main.nlogo

; Melisa Saichi & Thomas Bersez
; M2 GENIOHME, fall semester 2018
;-----------------------------------------------------------------------
patches-own [
  act-c     ; activator concentration
  inh-c     ; inhibitor concentration
  act-n     ; activator concentration
  inh-n     ; activator concentration
]
;----------------------------------------------------------------------
; Procedures
to show-concentration
  ask patches [
    set pcolor scale-color
    green act-c
    2 ; residual
    80 ; maximum
  ]
end

to setup
  clear-all
  random-seed 137 ; to allow reproducibility, random seed is manualy fixed
  ask patches [ set act-c random-float 50.0
    set inh-c random-float 50.0 ] ; random concentrations are set
end

to copy-concentration
  ask patches [
    set act-n ( act-c )
    set inh-n ( inh-c )
  ]
end

to production-decay ; autonomous syntesis and decay for act & inh
  ask patches [
    set act-n ( act-c + ActivatorProduction - ( ActivatorDecayRate * act-c ) )
    set inh-n ( inh-c + InhibitorProduction - ( InhibitorDecayRate * inh-c ) )
  ]
end

to act-inh-dependent-production
    ask patches [
    if act-c < 100
    [
      ifelse inh-c > 0
      [ set act-n ( act-n + ( InteractionRate * ( ( act-c * act-c ) / inh-c ) ) ) ]
      [ set act-n ( act-n + ( InteractionRate * ( ( act-c * act-c ) ) ) ) ]
    ]
    if inh-c < 100
    [ set inh-n ( inh-n + ( InteractionRate * ( act-c * act-c ) ) ) ]
  ]
end

to diffusion
    ask patches [

    let ACT ( act-c )
    let INH ( inh-c )

    ; define activator diffusion coefficient according to mode

    if Mode = "OneDim"
    [ let onedim ( abs  ( cos ( Multact * pxcor ) ) )
    set act-n ( act-n - ( onedim * act-n ) )
    set inh-n ( inh-n - ( InhibitorDiffusionRate * act-n ) )
      ask neighbors [
        set act-n ( act-n + ( ( onedim * ACT ) / 8  ) )
        set inh-n ( inh-n + ( ( InhibitorDiffusionRate * INH ) / 8 ) )
      ]
    ]

    if Mode = "TwoDim"
    [ let twodim ( abs ( 0.5 * ( cos ( Multact * pxcor ) + cos ( Multact * pycor) ) ) )
      set act-n ( act-n - ( twodim * act-n ) )
      set inh-n ( inh-n - ( InhibitorDiffusionRate * act-n ) )
        ask neighbors [
        set act-n ( act-n + ( ( twodim * ACT ) / 8  ) )
        set inh-n ( inh-n + ( ( InhibitorDiffusionRate * INH ) / 8 ) )
      ]
    ]

    if Mode = "Homogenous"
    [ set act-n ( act-n - ( ActivatorDiffusionRate * act-n ) )
    set inh-n ( inh-n - ( InhibitorDiffusionRate * act-n ) )
        ask neighbors [
        set act-n ( act-n + ( ( ActivatorDiffusionRate * ACT ) / 8  ) )
        set inh-n ( inh-n + ( ( InhibitorDiffusionRate * INH ) / 8 ) )
      ]
    ]
  ]
end

to next-turn
    ask patches [
    ifelse act-n < 0
    [ set act-c ( 0 ) ]
    [ set act-c ( act-n ) ]
    ifelse inh-n < 0
    [ set inh-c ( 0 ) ]
    [ set inh-c ( inh-n ) ]
  ]
  show-concentration
end
@#$#@#$#@
GRAPHICS-WINDOW
91
10
500
420
-1
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1.0
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ticks
30.0

BUTTON
9
12
73
45
Setup
setup\nshow-concentration\n
NIL
1
T
OBSERVER
NIL
NIL
NIL
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1

BUTTON
191
439
394
472
Start
copy-concentration\nproduction-decay\nact-inh-dependent-production\ndiffusion\nnext-turn
T
1
T
OBSERVER
NIL
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1

SLIDER
510
294
682
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InteractionRate
InteractionRate
0
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1
NIL
HORIZONTAL

INPUTBOX
507
10
662
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ActivatorProductionRate
1.0
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0
Number

INPUTBOX
669
10
824
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InhibitorProductionRate
0.5
1
0
Number

INPUTBOX
507
78
662
138
ActivatorDecayRate
0.3
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Number

INPUTBOX
670
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825
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InhibitorDecayRate
0.1
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Number

INPUTBOX
507
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662
206
ActivatorDiffusionRate
0.1
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Number

INPUTBOX
670
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InhibitorDiffusionRate
0.6
1
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Number

INPUTBOX
508
214
663
274
ActivatorProduction
28.0
1
0
Number

INPUTBOX
670
214
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InhibitorProduction
3.0
1
0
Number

CHOOSER
690
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828
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Mode
Mode
"Homogenous" "OneDim" "TwoDim"
2

INPUTBOX
835
10
990
70
Multact
1.0
1
0
Number

@#$#@#$#@
## WHAT IS IT?

(a general understanding of what the model is trying to show or explain)

## HOW IT WORKS

(what rules the agents use to create the overall behavior of the model)

## HOW TO USE IT

(how to use the model, including a description of each of the items in the Interface tab)

## THINGS TO NOTICE

(suggested things for the user to notice while running the model)

## THINGS TO TRY

(suggested things for the user to try to do (move sliders, switches, etc.) with the model)

## EXTENDING THE MODEL

(suggested things to add or change in the Code tab to make the model more complicated, detailed, accurate, etc.)

## NETLOGO FEATURES

(interesting or unusual features of NetLogo that the model uses, particularly in the Code tab; or where workarounds were needed for missing features)

## RELATED MODELS

(models in the NetLogo Models Library and elsewhere which are of related interest)

## CREDITS AND REFERENCES

(a reference to the model's URL on the web if it has one, as well as any other necessary credits, citations, and links)
@#$#@#$#@
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@#$#@#$#@
NetLogo 6.0.4
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default
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0
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