Large scale neocortical model for PGENESIS (Crone et al 2019)

 Download zip file 
Help downloading and running models
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
// Neocortex - celldefs.g

// Define P23RSa cells

include config_neuron/protodefs/P23RSaprotodefs.g

// Build the cell from a parameter file using the cell reader
readcell config_neuron/parameters/P23RSacell3D.p /P23RSa -hsolve

include config_neuron/synapsedefs/P23RSa_synapsedefs.g

setfield /P23RSa/apdend3 inject 0.0

delete /library

// Define P23RSb cells

include config_neuron/protodefs/P23RSbprotodefs.g

// Build the cell from a parameter file using the cell reader
readcell config_neuron/parameters/P23RSbcell3D.p /P23RSb -hsolve

include config_neuron/synapsedefs/P23RSb_synapsedefs.g

delete /library

// Define P23RSc cells

include config_neuron/protodefs/P23RScprotodefs.g 

// Build the cell from a parameter file using the cell reader
readcell config_neuron/parameters/P23RSccell3D.p /P23RSc -hsolve

include config_neuron/synapsedefs/P23RSc_synapsedefs.g

delete /library

// Define P23RSd cells

include config_neuron/protodefs/P23RSdprotodefs.g

// Build the cell from a parameter file using the cell reader
readcell config_neuron/parameters/P23RSdcell3D.p /P23RSd -hsolve

include config_neuron/synapsedefs/P23RSd_synapsedefs.g

delete /library

// Define B23FS cells

include config_neuron/protodefs/B23FSprotodefs.g

// Build the cell from a parameter file using the cell reader
readcell config_neuron/parameters/B23FScell3D.p /B23FS -hsolve

include config_neuron/synapsedefs/B23FS_synapsedefs.g

delete /library

// Define P5IBa cells

include config_neuron/protodefs/P5IBaprotodefs.g

// Build the cell from a parameter file using the cell reader
readcell config_neuron/parameters/P5IBacell3D.p /P5IBa -hsolve

include config_neuron/synapsedefs/P5IBa_synapsedefs.g

delete /library

// Define P5IBb cells

include config_neuron/protodefs/P5IBbprotodefs.g

// Build the cell from a parameter file using the cell reader
readcell config_neuron/parameters/P5IBbcell3D.p /P5IBb -hsolve

include config_neuron/synapsedefs/P5IBb_synapsedefs.g

delete /library

// Define P5IBc cells
    
include config_neuron/protodefs/P5IBcprotodefs

// Build the cell from a parameter file using the cell reader
readcell config_neuron/parameters/P5IBccell3D.p /P5IBc -hsolve

include config_neuron/synapsedefs/P5IBc_synapsedefs.g

delete /library 

// Define P5IBd cells

include config_neuron/protodefs/P5IBdprotodefs.g

// Build the cell from a parameter file using the cell reader
readcell config_neuron/parameters/P5IBdcell3D.p /P5IBd -hsolve

include config_neuron/synapsedefs/P5IBd_synapsedefs.g

delete /library

// Define B5FS cells

include config_neuron/protodefs/B5FSprotodefs.g

// Build the cell from a parameter file using the cell reader
readcell config_neuron/parameters/B5FScell3D.p /B5FS -hsolve

include config_neuron/synapsedefs/B5FS_synapsedefs.g

delete /library

// Define P6RSa cells

include config_neuron/protodefs/P6RSaprotodefs.g

// Build the cell from a parameter file using the cell reader
readcell config_neuron/parameters/P6RSacell3D.p /P6RSa -hsolve

include config_neuron/synapsedefs/P6RSa_synapsedefs.g

delete /library

// Define P6RSb cells

include config_neuron/protodefs/P6RSbprotodefs.g

// Build the cell from a parameter file using the cell reader
readcell config_neuron/parameters/P6RSbcell3D.p /P6RSb -hsolve

include config_neuron/synapsedefs/P6RSb_synapsedefs.g

delete /library

if ({columntype == 0})

     // Define P6RSc cells

     include config_neuron/protodefs/P6RScprotodefs.g

     // Build the cell from a parameter file using the cell reader
     readcell config_neuron/parameters/P6RSccell3D.p /P6RSc -hsolve

     include config_neuron/synapsedefs/P6RSc_synapsedefs.g

     delete /library

     // Define P6RSd cells

     include config_neuron/protodefs/P6RSdprotodefs.g

     // Build the cell from a parameter file using the cell reader
     readcell config_neuron/parameters/P6RSdcell3D.p /P6RSd -hsolve

     include config_neuron/synapsedefs/P6RSd_synapsedefs.g

     delete /library

end

// Define C23FS cells

include config_neuron/protodefs/C23FSprotodefs.g

// Build the cell from a parameter file using the cell reader
readcell config_neuron/parameters/C23FScell3D.p /C23FS -hsolve

include config_neuron/synapsedefs/C23FS_synapsedefs.g

delete /library

// Define C5FS cells

include config_neuron/protodefs/C5FSprotodefs.g

// Build the cell from a parameter file using the cell reader
readcell config_neuron/parameters/C5FScell3D.p /C5FS -hsolve

include config_neuron/synapsedefs/C5FS_synapsedefs.g

delete /library

// Define ST4RS cells

include config_neuron/protodefs/ST4RSprotodefs.g

// Build the cell from a parameter file using the cell reader
readcell config_neuron/parameters/ST4RScell3D.p /ST4RS -hsolve

include config_neuron/synapsedefs/ST4RS_synapsedefs.g

delete /library

// Define I23LTS cells

include config_neuron/protodefs/I23LTSprotodefs.g

// Build the cell from a parameter file using the cell reader
readcell config_neuron/parameters/I23LTScell3D.p /I23LTS -hsolve

include config_neuron/synapsedefs/I23LTS_synapsedefs.g

delete /library

// Define I5LTS cells

include config_neuron/protodefs/I5LTSprotodefs.g

// Build the cell from a parameter file using the cell reader
readcell config_neuron/parameters/I5LTScell3D.p /I5LTS -hsolve

include config_neuron/synapsedefs/I5LTS_synapsedefs.g

delete /library

// Define TCR cells

if ({thalamocortical == 1})

     include config_neuron/protodefs/TCRprotodefs.g

// Build the cell from a parameter file using the cell reader

     readcell config_neuron/parameters/TCRcell.p /TCR -hsolve

     include config_neuron/synapsedefs/TCR_synapsedefs.g

     delete /library

     include config_neuron/protodefs/nRTprotodefs.g

// Build the cell from a parameter file using the cell reader

     readcell config_neuron/parameters/nRTcell.p /nRT -hsolve

     include config_neuron/synapsedefs/nRT_synapsedefs.g

     delete /library

end

// Define P23FRBa cells

include config_neuron/protodefs/P23FRBaprotodefs.g

// Build the cell from a parameter file using the cell reader
readcell config_neuron/parameters/P23FRBacell3D.p /P23FRBa -hsolve

include config_neuron/synapsedefs/P23FRBa_synapsedefs.g

delete /library

// Define P5RSa cells

include config_neuron/protodefs/P5RSaprotodefs.g

// Build the cell from a parameter file using the cell reader
readcell config_neuron/parameters/P5RSacell3D.p /P5RSa -hsolve

include config_neuron/synapsedefs/P5RSa_synapsedefs.g

delete /library

Loading data, please wait...