Team:Valencia UPV/Modeling/sexyplants.nlogo

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breed [ moths moth ] breed [ females female ] breed [ standers stander ]


moths-own [

 number-encounter
 count-down
 ocupado     ;1 mating _ 0 free
 flockmates
 nearest-neighbor

]

females-own [

 count-down
 ocupado    ;1 mating _ 0 free
 wait-time  ;after mating, females don't emit pheromone and shouldn't mate a male

]


patches-own [

 old-pheromonelevel   ; the pheromonelevel of the patch the last time thru go
 pheromonelevel       ; the current pheromonelevel of the patch

]

globals [

 plate-size           ; the size of the plate on which pheromone is diffusing                    
 min-pherolevel       ; the minimum pheromonelevel 
 max-pherolevel       ; the maximum pheromonelevel                       
 old-number-encounter
]


Setup Procedures ;;;

to setup

 clear-all
 set plate-size max-pxcor 
  
 
;TO SEE STANDARS JUST REMOVE ; FROM THE FIVE LINES BELOW 
 ;create-standers 20000
 ;[
  ; setxy random-xcor random-ycor
  ; set color gray
   ;set size 0.5
; ]
 
 ask patches
 [
   set pcolor white
   set-initial-pheromonelevels
   ;set-edge-pheromonelevels
   set old-pheromonelevel pheromonelevel
 ]
 set min-pherolevel min [old-pheromonelevel] of patches
 set max-pherolevel max [old-pheromonelevel] of patches
 ask patches [ draw-plate ]
 
 
 set-default-shape moths "butterfly"
 make-moths number-moths
 
 set-default-shape females "butterfly"
 make-females number-females
 
 

;SEXYPLANTS
 crt 1 [set shape "flower" set size 5 set xcor 0 set ycor 0 set color 86 ]
 crt 1 [set shape "flower" set size 5 set xcor 20 set ycor 20 set color 86 ]
 crt 1 [set shape "flower" set size 5 set xcor -20 set ycor 20 set color 86]
 crt 1 [set shape "flower" set size 5 set xcor 20 set ycor -20 set color 86]
 crt 1 [set shape "flower" set size 5 set xcor -20 set ycor -20 set color 86]
 
;CROP   
 crt 1 [set shape "plant" set size 2 set xcor 0 set ycor 20 set color 44]
 crt 1 [set shape "plant" set size 2 set xcor 20 set ycor 0 set color 44]
 crt 1 [set shape "plant" set size 2 set xcor -20 set ycor 0 set color 44]
 crt 1 [set shape "plant" set size 2 set xcor 0 set ycor -20 set color 44]
 crt 1 [set shape "plant" set size 2 set xcor 10 set ycor 0 set color 44]
 crt 1 [set shape "plant" set size 2 set xcor -10 set ycor 0 set color 44]
 crt 1 [set shape "plant" set size 2 set xcor -10 set ycor -20 set color 44]
 crt 1 [set shape "plant" set size 2 set xcor 10 set ycor -20 set color 44]
 crt 1 [set shape "plant" set size 2 set xcor -10 set ycor 20 set color 44]
 crt 1 [set shape "plant" set size 2 set xcor 10 set ycor 20 set color 44]
 crt 1 [set shape "plant" set size 2 set xcor -30 set ycor 0 set color 44]
 crt 1 [set shape "plant" set size 2 set xcor -30 set ycor 20 set color 44]
 crt 1 [set shape "plant" set size 2 set xcor 30 set ycor 0 set color 44]
 crt 1 [set shape "plant" set size 2 set xcor 30 set ycor 20 set color 44]
 crt 1 [set shape "plant" set size 2 set xcor 30 set ycor -20 set color 44]
 crt 1 [set shape "plant" set size 2 set xcor -30 set ycor -20 set color 44]
; crt 1 [set shape "plant" set size 2 set xcor 0 set ycor 10 set color 44]
; crt 1 [set shape "plant" set size 2 set xcor 0 set ycor -10 set color 44]
; crt 1 [set shape "plant" set size 2 set xcor 40 set ycor 0 set color 44]
; crt 1 [set shape "plant" set size 2 set xcor 0 set ycor 40 set color 44]
; crt 1 [set shape "plant" set size 2 set xcor -40 set ycor 0 set color 44]
; crt 1 [set shape "plant" set size 2 set xcor 0 set ycor -40 set color 44]
; crt 1 [set shape "plant" set size 2 set xcor 0 set ycor 60 set color 44]
; crt 1 [set shape "plant" set size 2 set xcor 0 set ycor -60 set color 44]
; crt 1 [set shape "plant" set size 2 set xcor 60 set ycor 0 set color 44]
; crt 1 [set shape "plant" set size 2 set xcor -60 set ycor 0 set color 44]
; crt 1 [set shape "plant" set size 2 set xcor 40 set ycor 20 set color 44]
; crt 1 [set shape "plant" set size 2 set xcor -40 set ycor -20 set color 44]
; crt 1 [set shape "plant" set size 2 set xcor 40 set ycor -20 set color 44]
; crt 1 [set shape "plant" set size 2 set xcor -40 set ycor 20 set color 44]
; crt 1 [set shape "plant" set size 2 set xcor 40 set ycor 20 set color 44]  
; crt 1 [set shape "plant" set size 2 set xcor -40 set ycor 40 set color 44]
 
 reset-ticks

end

to make-moths [ number ]

 create-moths number [
   set color brown
   jump random-float max-pxcor
   set size 2
   set number-encounter 0
   set count-down 40
   set ocupado 0
 ]

end

to make-females [ number ]

 create-females number [
   set color 125
   jump random-float max-pxcor
   set size 2
   set count-down 40
   set ocupado 0
   set wait-time 0
 ]

end

Sets the pheromonelevel for inside of the plate

to set-initial-pheromonelevels  ;; Patch Procedure

 if ((abs pycor) < plate-size) and ((abs pxcor) < plate-size)
 [set pheromonelevel initial-plate-pherolevel]                     ;we consider no pheromone concentration in the field for t=0
 
 ;Sexyplants
 if ( (pycor)= 0 ) and ( (pxcor) = 0)
 [set pheromonelevel releaserate-sexyplant]
   if ( (pycor)= 20 ) and ( (pxcor) = 20)
 [set pheromonelevel releaserate-sexyplant]
   if ( (pycor)= 20 ) and ( (pxcor) = -20)
 [set pheromonelevel releaserate-sexyplant]
     if ( (pycor)= -20 ) and ( (pxcor) = 20)
 [set pheromonelevel releaserate-sexyplant]
   if ( (pycor)= -20 ) and ( (pxcor) = -20)
 [set pheromonelevel releaserate-sexyplant]
 

end


Sets the pheromonelevels of the plate edges and corners
In this simulation this command is not activated, since the we consider an opened volume.

to set-edge-pheromonelevels  ;; patch procedure

 ; set the pheromonelevels of the edges
 if (pxcor >= plate-size) and ((abs pycor) < plate-size)
 [set pheromonelevel 0]
 if (pxcor <= (- plate-size)) and ((abs pycor) < plate-size)
 [set pheromonelevel 0]
 if (pycor >= plate-size) and ((abs pxcor) < plate-size)
 [set pheromonelevel 0]
 if (pycor <= (- plate-size)) and ((abs pxcor) < plate-size )
 [set pheromonelevel 0]
 ; set the pheromonelevels of the corners
 if (pxcor >= plate-size) and (pycor >= plate-size)
 [set pheromonelevel 0]
 if (pxcor >= plate-size) and (pycor <= (- plate-size))
 [set pheromonelevel 0]
 if (pxcor <= (- plate-size)) and (pycor >= plate-size)
 [set pheromonelevel 0]
 if (pxcor <= (- plate-size)) and (pycor <= (- plate-size))
 [set pheromonelevel 0]


end


Runtime Procedures ;;;
Runs the simulation through a loop

to go

 set max-pherolevel max [old-pheromonelevel] of patches
 set min-pherolevel min [old-pheromonelevel] of patches
 
 ask females [set color 125]
 ask standers [set color gray]
 
 move-thru-field ;males
     
 move-thru-field-females
 
 ask patches [
   ;Diffusion process with advection (wind)
   set pheromonelevel (pheromone-diffusivity * (sum [old-pheromonelevel] of neighbors4) - wind-forcey * ([old-pheromonelevel] of patch-at-heading-and-distance 0 1) - wind-forcex * ([old-pheromonelevel] of patch-at-heading-and-distance 90 1)) + ((1 - ( 4 * pheromone-diffusivity - 1 * wind-forcey - 1 * wind-forcex )) * old-pheromonelevel)
   ;set-edge-pheromonelevels
   set old-pheromonelevel pheromonelevel
   draw-plate
   ]

   
 if switch = TRUE [
 ask patches
 [
   ;; diffuse the pheromone of a patch with its neighbors
   if ( (pycor)= 0 ) and ( (pxcor) = 0)
   [set pheromonelevel (pheromone-diffusivity * (sum [old-pheromonelevel] of neighbors4)) + ((1 - ( 4 * pheromone-diffusivity )) * old-pheromonelevel + releaserate-sexyplant)]
   if ( (pycor)= 20 ) and ( (pxcor) = 20)
   [set pheromonelevel (pheromone-diffusivity * (sum [old-pheromonelevel] of neighbors4)) + ((1 - ( 4 * pheromone-diffusivity )) * old-pheromonelevel + releaserate-sexyplant)]
    if ( (pycor)= 20 ) and ( (pxcor) = -20)
   [set pheromonelevel (pheromone-diffusivity * (sum [old-pheromonelevel] of neighbors4)) + ((1 - ( 4 * pheromone-diffusivity )) * old-pheromonelevel + releaserate-sexyplant)]
    if ( (pycor)= -20 ) and ( (pxcor) = 20)
   [set pheromonelevel (pheromone-diffusivity * (sum [old-pheromonelevel] of neighbors4)) + ((1 - ( 4 * pheromone-diffusivity )) * old-pheromonelevel + releaserate-sexyplant)]
    if ( (pycor)= -20 ) and ( (pxcor) = -20)
   [set pheromonelevel (pheromone-diffusivity * (sum [old-pheromonelevel] of neighbors4)) + ((1 - ( 4 * pheromone-diffusivity )) * old-pheromonelevel + releaserate-sexyplant)]
   ; set the edges back to their constant pheromone
   ;set-edge-pheromonelevels
   set old-pheromonelevel pheromonelevel
   draw-plate
  ]
  
   ] 
 tick

end


to move-thru-field  ; turtle procedure for male moths behavior

  ask moths
  [
  ;MATING PROCEDURE
  ifelse (ocupado = 1) ;If i am mating
     [
         stay
     ]
     [
         ifelse any? (females-on neighbors) 
         [       
         set flockmates other females-on neighbors
         set nearest-neighbor min-one-of flockmates [distance myself]
         ifelse (([ocupado] of nearest-neighbor) = 0 and ([wait-time] of nearest-neighbor) = 0 )
            [
            set ocupado 1
            reset-count-down
            stay
            ]   ;If she is free and can
            [
            continue
            ]
         ][continue]   
     ]
  ] 

end

to stay

 ifelse count-down = 0 
   [  
     set number-encounter number-encounter + 1
     set label number-encounter         
     reset-count-down
     set ocupado 0
   ] 
   [
     set count-down count-down - 1   ;decrement-timer
     set label count-down   
   ]   

end

to continue  ;MALE MOTH RESPONSE


 ifelse ( pheromonelevel <= detectionthreshold)         
 [                                                            
   ; if there is no detectable pheromone move randomly
   ; flight by non-responding male moths involves short, fast movements in random directions  (J.N. Perry and C.Wall, 1984)
   rt flutter-amount 45    ;RANDOM FLIGHT                                   
 fd 1
 ]                                                            
 [                                                           
   ifelse (random 25 = 0)                                     
   ; add some additional randomness to the moth's movement, this allows some small
   ; probability that the moth might "escape"
   [
     rt flutter-amount 60
   fd 1
   ]
   [
     ifelse (pheromonelevel <= saturationlevel) 
     [       
      maximize 
      if (xcor = 0) and (ycor = 0)       ;flying around our sexy plants
      [jump 2
        rt flutter-amount 70
        fd 1
        ]
      if (xcor = 20) and (ycor = 20)       
      [jump 2
        rt flutter-amount 70
        fd 1]
      if (xcor = -20) and (ycor = -20)       
      [jump 2
        rt flutter-amount 70
        fd 1]
      if (xcor = 20) and (ycor = -20)       
      [jump 2
        rt flutter-amount 70
        fd 1]
      if (xcor = -20) and (ycor = 20)       
      [jump 2
        rt flutter-amount 70
        fd 1]
     ]
    
     [
       rt flutter-amount 60
       fd 1
       ]                                                     
   ]
 ]                                                              
 if not can-move? 1
   [ maximize ]

end

to move-thru-field-females  ; turtle procedure for female moths behavior

  ask females 
  [
    
   ;MATING PROCEDURE 
   ifelse (ocupado = 1)
   [
     stayfemale
   ]
   [  ;If i am free
      ifelse (any? moths-on neighbors) ;There are neighbors
      [  
          let flockmates-fem moths-on neighbors
          let nearest-neighbor-fem min-one-of flockmates-fem [distance myself]
          ifelse (([nearest-neighbor] of nearest-neighbor-fem) != 0) [
          ifelse ( ([who] of self)  = ( [who] of ([nearest-neighbor] of nearest-neighbor-fem) ) and (wait-time = 0) ) ;ask if the neighbor of my neighbor is me:  who-of myself
          [                    
          set ocupado 1
          set color 85    ;change its colour in order to differentiate it by the observer
          stayfemale
          ] [          continuefemale       ]][continuefemale]
      ]
      [
         continuefemale
      ] 
    ]
   ]

end

to stayfemale

 ifelse (count-down = 0)
   [      
     reset-count-down
     set ocupado 0
     set wait-time 100
     continuefemale
    ]
   [ set count-down count-down - 1   ;decrement-timer
 set label count-down    
   ]

end

to continuefemale

      ifelse wait-time > 0 
       [set wait-time wait-time - 1]  ;decrement timer for females after mating
       [pheromone-emission]                                          
      rt flutter-amount 45      ;RANDOM FLIGHT                                            
      if not can-move? 1
      [rt flutter-amount 60]
      fd 1  

end

to pheromone-emission

  ask patches in-radius 1[  
  set pheromonelevel releaserate
  set pheromonelevel (pheromone-diffusivity * (sum [old-pheromonelevel] of neighbors4)) + ((1 - ( 4 * pheromone-diffusivity )) * old-pheromonelevel + releaserate)
  set old-pheromonelevel pheromonelevel  
  draw-plate ] 

end

to-report flutter-amount [limit]

 ;; This routine takes a number as an input and returns a random value between
 ;; (+1 * input value) and (-1 * input value).
 ;; It is used to add a random flutter to the moth's movements
 report random-float (2 * limit) - limit

end

CHEMOATTRACTION

to maximize  ;; turtle procedure male moth

 move-to patch-here  
 let p max-one-of neighbors [pheromonelevel]  
 let gradient_p [pheromonelevel] of p - pheromonelevel
 ifelse (gradient_p > delta) [
 face p 
 rt random-normal 0 (0.2 * (5 / gradient_p))    ;; RANDOM TURNING ANGLE INVERSELY RELATED TO THE GRADIENT OF PHEROMONE CONCENTRATION (model project approximation)
 fd 1
 ]
   [rt flutter-amount 60
     fd 1] 

end

Draws the patches that are within the plate

to draw-plate  ;; Patch Procedure

 if ((abs pycor) <= plate-size) and ((abs pxcor) <= plate-size)
 [color-patch]

end

color the patch based on its pheromonelevel

to color-patch  ;; Patch Procedure

 set pcolor scale-color 123 pheromonelevel 50 0

end

to-report releaserate

 report 3 * release-rate 

end


to-report releaserate-sexyplant

 report 3 * release-rate-sexyplant         ;Primary sex pheromone components are approximately defined as those emitted by the calling insect that are obligatory

end  ;for trap catch in the field at component emission rates similar to that used by the insect.

                                           ;(W. L. Roelofs and R. T. Carde. Responses of Lepidoptera to Synthetic Sex Pheromone Chemicals and their Analogues, Page 386.
report the pheromone diffusivity constant that we use for the calculations of pheromone diffusion

to-report pheromone-diffusivity

 report number-diffusivity 

end

to-report wind-forcex

 report wind-force-x

end

to-report wind-forcey

 report wind-force-y

end

to-report delta

 report 5 - moth-sensitivity
  

end


to-report saturationlevel

 report saturation-level-threshold 

end

to-report detectionthreshold

 report detection-threshold

end


to reset-count-down

 set count-down 40 

end



Copyright 2014 Valencia_UPV iGEM team
See Info tab for full copyright and license.

@#$#@#$#@ GRAPHICS-WINDOW 976 12 1581 627 50 49 5.9 1 2 1 1 1 0 1 1 1 -50 50 -49 49 1 1 1 ticks 20.0

SLIDER 978 637 1178 670 initial-plate-pherolevel initial-plate-pherolevel 0 25 0 1 1 NIL HORIZONTAL

BUTTON 1480 640 1545 673 Go go T 1 T OBSERVER NIL NIL NIL NIL 1

BUTTON 1273 639 1389 672 Setup setup NIL 1 T OBSERVER NIL NIL NIL NIL 1

BUTTON 1398 640 1471 673 Go Once go NIL 1 T OBSERVER NIL NIL NIL NIL 1

SWITCH 1216 12 1317 45 switch switch 1 1 -1000

SLIDER 32 33 204 66 number-moths number-moths 0 100 5 1 1 u HORIZONTAL

SLIDER 33 78 205 111 number-females number-females 0 50 5 1 1 u HORIZONTAL

SLIDER 32 443 245 476 number-diffusivity number-diffusivity 0.01 0.2 0.177 0.001 1 cm^2/s HORIZONTAL

PLOT 273 337 957 640 Meetings in time Time Number of meeting 0.0 1000.0 0.0 10.0 true false "" "" PENS "males mating" 1.0 0 -2674135 true "" "plot sum [ocupado] of moths"

SLIDER 27 304 199 337 moth-sensitivity moth-sensitivity 0 5 4.6 0.001 1 NIL HORIZONTAL

SLIDER 26 262 214 295 saturation-level-threshold saturation-level-threshold 1 100 8 1 1 NIL HORIZONTAL

MONITOR 306 369 575 422 number of encounters at this instant sum [ocupado] of moths 17 1 13

PLOT 275 12 955 329 Total number of encounters in time Time Number of encounters 0.0 1000.0 0.0 100.0 true true "" "" PENS "total number of encounters up to now" 1.0 0 -14070903 true "" "plot sum [number-encounter] of moths" "males mating at this moment" 1.0 0 -2674135 true "" "plot sum [ocupado] of moths"

MONITOR 314 39 507 93 total number of encounters sum [number-encounter] of moths 17 1 13

SLIDER 27 217 198 250 detection-threshold detection-threshold 0.5 5 1.2 0.1 1 NIL HORIZONTAL

SLIDER 32 488 176 521 wind-force-x wind-force-x -0.1 0.1 0 0.01 1 NIL HORIZONTAL

SLIDER 33 534 172 567 wind-force-y wind-force-y -0.1 0.1 0 0.01 1 NIL HORIZONTAL

SLIDER 27 178 198 211 release-rate release-rate 0 1 0.999 0.001 1 µg/h HORIZONTAL

SLIDER 27 346 246 379 release-rate-sexyplant release-rate-sexyplant 0 1 0.998 0.001 1 µg/h HORIZONTAL

@#$#@#$#@

    1. WHAT IS IT?

This model simulates pheromone diffusion processes and its influence in moths response. https://2014.igem.org/Team:Valencia_UPV

    1. HOW IT WORKS

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    1. HOW TO USE IT

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    1. THINGS TO TRY

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    1. THINGS TO NOTICE

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    1. EXTENDING THE MODEL

This model simulates a classic partial differential equation problem (that of heat diffusion with advection).


    1. HOW TO CITE

If you mention this model in a publication, we ask that you include these citations for the model itself and for the NetLogo software:

  • Valencia_UPV iGEM, Alejandra González Boscá (2014) Pheromone diffusion and moths response with Sexyplants


    1. COPYRIGHT AND LICENSE

Valencia_UPV iGEM 2014

Alejandra González Boscá


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triangle false 0 Polygon -7500403 true true 150 30 15 255 285 255

triangle 2 false 0 Polygon -7500403 true true 150 30 15 255 285 255 Polygon -16777216 true false 151 99 225 223 75 224

truck false 0 Rectangle -7500403 true true 4 45 195 187 Polygon -7500403 true true 296 193 296 150 259 134 244 104 208 104 207 194 Rectangle -1 true false 195 60 195 105 Polygon -16777216 true false 238 112 252 141 219 141 218 112 Circle -16777216 true false 234 174 42 Rectangle -7500403 true true 181 185 214 194 Circle -16777216 true false 144 174 42 Circle -16777216 true false 24 174 42 Circle -7500403 false true 24 174 42 Circle -7500403 false true 144 174 42 Circle -7500403 false true 234 174 42

turtle true 0 Polygon -10899396 true false 215 204 240 233 246 254 228 266 215 252 193 210 Polygon -10899396 true false 195 90 225 75 245 75 260 89 269 108 261 124 240 105 225 105 210 105 Polygon -10899396 true false 105 90 75 75 55 75 40 89 31 108 39 124 60 105 75 105 90 105 Polygon -10899396 true false 132 85 134 64 107 51 108 17 150 2 192 18 192 52 169 65 172 87 Polygon -10899396 true false 85 204 60 233 54 254 72 266 85 252 107 210 Polygon -7500403 true true 119 75 179 75 209 101 224 135 220 225 175 261 128 261 81 224 74 135 88 99

wheel false 0 Circle -7500403 true true 3 3 294 Circle -16777216 true false 30 30 240 Line -7500403 true 150 285 150 15 Line -7500403 true 15 150 285 150 Circle -7500403 true true 120 120 60 Line -7500403 true 216 40 79 269 Line -7500403 true 40 84 269 221 Line -7500403 true 40 216 269 79 Line -7500403 true 84 40 221 269

x false 0 Polygon -7500403 true true 270 75 225 30 30 225 75 270 Polygon -7500403 true true 30 75 75 30 270 225 225 270

@#$#@#$#@ NetLogo 5.1.0 @#$#@#$#@ @#$#@#$#@ @#$#@#$#@ @#$#@#$#@ @#$#@#$#@ default 0.0 -0.2 0 0.0 1.0 0.0 1 1.0 0.0 0.2 0 0.0 1.0 link direction true 0 Line -7500403 true 150 150 90 180 Line -7500403 true 150 150 210 180

@#$#@#$#@ 0 @#$#@#$#@