A Federated Design for a Neurobiological Simulation Engine: The CBI federated software architecture.

Cornelis H, Coop AD, and Bower JM

Supplementary Materials 2:

RSnet.g is a customizeable GENESIS 2 script for creating a network of simplified Regular Spiking neocortical neurons with local excitatory connections. The simulation script is analyzed and explained in the GENESIS Neural Modeling Tutorials (http://www.genesis-sim.org/GENESIS/Tutorials/).

This version RSnet2.g has been reorganized and modularized for eventual use under GENESIS 3.

The following snippet (source code lines 12–15) mix up the solver method used and coordinates of the neurons to be simulated.

// If hsolve is used, make a solver for cell[0] and duplicate for others  
    pushe /network/cell[0]  
    create hsolve solver  
    setmethod solver 11  
    setfield solver chanmode {hsolve_chanmode} path "../[][TYPE=compartment]"  
    call solver SETUP  
    int i  
    for (i = 1 ; i < {NX*NY} ; i = i  1)  
        call solver DUPLICATE \  
            /network/cell[{i}]/solver  ../##[][TYPE=compartment]  
             setfield /network/cell[{i}]/solver \  
               x {getfield /network/cell[{i}]/soma x} \  
               y {getfield /network/cell[{i}]/soma y} \  
               z {getfield /network/cell[{i}]/soma z}