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;
//P23RS

float CondmaxP23RSAMPA_P23RS=0.25e-9

float CondmaxP23RSNMDA_P23RS=0.025e-9

float CondmaxB23FSGABAa_P23RS=1.2e-9

float CondmaxP5IBAMPA_P23RS=0.5e-9

float CondmaxP5IBNMDA_P23RS=0.05e-9

float CondmaxP6RSAMPA_P23RS=0.50e-9

float CondmaxP6RSNMDA_P23RS=0.05e-9

float CondmaxC23FSGABAa_P23RS=1.2e-9

float CondmaxC5FSGABAa_P23RS=1.0e-9

float CondmaxST4RSAMPA_P23RS=1.00e-9

float CondmaxST4RSNMDA_P23RS=0.10e-9

float CondmaxI23LTSGABAa_P23RS=0.01e-9

float CondmaxI5LTSGABAa_P23RS=0.01e-9

float CondmaxTCRAMPA_P23RS=0.50e-9

float CondmaxTCRNMDA_P23RS=0.05e-9

float CondmaxP23FRBAMPA_P23RS=0.25e-9

float CondmaxP23FRBNMDA_P23RS=0.025e-9

float CondmaxP5RSAMPA_P23RS=0.5e-9

float CondmaxP5RSNMDA_P23RS=0.05e-9

//B23FS

float CondmaxP23RSAMPA_B23FS=3.0e-9

float CondmaxP23RSNMDA_B23FS=0.15e-9

float CondmaxB23FSGABAa_B23FS=0.2e-9  //

float CondmaxP5IBAMPA_B23FS=1.0e-9

float CondmaxP5IBNMDA_B23FS=0.15e-9

float CondmaxP6RSAMPA_B23FS=1.0e-9

float CondmaxP6RSNMDA_B23FS=0.10e-9

float CondmaxST4RSAMPA_B23FS=1.0e-9

float CondmaxST4RSNMDA_B23FS=0.15e-9

float CondmaxI23LTSGABAa_B23FS=0.01e-9  //.01e-9

float CondmaxI5LTSGABAa_B23FS=0.01e-9  //.01e-9

float CondmaxTCRAMPA_B23FS=0.1e-9

float CondmaxTCRNMDA_B23FS=0.01e-9

float CondmaxP23FRBAMPA_B23FS=3.0e-9

float CondmaxP23FRBNMDA_B23FS=0.10e-9

float CondmaxP5RSAMPA_B23FS=1.0e-9

float CondmaxP5RSNMDA_B23FS=0.15e-9

//P5IB

float CondmaxP23RSAMPA_P5IB= 0.10e-9

float CondmaxP23RSNMDA_P5IB=0.010e-9

float CondmaxB5FSGABAa_P5IB=0.7e-9

float CondmaxP5IBAMPA_P5IB=2.00e-9

float CondmaxP5IBNMDA_P5IB=0.20e-9

float CondmaxP6RSAMPA_P5IB=1.00e-9

float CondmaxP6RSNMDA_P5IB=0.10e-9

float CondmaxC23FSGABAa_P5IB=1.0e-9

float CondmaxC5FSGABAa_P5IB=1.0e-9

float CondmaxST4RSAMPA_P5IB=1.00e-9

float CondmaxST4RSNMDA_P5IB=0.10e-9

float CondmaxI23LTSGABAa_P5IB=0.02e-9

float CondmaxI5LTSGABAa_P5IB=0.05e-9

float CondmaxTCRAMPA_P5IB=1.50e-9

float CondmaxTCRNMDA_P5IB=0.15e-9

float CondmaxP23FRBAMPA_P5IB=0.10e-9

float CondmaxP23FRBNMDA_P5IB=0.010e-9

float CondmaxP5RSAMPA_P5IB=1.0e-9

float CondmaxP5RSNMDA_P5IB=0.10e-9

//B5FS

float CondmaxP23RSAMPA_B5FS=1.0e-9

float CondmaxP23RSNMDA_B5FS=0.1e-9

float CondmaxP5IBAMPA_B5FS=3.0e-9

float CondmaxP5IBNMDA_B5FS=0.15e-9

float CondmaxB5FSGABAa_B5FS=0.2e-9  //  .2  Boothe 1/2018

float CondmaxP6RSAMPA_B5FS=3.0e-9

float CondmaxP6RSNMDA_B5FS=0.10e-9

float CondmaxST4RSAMPA_B5FS=1.0e-9

float CondmaxST4RSNMDA_B5FS=0.15e-9

float CondmaxI23LTSGABAa_B5FS=0.01e-9  //.01e-9

float CondmaxI5LTSGABAa_B5FS=0.01e-9  //.01e-9

float CondmaxTCRAMPA_B5FS=1.5e-9

float CondmaxTCRNMDA_B5FS=0.10e-9

float CondmaxP23FRBAMPA_B5FS=1.0e-9

float CondmaxP23FRBNMDA_B5FS=0.1e-9

float CondmaxP5RSAMPA_B5FS=3.0e-9

float CondmaxP5RSNMDA_B5FS=0.1e-9

//P6RS

float CondmaxP23RSAMPA_P6RS=0.50e-9

float CondmaxP23RSNMDA_P6RS=0.050e-9

float CondmaxB5FSGABAa_P6RS=0.7e-9

float CondmaxP5IBAMPA_P6RS=2.00e-9

float CondmaxP5IBNMDA_P6RS=0.20e-9

float CondmaxP6RSAMPA_P6RS=1.00e-9

float CondmaxP6RSNMDA_P6RS=0.10e-9

float CondmaxC23FSGABAa_P6RS=1.0e-9

float CondmaxC5FSGABAa_P6RS=1.0e-9

float CondmaxST4RSAMPA_P6RS=1.00e-9

float CondmaxST4RSNMDA_P6RS=0.10e-9

float CondmaxI23LTSGABAa_P6RS=0.01e-9

float CondmaxI5LTSGABAa_P6RS=0.01e-9

float CondmaxTCRAMPA_P6RS=1.00e-9

float CondmaxTCRNMDA_P6RS=0.10e-9

float CondmaxP23FRBAMPA_P6RS=0.50e-9

float CondmaxP23FRBNMDA_P6RS=0.050e-9

float CondmaxP5RSAMPA_P6RS=1.0e-9

float CondmaxP5RSNMDA_P6RS=0.10e-9

//C23FS

float CondmaxP23RSAMPA_C23FS=3.0e-9

float CondmaxP23RSNMDA_C23FS=0.15e-9

float CondmaxB23FSGABAa_C23FS=0.2e-9  //  .2  Boothe 1/2018

float CondmaxP5IBAMPA_C23FS=1.0e-9

float CondmaxP5IBNMDA_C23FS=0.15e-9

float CondmaxP6RSAMPA_C23FS=1.0e-9

float CondmaxP6RSNMDA_C23FS=0.10e-9

float CondmaxST4RSAMPA_C23FS=1.0e-9

float CondmaxST4RSNMDA_C23FS=0.15e-9 

float CondmaxI23LTSGABAa_C23FS=0.01e-9  //.01e-9

float CondmaxI5LTSGABAa_C23FS=0.01e-9  //.01e-9

float CondmaxTCRAMPA_C23FS=0.1e-9

float CondmaxTCRNMDA_C23FS=0.01e-9

float CondmaxP23FRBAMPA_C23FS=3.0e-9

float CondmaxP23FRBNMDA_C23FS=0.10e-9 

float CondmaxP5RSAMPA_C23FS=1.0e-9 

float CondmaxP5RSNMDA_C23FS=0.15e-9 

//C5FS

float CondmaxP23RSAMPA_C5FS=1.0e-9

float CondmaxP23RSNMDA_C5FS=0.10e-9

float CondmaxP5IBAMPA_C5FS=3.0e-9

float CondmaxP5IBNMDA_C5FS=0.15e-9

float CondmaxB5FSGABAa_C5FS=0.2e-9  //  .2 Boothe 

float CondmaxP6RSAMPA_C5FS=3.0e-9

float CondmaxP6RSNMDA_C5FS=0.10e-9

float CondmaxST4RSAMPA_C5FS=1.0e-9

float CondmaxST4RSNMDA_C5FS=0.15e-9

float CondmaxI23LTSGABAa_C5FS=0.01e-9  //.01e-9

float CondmaxI5LTSGABAa_C5FS=0.01e-9   //.01e-9

float CondmaxTCRAMPA_C5FS=1.0e-9

float CondmaxTCRNMDA_C5FS=0.10e-9

float CondmaxP23FRBAMPA_C5FS=1.0e-9

float CondmaxP23FRBNMDA_C5FS=0.10e-9

float CondmaxP5RSAMPA_C5FS=3.0e-9

float CondmaxP5RSNMDA_C5FS=0.10e-9

//ST4RS

float CondmaxP23RSAMPA_ST4RS=0.1e-9

float CondmaxP23RSNMDA_ST4RS=0.01e-9

float CondmaxB23FSGABAa_ST4RS=0.1e-9

float CondmaxP5IBAMPA_ST4RS=0.5e-9

float CondmaxP5IBNMDA_ST4RS=0.05e-9

float CondmaxB5FSGABAa_ST4RS=1.5e-9

float CondmaxP6RSAMPA_ST4RS=0.5e-9

float CondmaxP6RSNMDA_ST4RS=0.05e-9

float CondmaxC23FSGABAa_ST4RS=0.1e-9

float CondmaxC5FSGABAa_ST4RS=1.5e-95

float CondmaxST4RSAMPA_ST4RS=0.01e-9 // made to be .01 Traub 2005 uses a "low" state of base X 0.25, or a "high" state of base X 2.0

float CondmaxST4RSNMDA_ST4RS=0.10e-9

float CondmaxI23LTSGABAa_ST4RS=0.01e-9

float CondmaxI5LTSGABAa_ST4RS=0.01e-9

float CondmaxTCRAMPA_ST4RS=1.0e-9

float CondmaxTCRNMDA_ST4RS=0.10e-9

float CondmaxP23FRBAMPA_ST4RS=0.1e-9

float CondmaxP23FRBNMDA_ST4RS=0.01e-9

float CondmaxP5RSAMPA_ST4RS=0.5e-9

float CondmaxP5RSNMDA_ST4RS=0.05e-9

//I23LTS

float CondmaxP23RSAMPA_I23LTS=2.0e-9

float CondmaxP23RSNMDA_I23LTS=0.15e-9

float CondmaxB23FSGABAa_I23LTS=0.5e-9

float CondmaxP5IBAMPA_I23LTS=1.0e-9

float CondmaxP5IBNMDA_I23LTS=0.15e-9

float CondmaxP6RSAMPA_I23LTS=1.0e-9

float CondmaxP6RSNMDA_I23LTS=0.10e-9

float CondmaxST4RSAMPA_I23LTS=1.0e-9

float CondmaxST4RSNMDA_I23LTS=0.15e-9

float CondmaxI23LTSGABAa_I23LTS=0.05e-9

float CondmaxI5LTSGABAa_I23LTS=0.05e-9

float CondmaxP23FRBAMPA_I23LTS=2.0e-9

float CondmaxP23FRBNMDA_I23LTS=0.10e-9

float CondmaxP5RSAMPA_I23LTS=1.0e-9

float CondmaxP5RSNMDA_I23LTS=0.15e-9

//I5LTS

float CondmaxP23RSAMPA_I5LTS=1.0e-9

float CondmaxP23RSNMDA_I5LTS=0.15e-9

float CondmaxP5IBAMPA_I5LTS=2.0e-9

float CondmaxP5IBNMDA_I5LTS=0.15e-9

float CondmaxB5FSGABAa_I5LTS=0.7e-9

float CondmaxP6RSAMPA_I5LTS=2.0e-9

float CondmaxP6RSNMDA_I5LTS=0.10e-9

float CondmaxST4RSAMPA_I5LTS=1.0e-9

float CondmaxST4RSNMDA_I5LTS=0.15e-9

float CondmaxI23LTSGABAa_I5LTS=0.05e-9

float CondmaxI5LTSGABAa_I5LTS=0.05e-9

float CondmaxP23FRBAMPA_I5LTS=1.0e-9

float CondmaxP23FRBNMDA_I5LTS=0.10e-9

float CondmaxP5RSAMPA_I5LTS=2.0e-9

float CondmaxP5RSNMDA_I5LTS=0.10e-9

//TCR

float CondmaxP6RSAMPA_TCR=0.75e-9

float CondmaxP6RSNMDA_TCR=0.075e-9

float CondmaxnRTGABAa_TCR=1.4e-9
// In the 2005 Traub model, this conductance is uniformly randomly distributed 
// from 0.7 - 2.1 nS

//nRT

float CondmaxP6RSAMPA_nRT=0.5e-9

float CondmaxP6RSNMDA_nRT=0.05e-9

float CondmaxTCRAMPA_nRT=0.75e-9

float CondmaxTCRNMDA_nRT=0.15e-9

float CondmaxnRTGABAa_nRT=0.30e-9

//P23FRB

float CondmaxP23RSAMPA_P23FRB=0.25e-9 

float CondmaxP23RSNMDA_P23FRB=0.025e-9 

float CondmaxB23FSGABAa_P23FRB=1.2e-9

float CondmaxP5IBAMPA_P23FRB=0.5e-9

float CondmaxP5IBNMDA_P23FRB=0.05e-9

float CondmaxP6RSAMPA_P23FRB=0.50e-9

float CondmaxP6RSNMDA_P23FRB=0.05e-9

float CondmaxC23FSGABAa_P23FRB=1.2e-9

float CondmaxC5FSGABAa_P23FRB=1.0e-9

float CondmaxST4RSAMPA_P23FRB=1.00e-9

float CondmaxST4RSNMDA_P23FRB=0.10e-9

float CondmaxI23LTSGABAa_P23FRB=0.01e-9

float CondmaxI5LTSGABAa_P23FRB=0.01e-9 

float CondmaxTCRAMPA_P23FRB=0.50e-9

float CondmaxTCRNMDA_P23FRB=0.05e-9

float CondmaxP23FRBAMPA_P23FRB=0.25e-9

float CondmaxP23FRBNMDA_P23FRB=0.025e-9

float CondmaxP5RSAMPA_P23FRB=0.5e-9

float CondmaxP5RSNMDA_P23FRB=0.05e-9

//P5RS

float CondmaxP23RSAMPA_P5RS=0.10e-9

float CondmaxP23RSNMDA_P5RS=0.010e-9

float CondmaxB5FSGABAa_P5RS=0.7e-9

float CondmaxP5IBAMPA_P5RS=2.00e-9

float CondmaxP5IBNMDA_P5RS=0.20e-9

float CondmaxP6RSAMPA_P5RS=1.00e-9

float CondmaxP6RSNMDA_P5RS=0.10e-9

float CondmaxC23FSGABAa_P5RS=1.0e-9

float CondmaxC5FSGABAa_P5RS=1.0e-9

float CondmaxST4RSAMPA_P5RS=1.00e-9

float CondmaxST4RSNMDA_P5RS=0.10e-9

float CondmaxI23LTSGABAa_P5RS=0.02e-9

float CondmaxI5LTSGABAa_P5RS=0.02e-9

float CondmaxTCRAMPA_P5RS=1.50e-9

float CondmaxTCRNMDA_P5RS=0.15e-9

float CondmaxP23FRBAMPA_P5RS=0.10e-9

float CondmaxP23FRBNMDA_P5RS=0.010e-9

float CondmaxP5RSAMPA_P5RS=1.0e-9

float CondmaxP5RSNMDA_P5RS=0.10e-9


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