Bacterial competition influenced by phage-encoded lysin

globals [red-nearby green-nearby red-toxin-area green-toxin-area lysin-area setup-size target feeding-radius radius nearby]
breed [lysins lysin] ;; creates a breed of turtles called "lysins" pluaral and "lysin" singular
lysins-own [age] ;; lysin specific variable used to calculate how old the molecule is
patches-own [ cells energy dormant time nutrient] ; variables for the patches
turtles-own [phage-time] ; a variable for phage used to track age

; Color Coding:
;Phage: Blue- normal phage that can move and attach 
;       Red- Phage that have attached to a cell and can no longer move 
;Lysins: Magenta- normal lysin that can move and attach 
;       Pink- lysins that have attached to cell and can no longer move
;Patches: Shades of Green and Red- normal bacterial cells, lighter shades represent more cells at a location, 
;         Yellow- a patch that only contains nutrient agar can be consumed for energy
;         Brown- a dead bacterial cell, can be consumed for energy
;         Grey- a green bacterial cell that has been infected with phage
;         Black- an empty patch
;
;
;

to setup
  clear-all
  reset-ticks
  set red-nearby circle-neighborhood red-radius
  set green-nearby circle-neighborhood green-radius
  set red-toxin-area circle-neighborhood red-toxin-radius 
  set green-toxin-area circle-neighborhood green-toxin-radius 
  set setup-size circle-neighborhood initial-size
  set feeding-radius circle-neighborhood 3
  ; sets up the model using the different modes
  if mode = "1 colony" ; 1 colony mode sets up a single green colony in the middle
  [
    ask patches [set pcolor 48] 
    ask patch (0) (0)
    [
      ask patches at-points setup-size [
        set pcolor 57
        set energy 0
        set cells 3
      ]
    ]
  ]
  if mode = "random positions" ; this mode spreads a specified number of green and red cells randomly across the grid
  [
    ask patches 
    [
      set pcolor 48
      set cells 0
      set nutrient initial-nutrient
    ] 
    while [count patches with [pcolor = 55] < number-of-green] [ask patch random-xcor random-ycor 
      [
        if pcolor = 48  
        [
          set pcolor 55
          set cells 1
          set nutrient initial-nutrient
        ]
      ]
    ]
    while [count patches with [pcolor = 15] < number-of-red] [ask patch random-xcor random-ycor [
      if pcolor = 48  
      [
        set pcolor 15
        set cells 1
        
        set nutrient initial-nutrient]
    ]
    ]
    
    
  ]
  if mode = "even spacing"
  [
    ask patches 
    [
      set pcolor 48
      set cells 0
      set nutrient initial-nutrient
    ] 
    while [count patches with [pcolor = 55] < number-of-green] [ask patch random-xcor random-ycor 
      [
        if pcolor = 48  
        [
          set pcolor 55
          set cells 1
          set nutrient initial-nutrient
        ]
      ]
    ]
    while [count patches with [pcolor = 15] < number-of-red] [ask patch random-xcor random-ycor [
      if pcolor = 48  
      [
        set pcolor 15
        set cells 1
        
        set nutrient initial-nutrient]
    ]
    ]
  ]
  if mode = "2 colonies" ; this mode makes a green colony and a red colony a specified distance apart
  [
    ;distance-apart is the distance between two colonies
    ask patches [set pcolor 48] 
    ask patch ((distance-apart / 2)) (0)
    [
      ask patches at-points setup-size 
      [
        set pcolor 57
        set energy 0
        set cells 3
      ]
    ]
    ask patch ((distance-apart / -2)) (0)
    [
      ask patches at-points setup-size 
      [
        set pcolor 17
        set energy 0
        set cells 3
        
      ]
    ]
  ]
  if mode = "central phage" ; a high density of green cells with phage in the center that has a delayed start
  [
    ask patches 
    [
      set pcolor one-of [48 57]
      if pcolor = 57
      [
        set energy 1
        set cells 3 
        set time random 10
      ]
    ]
  ]
  if phage?
  [
    setup-phage
  ]
end 

to go
  ;;  asksthe bacteria to eat and grow when possible, and asks the phage and lysins to move.
  ;if growth is disabled the bacteria will not grow.
  if growth? [
    ask patches with [ (pcolor = 55) or (pcolor = 56) or (pcolor = 57)]  
    [
      eat grow-green  
      set time time + 1
    ]
    ask patches with [(pcolor = 15) or (pcolor = 16) or (pcolor = 17)]  
    [
       eat grow-red  
      set time time + 1
    ]
  ]
  ask turtles ;; asks the phage to run their commands
  [
    move attach reproduce
    if mode = "2 colonies" ;; this command delays the phage from doing anything until after 200 ticks. This give the bacteria time to grow first
    [
     if ticks = 200
     [
      
      
       if color = orange
       [
        set color blue 
       ] 
      
     ] 
    ]
  ]
  ask lysins ; asks the lysins to run their commands
  [
   lysin-move lysin-attach grow-up
  ]
  ifelse hide-turtles? ;; hides all the phage if the switch is on
  [ ask turtles
    [
      hide-turtle
    ]
  ] 
  [
   ask turtles
   [
    show-turtle 
   ] 
  ]
  if mouse-down?  ; clicking the mouse on the grid will create a phage at that location
  [
    create-turtles 1 
    [ 
      set color blue
      setxy mouse-xcor mouse-ycor
    ]
  ]
  ifelse energy-label?  ;; will show how much energy each patch has, used only for trouble shooting
  [
    ask patches
    [ 
      set plabel energy
    ]
  ]
  [
    ask patches
    [ 
      set plabel ""
    ]
  ]
  ifelse show-lysin? ; this will show all the lysins if the switch is turned on
  [
    ask lysins
    [
      show-turtle 
    ]
  ]
  [
   ask lysins
   [
    hide-turtle 
   ] 
  ]
  
  tick
end 

to grow-green
  ;; 
  ;; the grow command works by asking a patch if its energy is less than 1. If the cell's "time" variable is hgih enough and has enough energy it will reproduce. The add-to-parent site variable is the probability it will preferentially
  ;; add the new cell to its own location rather than an adjacent one. After succesfully reproducing it will reduce its own energy and reset its time.  
  ;; The cell will ask one-of neighbors with cells < 2 (if it can't find a cell with cells < 2 it will return "nobody" and stop the reproduction event) after finding a cell with cells < 2 that's the right color
  ;; it will add a new cell to that location and change cell number and color accordingly.
 if time > 10
 [ 
  if energy >= 1
    [
      
        ifelse cells < 3
        [
          ifelse add-to-parent-site > random 100
          [
            set cells cells + 1
            set energy energy - 1
            if cells = 2 
            [
              set pcolor 56
            ]
            if cells = 3
            [
              set pcolor 57
            ]
          ]
          [ set target one-of neighbors with [cells < 3]
            
            if target != nobody
            [ 
              ask target
              [
                if ( pcolor = 55) or ( pcolor = 56) or ( pcolor = 57) or ( pcolor = black) or ( pcolor = 48) or (pcolor = brown)
                [
                  if cells = 0 
                  [ 
                    
                    set energy 0
                    set cells 1
                    set pcolor green
                    set time 0
                    ask myself [set energy energy - 1]
                    stop
                  ]
                  if cells = 1
                  [
                    set cells cells + 1
                    set pcolor 56
                    ask myself [set energy energy - 1]
                    stop
                  ]
                  if cells = 2
                  [
                    set cells cells + 1
                    set pcolor 57
                    ask myself [set energy energy - 1]
                    stop
                  ]
                ]
              ]
            ]
          ]
        ]
        [
          set target one-of neighbors with [cells < 3]
          
          if target != nobody 
          [
            ask target
            [
              if (pcolor = 55) or (pcolor = 56) or (pcolor = 57) or (pcolor = black) or (pcolor = 48) or (pcolor = brown)
              [
                if cells = 0 
                [ 
                  set energy 0
                  set cells 1
                  set time 0
                  set pcolor green
                  ask myself [set energy energy - 1]
                  stop
                ]
                if cells = 1
                [
                  set cells cells + 1
                  set pcolor 56
                  ask myself [set energy energy - 1]]
                stop
                if cells = 2
                [
                  set cells cells + 1
                  set pcolor 57
                  ask myself [set energy energy - 1]
                  stop
                ]
              ]
            ]
          ]
        ]
        set time 0
      ]
    ]
end 

to grow-red
  ;; same as green command but with colors switched
  if time > 10
  [ 
    if energy >= 1
    [
     
        ifelse cells < 3
        [
          ifelse add-to-parent-site > random 100
          [
            set cells cells + 1
            set energy energy - 1
            if cells = 2 
            [
              set pcolor 16
            ]
            if cells = 3
            [
              set pcolor 17
            ]
          ]
          [ set target one-of neighbors with [cells < 3]
            
            if target != nobody
            [ 
              ask target
              [
                if ( pcolor = 15) or ( pcolor = 16) or ( pcolor = 17) or ( pcolor = black) or ( pcolor = 48) or (pcolor = brown)
                [
                  if cells = 0 
                  [ 
                    
                    set energy 0
                    set cells 1
                    set pcolor red
                    set time 0
                    ask myself [set energy energy - 1]
                    stop
                  ]
                  if cells = 1
                  [
                    set cells cells + 1
                    set pcolor 16
                    ask myself [set energy energy - 1]
                    stop
                  ]
                  if cells = 2
                  [
                    set cells cells + 1
                    set pcolor 17
                    ask myself [set energy energy - 1]
                    stop
                  ]
                ]
              ]
            ]
          ]
        ]
        [
          set target one-of neighbors with [cells < 3]
          
          if target != nobody 
          [
            ask target
            [
              if (pcolor = 15) or (pcolor = 16) or (pcolor = 17) or (pcolor = black) or (pcolor = 48) or (pcolor = brown)
              [
                if cells = 0 
                [ 
                  set energy 0
                  set cells 1
                  set time 0
                  set pcolor red
                  ask myself [set energy energy - 1]
                  stop
                ]
                if cells = 1
                [
                  set cells cells + 1
                  set pcolor 16
                  ask myself [set energy energy - 1]]
                stop
                if cells = 2
                [
                  set cells cells + 1
                  set pcolor 17
                  ask myself [set energy energy - 1]
                  stop
                ]
              ]
            ]
          ]
        ]
        set time 0
      ]
    ]
end 

;; this is the reporter used to take a radius number (n) and create a list of all the cells in the neighborhood of the radius n and can store the list as a variable (ex. "red-nearby")

to-report circle-neighborhood [n]
  let result [list pxcor pycor] of patches with [(abs pxcor) ^ 2 + (abs pycor) ^ 2 <= n ^ 2]
  report result 
end 

to eat
  ;;a cell can eat a yellow patch for a set amount of energy or a dead brown patch for a set amount of energy.
  ;; this command works by looking for a patch to eat within its feeding radius.
  
 
    if energy < 1
    [
      
      ask one-of patches at-points feeding-radius
      [
        if nutrient > 0
        [
          set nutrient nutrient - 1
          ask myself 
          [
            set energy energy + 1 
          ] 
        ] 
      ] 
    ]
end 

to setup-phage  ;; different ways to start the phage
  ifelse mode = "central phage" ; this creates phage right on the origin of the grid
    [
      create-turtles initial-number
      ask turtles [setxy 0 0]
      ask turtles [set color blue]
    ]
    [
      ifelse mode = "2 colonies" ; starts phage in the center of the green colony
      [
        create-turtles initial-number    
      ask turtles [ setxy (distance-apart / 2) 0 ]
      ask turtles [ set color orange ]
      ]
      [ 
        ifelse mode = "even spacing"
        [
           create-turtles 1 [ setxy -15 15]
           create-turtles 1 [ setxy 0 15]
           create-turtles 1 [ setxy 15 15]
           create-turtles 1 [ setxy -15 -15]
           create-turtles 1 [ setxy 0 -15]
           create-turtles 1 [ setxy 15 -15]
           ask turtles [set color blue]
           
        ]
        [
          create-turtles initial-number    ; for all other modes the phage are given random starting locations
          ask turtles [ setxy random-xcor random-ycor ]
          ask turtles [ set color blue ]
        ]
      ]
    ]
end 

to move ;; the phage moves if it is blue
  if color = blue [
    right random 360
    forward .25
  ] 
  if color = red
  [
    set phage-time phage-time + 1
  ]
end 

to attach  ; blue phage can attach and turn red, and turn the patch grey. Red phage do not move.
  if color = blue
    [ if (pcolor = 55) or (pcolor = 56) or (pcolor = 57) or (pcolor = grey)
      [ if random 100 < attachment-chance
        [
          set color red
          set pcolor grey
          set phage-time 0
        ]
      ]
    ]
end 

to reproduce ; after being attached for the amount of time specified by phage-reproduction-time, the phage lyses the cell, produces offspring and reduces the cell count on a patch by 1, if the cell count equals zero the patch turns brown
  if color = red
  [
    if phage-time = phage-reproduction-time
    [ 
      
      hatch burst-size [ set color blue] 
      set color black
      ask patch-here
      [
        set cells cells - 1
        set nutrient nutrient + corpse-energy
        if lysin?
        [
          lyse
        ]
        if cells = 0
        [
          set pcolor brown
          ask turtles-here 
          [
            if color = red
            [
              set color black 
            ] 
          ]
        ] 
      ]
      
    ] 
  ]
end    

to lyse ;; a command for a patch to lyse and burst out lysin molecules
 
    sprout-lysins lysin-production
    [
      set color magenta
      set size 1
      set age 0
    ]
end 

to lysin-move  ; command to let the lysins move, only magenta lysins can move
  if color = magenta
  [
    right random 360
    forward lysin-speed
  ]
end 

to lysin-attach ; lysin can attach and turn pink, once the number of lysin attached is equal to the lethal-amount the cell dies and clears all attached lysin molecules
  if (pcolor = 15) or (pcolor = 16) or (pcolor = 17) 
  [
    if random 100 < lysin-attachment-chance
    [
      
      set color pink
      ask patch-here
        [
          if count lysins-here with [color = pink] = lethal-amount
            [
              
              set cells cells - 1
              set nutrient nutrient + corpse-energy
              if cells = 0
              [
                set pcolor brown
              ]
              ask lysins-here
              [
                if color = pink
                [
                  die 
                ] 
              ]
            ] 
        ]
    ]
  ]
end 

to grow-up ; lysins grow older each tick once they reach degradation-time they die
  
  ifelse age = degradation-time
  [
   die 
  ]
  [
  set age age + 1
  ]
end