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
//Gapdefs.g

// Create Gap Junctions

     include config_neuron_x_neuron/P23RSa_P23RSa_Gap.g
     include config_neuron_x_neuron/P23RSa_P23RSb_Gap.g
     include config_neuron_x_neuron/P23RSa_P23RSc_Gap.g
     include config_neuron_x_neuron/P23RSa_P23RSd_Gap.g

     include config_neuron_x_neuron/P23RSb_P23RSb_Gap.g
     include config_neuron_x_neuron/P23RSb_P23RSc_Gap.g
     include config_neuron_x_neuron/P23RSb_P23RSd_Gap.g

     include config_neuron_x_neuron/P23RSc_P23RSc_Gap.g
     include config_neuron_x_neuron/P23RSc_P23RSd_Gap.g

     include config_neuron_x_neuron/P23RSd_P23RSd_Gap.g

if ({columntype == 0})

     include config_neuron_x_neuron/B23FS_B23FS_Gap.g

end

if ({columntype == 1})

     include config_neuron_x_neuron/B23FS_B23FS_TraubGap.g

end

     include config_neuron_x_neuron/P5IBa_P5IBa_Gap.g
     include config_neuron_x_neuron/P5IBa_P5IBb_Gap.g
     include config_neuron_x_neuron/P5IBa_P5IBc_Gap.g
     include config_neuron_x_neuron/P5IBa_P5IBd_Gap.g

     include config_neuron_x_neuron/P5IBb_P5IBb_Gap.g
     include config_neuron_x_neuron/P5IBb_P5IBc_Gap.g
     include config_neuron_x_neuron/P5IBb_P5IBd_Gap.g

     include config_neuron_x_neuron/P5IBc_P5IBc_Gap.g
     include config_neuron_x_neuron/P5IBc_P5IBd_Gap.g

     include config_neuron_x_neuron/P5IBd_P5IBd_Gap.g

if ({columntype == 0})

     include config_neuron_x_neuron/B5FS_B5FS_Gap.g

end

if ({columntype == 1})

     include config_neuron_x_neuron/B5FS_B5FS_TraubGap.g

end

if ({columntype == 0})

     include config_neuron_x_neuron/P6RSa_P6RSa_Gap.g
     include config_neuron_x_neuron/P6RSa_P6RSb_Gap.g
     include config_neuron_x_neuron/P6RSa_P6RSc_Gap.g
     include config_neuron_x_neuron/P6RSa_P6RSd_Gap.g

     include config_neuron_x_neuron/P6RSb_P6RSb_Gap.g
     include config_neuron_x_neuron/P6RSb_P6RSc_Gap.g
     include config_neuron_x_neuron/P6RSb_P6RSd_Gap.g

     include config_neuron_x_neuron/P6RSc_P6RSc_Gap.g
     include config_neuron_x_neuron/P6RSc_P6RSd_Gap.g

     include config_neuron_x_neuron/P6RSd_P6RSd_Gap.g

end

if ({columntype == 1})

     include config_neuron_x_neuron/P6RSa_P6RSa_Gap.g
     include config_neuron_x_neuron/P6RSa_P6RSb_Gap.g

     include config_neuron_x_neuron/P6RSb_P6RSb_Gap.g

end

     include config_neuron_x_neuron/ST4RS_ST4RS_Gap.g

if ({columntype == 0})

     include config_neuron_x_neuron/I23LTS_I23LTS_Gap.g

end

if ({columntype == 1})

     include config_neuron_x_neuron/I23LTS_I23LTS_TraubGap.g

end

if ({columntype == 0})

     include config_neuron_x_neuron/I5LTS_I5LTS_Gap.g

end

if ({columntype == 1})

     include config_neuron_x_neuron/I5LTS_I5LTS_TraubGap.g

end

if ({thalamocortical == 1})

     if ({columntype == 0})

          include config_neuron_x_neuron/nRT_nRT_Gap.g

     end

     if ({columntype == 1})

          include config_neuron_x_neuron/nRT_nRT_TraubGap.g

     end

end

    include config_neuron_x_neuron/P5IBa_P5RSa_Gap.g
    include config_neuron_x_neuron/P5IBb_P5RSa_Gap.g
    include config_neuron_x_neuron/P5IBc_P5RSa_Gap.g
    include config_neuron_x_neuron/P5IBd_P5RSa_Gap.g

    include config_neuron_x_neuron/P5RSa_P5RSa_Gap.g

if ({columntype == 1})

          include config_neuron_x_neuron/P23RSa_P23FRBa_TraubGap.g
          include config_neuron_x_neuron/P23RSb_P23FRBa_TraubGap.g
          include config_neuron_x_neuron/P23RSc_P23FRBa_TraubGap.g
          include config_neuron_x_neuron/P23RSd_P23FRBa_TraubGap.g

end

if ({columntype == 0})

          include config_neuron_x_neuron/P23RSa_P23FRBa_Gap.g
          include config_neuron_x_neuron/P23RSb_P23FRBa_Gap.g
          include config_neuron_x_neuron/P23RSc_P23FRBa_Gap.g
          include config_neuron_x_neuron/P23RSd_P23FRBa_Gap.g

end

    include config_neuron_x_neuron/P23FRBa_P23FRBa_Gap.g

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