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

create xform /neotree [300,0,800,500]

// Creating the draw for the element tree.

create xdraw /neotree/draw [0,0,100%,93%]
setfield /neotree/draw xmin -2 xmax 20 ymin -1 ymax 5

//// Creating an xtree to help us move around the simulation.

//create xtree /tree/draw/tree 

//create xtoggle /tree/show_element [0,93%,100%,7%]
 
//// icons.g defines the icons for the different element types.
//// It is included here since it requires /tree/draw/tree.

//include icons.g 

//// Set tree parameters.

//setfield /tree/draw/tree \
//        path /##[]       \
//        treemode tree    \
//        sizescale 0.4    \
//        script "change_to_element.d1 <v>; zoom_tree.d2 <w> <v>; truncate.d3 <v>"

//echo xtree created
//reset

//function setup_tree
//    call /tree/draw/tree TRUNCATE /output
//    call /tree/draw/tree TRUNCATE /tree
//    call /tree/draw/tree TRUNCATE /xout
//// call /tree/draw/tree TRUNCATE /conn
//    call /tree/draw/tree TRUNCATE /library
//    call /tree/draw/tree TRUNCATE /control
//    call /tree/draw/tree TRUNCATE /xgraphs
//end

//setup_tree

//function reset_tree
//    call /tree/draw/tree RESET
//end

//// This function selects the element as the "working element"
//// and does a showfield on the element if the toggle is down.

//function change_to_element(item)
//    str item
//    int show_state

//    echo changing to element {item}
//    ce {item}
//    show_state = {getfield /tree/show_element state}
//    if (show_state)
//        showfield -all
//    end
//end

//// This function makes the selected element the base of the tree.

//function zoom_tree(widget, item)
//    str widget, item

//    if ({strcmp {getfield {widget} path} "/##[]"} != 0)
//        echo zooming tree out to /
//        setfield {widget} path /##[]
//	reset_tree
//	setup_tree
//    else
//        echo zooming in to {item}
//        setfield {widget} path {item}/../##  // this isn't quite right
//    end

//    reset_tree
//end



//// This function crunches the selected element and its children into a tree object.
//// This function is no longer strictly necessary.

//function truncate(item)
//    str item
//    call /tree/draw/tree TRUNCATE {item}
//    reset_tree
//end

//disable /tree

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