Skin microbiome and Shine coli

Skin microbiome and Shine coli preview image

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Default-person Caius Gibeily (Author)

Tags

microbiome 

Tagged by Caius Gibeily 21 days ago

Visible to everyone | Changeable by the author
Model was written in NetLogo 6.1.1 • Viewed 60 times • Downloaded 0 times • Run 0 times
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; (C) Caius Gibeily - Designer of Microbiome Simulator

patches-own [damage birth-tick age quorum_col2 quorum_col3 ]

to setup
  clear-all
  if Seed = True [
         random-seed seed-val
  ]
  ask patches [
    set pcolor one-of [green blue orange]
    set birth-tick 4
    set damage 0
    set quorum_col3 0
   set quorum_col2 0
  ]
  reset-ticks
end 

to go
  ask patches [
    set birth-tick ticks
    col-replication
    increment-age
    death

  ]
  if Model-type = "solar model" [
      ask up-to-n-of solar-flux patches [set damage (damage + damage-factor)
         UV-recovery
    ]
  ]
  if Model-type = "quorum sensing" [
    ask patches [
      quorum-sensing
    ]
  ]



if (count patches with [pcolor = green] = 0) and (count patches with [pcolor = orange] = 0) and (count patches with [pcolor = blue] = 0) [
    stop
  ]



  if (count patches with [pcolor = green] >= 21000) or (count patches with [pcolor = orange] >= 21000) or (count patches with [pcolor = blue] >= 21000) [
    print "All hail the new colony"
  ]
  if (ticks = N-cycles) and (N-cycles > 0) [
    stop]

  tick
end 

to increment-age
   let age-in-ticks birth-tick - ticks
    if (age-in-ticks >= 0) and (age-in-ticks mod 2 = 0) [
    set age (1 + age)
  ]
end 

to quorum-sensing

  ask self [
    ifelse (pcolor = blue) and (age >= col2-doublingt) [
      set quorum_col2 quorum_col2 + 1
    let amount quorum_col2 * col2-secretion
    let neighbor-share amount / 8
    ask neighbors4 [set quorum_col2 quorum_col2 + neighbor-share]
  ]


     [if (pcolor = orange) and (age >= col3-doublingt) [
      set quorum_col3 quorum_col3 + 1
    let amount2 quorum_col3 * col3-secretion
    let neighbor-share2 amount2 / 8
    ask neighbors4 [set quorum_col3 quorum_col3 + neighbor-share2]
  ]
  ]
  ]
end 

to col-replication
  ask self [
    if (pcolor = cyan) and (age = 3) [
      if random-float 120 < shine-replication [
        set birth-tick ticks
        set age 0
          ask neighbors4 [
          set pcolor cyan
          set birth-tick ticks
          set age 0
        ]
        ]
    ]
     if (pcolor = green) and (age = col1-doublingt) [
      if random-float 100 < col1-replication [
        set birth-tick ticks
        set age 0
          ask neighbors4 [
          set pcolor green
          set birth-tick ticks
          set age 0
        ]
        ]
    ]

 ifelse (Model-type = "quorum sensing") and (pcolor = blue) and (age = col2-doublingt) [

  ifelse (pcolor = blue) and (age = col2-doublingt) and (quorum_col2 > 5) [
        if random-float 40 < col2-replication [
          set birth-tick ticks
          set age 0
          set quorum_col2 0
          ask neighbors4 [
          set pcolor blue
          set birth-tick ticks
          set age 0

          ]
        ]
      ]


     [ifelse (pcolor = blue) and (age = col2-doublingt) and (quorum_col2 < 5) [
          if random-float 150 < col2-replication [
          set birth-tick ticks
          set quorum_col2 0
        set age 0
        ask neighbors4 [
          set pcolor blue
          set birth-tick ticks
          set age 0

          ]
        ]
        ]
        [if (pcolor = blue) and (age = col2-doublingt) and (quorum_col2 < quorum_col3) [
          ifelse random-float 140 < col2-replication [
        set birth-tick ticks
        set age 0
            set quorum_col2 0
        ask neighbors4 [
          set pcolor blue
          set birth-tick ticks
          set age 0
              set quorum_col2 0

            ]
          ]
          [set pcolor orange
          ask neighbors4 [
          set pcolor orange
          set birth-tick ticks
          set age 0
              set quorum_col2 0
              set quorum_col3 1
          ]
          ]

      ]
    ]
      ]
    ]

    [if (Model-type = "dark microbiome") or (Model-type = "solar model") and (pcolor = blue) and (age = col2-doublingt)[
    if random-float 100 < col2-replication [
        set birth-tick ticks
        set age 0
        ask neighbors4 [
          set pcolor blue
          set birth-tick ticks
          set age 0
    ]
  ]
    ]
    ]











       ifelse (Model-type = "quorum sensing") and (pcolor = orange) and (age = col3-doublingt)[

  ifelse (pcolor = orange) and (age = col3-doublingt) and (quorum_col3 > 5) [
        if random-float 40 < col3-replication [
          set birth-tick ticks
          set age 0
          set quorum_col3 0
          ask neighbors4 [
          set pcolor orange
          set birth-tick ticks
          set age 0

          ]
        ]
      ]


     [ifelse (pcolor = orange) and (age = col3-doublingt) and (quorum_col3 < 5) [
          if random-float 150 < col3-replication [
          set birth-tick ticks
        set age 0
          set quorum_col3 0
        ask neighbors4 [
          set pcolor orange
          set birth-tick ticks
          set age 0
          ]
        ]
        ]
        [if (pcolor = orange) and (age = col3-doublingt) and (quorum_col3 < quorum_col2) [
          ifelse random-float 140 < col3-replication [
        set birth-tick ticks
        set age 0
        ask neighbors4 [
          set pcolor orange
          set birth-tick ticks
          set age 0
          set quorum_col3 0
            ]
          ]
          [set pcolor blue
          ask neighbors4 [
          set pcolor blue
          set birth-tick ticks
          set age 0
                set quorum_col3 0
              set quorum_col2 1
          ]
          ]

      ]
    ]
      ]
    ]

    [if (Model-type = "dark microbiome") or (Model-type = "solar model") and (pcolor = orange) and (age = col3-doublingt)[

    if random-float 100 < col3-replication [
        set birth-tick ticks
        set age 0
        ask neighbors4 [
          set pcolor orange
          set birth-tick ticks
          set age 0
    ]
  ]
    ]
    ]
      ]
end 

to UV-recovery
      ask self [
      if (pcolor = brown) and (age >= 5) [
      if random-float 20 < 10 [
      set pcolor [pcolor] of one-of neighbors4
      set damage 0
      ]
      if pcolor = cyan [
        ask patches in-radius electrosphere [
          set damage 0
    ]
  ]
    ]
  ]
end 

to col
  ask self [
    if age > 100 [
    set pcolor white
  ]
  ]
end 

to death
  ask self [
    if (age >= death-age-def3) and (pcolor = one-of [blue orange green cyan])  [set pcolor [black] of myself]
    if Model-type = "solar model" [
          if (damage > green-damage-threshold) and (pcolor = green)
    [set pcolor brown
      set damage 0
    ]
    if (damage > orange-damage-threshold) and (pcolor = orange)
    [set pcolor brown
      set damage 0
    ]
    if (damage > blue-damage-threshold) and (pcolor = blue)
    [set pcolor brown
      set damage 0
    ]
  ]
  ]
end 

to-report colony-orange
  report patches with [pcolor = orange]
end 

to-report colony-blue
  report patches with [pcolor = blue]
end 

to-report colony-green
  report patches with [pcolor = green]
end 

to-report thanos
  report patches with [pcolor = black]
end 

to-report age-check
  report patches with [age > 3]
end 

There are 4 versions of this model.

Uploaded by When Description Download
Caius Gibeily 21 days ago Debugged quorum Download this version
Caius Gibeily 21 days ago Change 3D model to 2D model Download this version
Caius Gibeily 21 days ago Change 3D model to 2D model Download this version
Caius Gibeily 21 days ago Initial upload Download this version

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