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Code: Select all

load_file("nrngui.hoc")


print "-{ create cells }-"

begintemplate simpleIAFcell




  public soma1, soma2, soma3
  public IAF
  public x, y, z, x1, y1, z1, x2, y2, z2
  public addConnection

  objref IAF

  create soma1

  proc init() {
     x = $1
     y = $2 
     z = $3

     soma1 {
       // set lattice position of the cell
       pt3dclear()
       pt3dadd(x, y, z, 5)
       pt3dadd(x+5, y, z, 5)

       // insert IntFire1 point process
       IAF = new IntFire1(0.5)
       IAF.tau = 10
       IAF.refrac = 5
     }
  }

  proc addConnection() {
     soma1 {
       pt3dadd(x+5, y, z, 1)
       pt3dadd($1+5, $2, $3, 1)
     }
  }

//=======================================================================

  create soma2

  proc init() {
     x1 = $4
     y1 = $5 
     z1 = $6

     soma2 {
       // set lattice position of the cell
       pt3dclear()
       pt3dadd(x1, y1, z1, 10)
       pt3dadd(x1+2, y1, z1, 10)

       // insert IntFire1 point process
       IAF = new IntFire1(0.5)
       IAF.tau = 10
       IAF.refrac = 5
     }
  }

  proc addConnection() {
     soma2 {
       pt3dadd(x1+2, y1, z1, 1)
       pt3dadd($4+2, $5, $7, 1)
     }
  }

//========================================================================

  create soma3

  proc init() {
     x2 = $7
     y2 = $8 
     z2 = $9

     soma3 {
       // set lattice position of the cell
       pt3dclear()
       pt3dadd(x2, y2, z2, 8)
       pt3dadd(x2+10, y2, z2, 8)

       // insert IntFire1 point process
       IAF = new IntFire1(0.5)
       IAF.tau = 10
       IAF.refrac = 5
     }
  }

  proc addConnection() {
     soma3 {
       pt3dadd(x2+8, y2, z2, 1)
       pt3dadd($7+8, $8, $9, 1)
     }
  }


//Connect somas together

  objref prob
  prob = new Random()

  aprob = prob.uniform(0,1)
   

  objref CellConnections

    CellConnections = new NetCon(soma1, soma2, 10, 1, 0.3)

endtemplate simpleIAFcell

Code: Select all

load_file("nrngui.hoc")


objref IAF

create soma1, soma2, soma3


    soma1 {
       nseg = 1
       diam = 100
       L = 100
       Ra = 123.0

       // insert IntFire1 point process
       IAF = new IntFire1(0.5)
       IAF.tau = 10
       IAF.refrac = 5
    }
    
     soma2 {
        nseg = 1
        diam = 50
        L = 100
        Ra = 123.0

        // insert IntFire1 point process
        IAF = new IntFire1(0.5)
        IAF.tau = 10
        IAF.refrac = 5
     }

     soma3 {
        nseg = 1
        diam = 80
        L = 100
        Ra = 123.0

        // insert IntFire1 point process
        IAF = new IntFire1(0.5)
        IAF.tau = 10
        IAF.refrac = 5
     }


// network connection

  objref CellConnections    

    CellConnections = new NetCon(soma1, soma2, 10, 1, 0.5)

Code: Select all

load_file("nrngui.hoc")
load_file("cobacell.hoc") // now the CobaCell class has been defined

///// create cell instances
objref cells
cells = new List()
proc create_cells() { local i
  for i=0,$1-1 cells.append(new CobaCell())
}

///// connect the instances
objref nclist
nclist = new List()
// $1 is index of presynaptic cell
// $2 is index of postsynaptic cell
// $3 is index of synapse on target cell
proc connect_cells() { localobj nc
  nc = cells.o($1).connect2target(cells.o($2).synlist.o($3))
  nclist.append(nc)
}
// make first cell excite 2nd cell
// and 2nd cell inhibit first cell
connect_cells(0, 1, 0)
connect_cells(1, 0, 1)
// don't forget to specify the weights and delays of the NetCons in nclist!

///// create a source of afferent spikes that will drive the network
objref ns, afferent
ns = new NetStim()
  // don't forget to specify properties of NetStim()!
afferent = new NetCon(ns, cells.o(0).synlist.o(0))
  // don't forget to specify properties of this NetCon!

///// capture spike times and plot them
// left as an exercise to the reader
// --see examples of raster plot code in the NEURON Forum

Code: Select all

    NEURON {
	ARTIFICIAL_CELL IntFire1
	RANGE tau, m, refrac
}

PARAMETER { 
  tau = 10 (ms)
  refrac = 5 (ms)
}

ASSIGNED {
  m
  t0 (ms)
  refractory (ms)
}

INITIAL {
  m = 0
  t0 = 0
  refractory = 0
}

NET_RECEIVE (w) {
  if (refractory == 0) {
    m = m*exp(-(t - t0)/tau)
    m = m + w
    t0 = t
    if (m > 1) {
       net_event(t)
       refractory = 1
       net_send(refrac, refractory)
    }
  } else if (flag == 1) {
     : self-event arrived, so terminate refractory period
    refractory = 0
    m = 0
    t0 = t
  } : else ignore the external event  
}

FUNCTION M() {
  if (refractory == 0) {
    M = m*exp(-(t - t0)/tau)
  } else if (refractory == 1) {
    if (t-t0 < 0.5) {
      M = 2
    } else {
      M = -1
    }
  }
}

Code: Select all

obfunc newcell() {localobj cell
        cell =  new IntFire1()
        cell.tau = 10
        cell.refrac = 5
        return cell
}