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

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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. ..."
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;
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];
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;
str element
str shortelement
str mysource
str mydest
str outfile

// By synapse target:
// List source, dest coordinates and weight
//foreach element ({el /#net/#[]/#/Inh_ch#,/#net/#[]/#/Ex_ch#})
//   int syncount = {getsyncount {element}}
//   outfile = {"./data-latest/connections/" @ {myzeropadnode} @ {strsub {element} / _ -all} @ ".txt"}
//   for (i=0; i<=syncount-1; i=i+1) 
//      mysource = {getsynsrc {element} {i}}
//      //if ({mysource} != "/post")
//         echo {getsynsrc {element} {i}} {getfield {getsynsrc {element} {i}} x} {getfield {getsynsrc {element} {i}} y} {getfield {getsynsrc {element} {i}} z} {element} {getfield {element} x} {getfield {element} y} {getfield {element} z} {getfield {element} synapse[{i}].weight} >> {outfile}
//      //end
//   end

//// By spike generator (soma):
//// List source, dest coordinates using rshowmsg
//// Using rshowmsg for efficiency (instead of personally iterating over each destination element)
int thisnode
for (thisnode=0; {thisnode < {Nnodes}}; thisnode={{thisnode}+1})
    if ({thisnode} == {mynode})

		// Synaptic connections to other neurons
        echo Listing connections for node {mynode}
        foreach element ({el /#net/#[]/soma/spk#})
            outfile = {"./data-latest/connections/" @ {myzeropadnode} @ {strsub {element} / _ -all} @ ".txt"}
            echo {mynode} {element} {getfield {element} x} {getfield {element} y} {getfield {element} z} {getfield {element}/../.. rotation} >> {outfile}
            rshowmsg {element} >> {outfile}
            //echo {thisnode} {element} {getfield {element} x} {getfield {element} y} {getfield {element} z} {getfield {element}/../.. rotation} > /dev/null
            //async rshowmsg {element} > /dev/null
		// Get random spike connections too
		echo Listing random connections for node {mynode}
		foreach element ({el /randomspike#})
			outfile = {"./data-latest/connections/" @ {myzeropadnode} @ {strsub {strsub {element} randomspike randomspike_ -all} / _ -all} @ ".txt"}
			echo {getsyndest {element} 0} {getfield {getsyndest {element} 0}/../.. x} {getfield {getsyndest {element} 0}/../.. y} {getfield {getsyndest {element} 0}/../.. z} {element} {getfield {getsyndest {element} 0} synapse[0].weight} >> {outfile}
			rshowmsg {element} >> {outfile}
			//echo {thisnode} {element} {getfield {element} x} {getfield {element} y} {getfield {element} z} {getfield {element}/../.. rotation} > /dev/null
			//async rshowmsg {element} > /dev/null

// It's not currently possible to get the synaptic weight for remote
// connections, e.g.:
// echo {getfield@1 /C23FSnet/C23FS/distdendSmidb/Ex_ch15P23RSAMPA synapse[7].weight}
// This is because they're all routed through the /post object.

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