Complete Netlogo Tutorial_Surber

links-own [ tDCfree ]
globals [ dt ds tcell-step nDCmeet]
; dt = duration of one step in min/time step
; ds= size of one patch in um/patch
; tcell-step = size of tcell step in patches/time step
; nDCmeet = number of DC-T cell encounters
breed [tcells tcell] ; the T cells
breed [DCs DC] ; the dentric cells (DCs)

to setup
  clear-all
  set-default-shape turtles "circle" ; all turtles will be circles (spheres)
  create-tcells 100 [
    set color green ; make T cell green
    setxyz random-xcor random-ycor random-zcor ; put T cell at random location
  ]
  create-DCs 2 [
    set size 2 ; make DC of size 2 (twice that of T cells)
    set color red ; make DC red
    setxyz random-xcor random-ycor random-zcor
  ]
  set dt 0.5 ; 0.5 min per time step
  set ds 8 ; 8 um per patch
  set tcell-step 16 / ds * dt ; (16 um/min)*(1 patch/8 um)*(0.5 min/time step)
end 

to go
  move-tcells ; move T cell movement commands into a function
  identify-DCbound-tcells ; new function to identify DC-bound T cells
  update-link-status ; new function to update DC-T cell links
  plotxy ticks nDCmeet
  tick-advance dt
end 

to move-tcells ; function for T cell motion
  ask tcells [
    right random-normal 0 90
    roll-right random-normal 0 90
    forward tcell-step
  ]
end 

to identify-DCbound-tcells ; function to identify DC-bound T cells
  ask DCs [
    create-links-to tcells with [ color != blue ] in-radius 2 [
      set color red ; make the link red
      set tDCfree 3 ; bound for 3 minutes
      ask end2 [ set color blue ] ; make the linked T cell blue
      set nDCmeet nDCmeet + 1
    ]
  ]
end 

to update-link-status ; function to update the DC-T cell links
  ask links [
    set tDCfree tDCfree - dt ; update time remaining for link
    if tDCfree < 0 [ ; if tDCfree has elapsed
      ask end2 [ set color green] ; set T cell to its green colour
    ]
  ]
reset-ticks
end