_spk13longrange
//      addmsg /P6RSc/soma /P6RSc/soma/spk13longrange INPUT Vm
//      ce /
// 
//      ce /P6RSd/soma
//      make_spk14longrange
//      addmsg /P6RSd/soma /P6RSd/soma/spk14longrange INPUT Vm
//      ce /
// 
// end
// 
// ce /C23FS/soma
// make_spk15longrange
// addmsg /C23FS/soma /C23FS/soma/spk15longrange INPUT Vm
// ce /
// 
// ce /C5FS/soma
// make_spk16longrange
// addmsg /C5FS/soma /C5FS/soma/spk16longrange INPUT Vm
// ce /
// 
// ce /ST4RS/soma
// make_spk17longrange
// addmsg /ST4RS/soma /ST4RS/soma/spk17longrange INPUT Vm
// ce /
// 
// ce /I23LTS/soma
// make_spk18longrange
// addmsg /I23LTS/soma /I23LTS/soma/spk18longrange INPUT Vm
// ce /
// 
// ce /I5LTS/soma
// make_spk19longrange
// addmsg /I5LTS/soma /I5LTS/soma/spk19longrange INPUT Vm
// ce /
// 
// if ({thalamocortical == 1})
// 
//      ce /TCR/soma
//      make_spk20longrange
//      addmsg /TCR/soma /TCR/soma/spk20longrange INPUT Vm
//      ce /
// 
//      ce /nRT/soma
//      make_spk21longrange
//      addmsg /nRT/soma /nRT/soma/spk21longrange INPUT Vm
//      ce /
// 
// end

    ce /P23FRBa/soma
    make_spk22longrange
    addmsg /P23FRBa/soma /P23FRBa/soma/spk22longrange INPUT Vm
    ce /

    ce /P5RSa/soma
    make_spk23longrange
    addmsg /P5RSa/soma /P5RSa/soma/spk23longrange INPUT Vm
    ce /
end

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