; Bacterial Chemotaxis and Movement
; Adaptive Systems Project
; Ken Webb
; (C) Copyright 2004 Ken Webb
; All rights reserved
; April 12, 2004
; AdapSysProj_7.nlogo

; There are three types of objects in this system (as in all NetLogo programs):
; - a single observer object,
; - a large number of patch objects,
; - a large number of protein objects (a breed of turtle).
; Using standard NetLogo practice, each procedure in this program is identified
; as being an observer procedure, a patches procedure, or a protein procedure.

;                                     PROGRAM DECLARATIONS
;                                     ====================

; Bacteria
; --------
; this is a built-in NetLogo command that declares protein as a breed of turtle
breeds [
  eColi
]

; Chemical variables
; ------------------
; this is a built-in NetLogo command that declares instance variables that belong to all patches
patches-own [
  ; Concentration: a proportion from 0.0 (none) to 1.0 (100% that chemical)
  aspartateConcEnv ; Aspartate concentration
  glucoseConcEnv   ; Glucose concentration
  phenolConcEnv    ; Phenol concentration
]

; eColi variables
; -----------------
; this is a built-in NetLogo command that declares instance variables that belong to all eColi
eColi-own [
  aspartateConc ; Aspartate concentration
  glucoseConc   ; Glucose concentration
  phenolConc    ; Phenol concentration
  runCounter  ; current length of current run (time between tumbles)
  nextOn ; current sliding window values
  nextOff
]

; Global Constants and Variables
; ------------------------------
; this is a built-in NetLogo command that declares global constants and variables
globals [
  timeStep
  aspartateType  glucoseType  phenolType
  aspartateColor glucoseColor phenolColor
  typeList
  colorList
  xList yList
  numChemicals ; number of chemicals to use
  concParm
  dCountMaxParm
  diffuseParm
  runList ; list of all run lengths for all eColi instances

  ; Chromosome and other Probability values
  rMax ; max random number
  chromosome ; list of lists of possible behavior probability values
  ; Probability matrix
  ;   Gt = greater than
  ;   Eq = equal
  ;   Lt = less than
  P_AspGt P_AspEq P_AspLt ; Aspartate
  P_GluGt P_GluEq P_GluLt ; Glucose
  P_PheGt P_PheEq P_PheLt ; Phenol
]

;                                              SETUP
;                                              =====

; Setup - invoked when user presses the setup button in the GUI
; -----
to setup ; observer procedure
  ca ; clear all
  ;clear-output ; clear the output window
  set-globals
  set-probabilities ChromosomeNum chromosome
  if Experiment = "No chemicals"
    [expNoChemicals]
  if Experiment = "Constant level aspartate"
    [expConstantAspartate]
  if Experiment = "Rectangular gradient"
    [expRectangularGradient]
  if Experiment = "Three diffusing chemicals"
    [expThreeDiffusingChems]
  if Experiment = "Micropipette"
    [expMicropipette]
  if Experiment = "Long gradient"
    [expLongGradient]
  if Experiment = "Long uniform"
    [expLongUniform]
  if Experiment = "Long combination"
    [expLongCombination]
  if Experiment = "Brownian motion"
    [expBrownian]
end

; Experiment 1
to expNoChemicals ; observer procedure
  initialize-eColi
end

; Experiment 2
to expConstantAspartate ; observer procedure
  ask patches [set aspartateConcEnv AspartateConcentration]
  ask patches [set-colors]
  initialize-eColi
end

; Experiment 3
to expRectangularGradient ; observer procedure
  ask patches [set aspartateConcEnv (abs(pycor) / screen-edge-y)]
  ask patches [set-colors]
  initialize-eColi
end

; Experiment 4
to expThreeDiffusingChems ; observer procedure
  ifelse RandomizeConfiguration
    [
    initialize-3-chemical-circles ; patches
    initialize-eColi
    ]
    [import-world "world.csv"
    initialize-eColi
    ]
end

; Experiment 5
to expMicropipette ; observer procedure
  print "Micropipette Experiment: not yet implemented"
end

; Experiment 6
to expLongGradient ; observer procedure
  ask patches [set aspartateConcEnv ((pycor + screen-edge-y) / screen-size-y)]
  ask patches [set-colors]
  no-display
  initialize-eColi
  ask eColi [setxy xcor -1 * screen-edge-y]
  ask eColi [set heading 0]
  display
  ask eColi [internalize-environment]
end

; Experiment 7
to expLongUniform ; observer procedure
  ask patches [set aspartateConcEnv 0.0]
  ask patches [set-colors]
  no-display
  initialize-eColi
  ask eColi [setxy xcor -1 * screen-edge-y]
  ask eColi [set heading 0]
  display
  ask eColi [internalize-environment]
end

; Experiment 8
to expLongCombination ; observer procedure
  ask patches with [pycor < 0] [set aspartateConcEnv 0.0]
  ask patches with [pycor >= 0] [set aspartateConcEnv (pycor / screen-edge-y)]
  ask patches [set-colors]
  no-display
  initialize-eColi
  ask eColi [setxy xcor -1 * screen-edge-y / 2]
  ask eColi [set heading 0]
  display
  ask eColi [internalize-environment]
end

; Experiment 9
to expBrownian ; observer procedure
  initialize-eColi
end

to set-globals ; observer procedure
  ; Constants
  set aspartateType 1
  set glucoseType  2
  set phenolType  3
  set aspartateColor red
  set glucoseColor green
  set phenolColor blue
  set typeList  (list aspartateType  glucoseType  phenolType)
  set colorList (list aspartateColor glucoseColor phenolColor)
  set xList (list -21 -30  23) ; x coordinate of center of each chemical type
  set yList (list  29 -30   1) ; y coordinate
  set numChemicals 3
  set concParm 500.0 ; initialize-chemicals (default: 500.0)
  set dCountMaxParm 200 ; initialize-chemicals (default: 200) 10
  set diffuseParm 0.6 ; initialize-chemicals (default: 0.6)
  ; Variables
  set timeStep 0
  set runList []

  ; Chromosome and probabilites
  ; ---------------------------
  set rMax 100
  ; ChromosomeNum is the first value in each sub-list, 1, 2, ...
  ; in order by:
  ;  P_AspGt P_AspEq P_AspLt  P_GluGt P_GluEq P_GluLt   P_PheGt P_PheEq P_PheLt
  set chromosome [
    [1 [10 40 70   10 40 70   90 60 30]] ; default
    [2 [20 30 60   30 40 50   80 50 20]]
    [3 [50 50 50   50 50 50   50 50 50]] ; random
  ]
end

; Set the probability variables from values in chromosome list
; ------------------------------------------------------------
; this is a standard lisp-like recursive function
to set-probabilities [probID pList] ; observer procedure
  ifelse empty? pList
    [print "Can't find pList"]
    [ifelse first first pList = probID
      [set-prob-detail 1 first but-first first pList]
      [set-probabilities probID but-first pList]
    ]
end

; Set value for one probability variable (for use only by set-probabities)
; --------------------------------------
to set-prob-detail [itemID pList] ; observer procedure
  if itemID = 1 [set P_AspGt first pList]
  if itemID = 2 [set P_AspEq first pList]
  if itemID = 3 [set P_AspLt first pList]
  if itemID = 4 [set P_GluGt first pList]
  if itemID = 5 [set P_GluEq first pList]
  if itemID = 6 [set P_GluLt first pList]
  if itemID = 7 [set P_PheGt first pList]
  if itemID = 8 [set P_PheEq first pList]
  if itemID = 9 [set P_PheLt first pList]
  ; recursively handle next value in the list
  if itemID < 10
    [set-prob-detail itemID + 1 but-first pList]
end

; Initialize three color circles, with diffusion
to initialize-3-chemical-circles ; observer procedure
  locals [cCount dCount chemType x y maxA maxG maxP]
  ; establish random numChemicals (three) centers of chemical diffusion
  set cCount 0
  while [cCount < numChemicals] [
    ifelse RandomizeLocations
      [
      set x (random screen-size-x) - screen-edge-x
      set y (random screen-size-y) - screen-edge-y
      ]
      [
      set x item cCount xList
      set y item cCount yList
      ]
    ask (patch x y) [
      set chemType item cCount typeList
      if chemType = aspartateType [set aspartateConcEnv concParm]
      if chemType = glucoseType   [set glucoseConcEnv   concParm]
      if chemType = phenolType    [set phenolConcEnv    concParm]
      ]
    set cCount cCount + 1
  ]
  ; Diffuse the chemical concentrations
  set dCount 0
  while [dCount < dCountMaxParm] [
    diffuse aspartateConcEnv diffuseParm
    diffuse glucoseConcEnv   diffuseParm
    diffuse phenolConcEnv    diffuseParm
    set dCount dCount + 1
  ]
  ; Normalize the concentrations to range 0.0 to 1.0
  set maxA max values-from patches [aspartateConcEnv]
  set maxG max values-from patches [glucoseConcEnv]
  set maxP max values-from patches [phenolConcEnv]
  ask patches [
    set aspartateConcEnv aspartateConcEnv / maxA
    set glucoseConcEnv   glucoseConcEnv   / maxG
    set phenolConcEnv    phenolConcEnv    / maxP
  ]
  ask patches [set-colors]
end

; Interpret the concentrations as color RGB values in range 0.0 to 1.0
to set-colors ; patches procedure
  ; Verify that all colors will be in correct range
  if aspartateConcEnv > 1.0 or aspartateConcEnv < 0.0 [show aspartateConcEnv]
  if glucoseConcEnv   > 1.0 or glucoseConcEnv   < 0.0 [show glucoseConcEnv]
  if phenolConcEnv    > 1.0 or phenolConcEnv    < 0.0 [show phenolConcEnv]
  ; Set the patch color
  set pcolor rgb aspartateConcEnv glucoseConcEnv phenolConcEnv
end

to initialize-eColi ; observer procedure
  set-default-shape eColi "arrow"
  create-custom-eColi NumEColi [
    ifelse PnDn ; GUI switch
      [pen-down]
      [pen-up]
    setxy (random screen-size-x) (random screen-size-y)
    set heading random 360
    ask eColi [init-concentrations]
    ask eColi [internalize-environment]
    set runCounter 0
    fd 1
  ]
end

to init-concentrations
  locals [i]
  set nextOn 0
  set nextOff SlidingWindowSize - 1
  set aspartateConc []
  set glucoseConc  []
  set phenolConc  []
  set i 0
  while [i < SlidingWindowSize]
  [
    set aspartateConc lput aspartateConcEnv aspartateConc
    set glucoseConc   lput glucoseConcEnv   glucoseConc
    set phenolConc    lput phenolConcEnv    phenolConc
    set i i + 1
  ]
end

; Set internal concentrations to those of the environment.
; Creates an internal representation of the current environment,
; so it can compare this with the environment a short time later.
to internalize-environment ; eColi procedure
  set aspartateConc (replace-item nextOn aspartateConc aspartateConcEnv)
  set glucoseConc (replace-item nextOn  glucoseConc  glucoseConcEnv)
  set phenolConc (replace-item nextOn  phenolConc  phenolConcEnv)
  set nextOn (nextOn + 1) mod SlidingWindowSize
end

;                                                   PROCESS
;                                                   =======

; Go - invoked when user presses the go button in the GUI
; --
to go ; observer procedure
  if timeStep >= MaxTimeSteps
  [
    outputStats
    stop
  ]
  ifelse (Experiment = "Brownian motion")
    [ask eColi [doBrownian]]
    [ask eColi [behave]]
  set timeStep timeStep + 1
end

to outputStats
  locals [statsType]
  set statsType 2
  ifelse statsType = 1
  [
    type "Experiment: "
    print Experiment
    type "Time step: "
    print timeStep
    type "Sliding window size: "
    print slidingWindowSize
    type "Mean: "
    print mean runList
    type "Std: "
    print standard-deviation runList
    type "Min: "
    print min runList
    type "Max: "
    print max runList
    type "Median: "
    print median runList
  ]
  [
    type Experiment
    type ","
    type timeStep
    type ","
    type mean runList
    type ","
    print standard-deviation runList
  ]
end

; Do Brownian motion, for comparison with more intelligent bacterial movement
to doBrownian ; eColi procedure
  rt random 360
  fd 1
end

; Do some behavior
to behave ; eColi procedure

  ; Aspartate (food; move towards)
  ifelse (aspartateConcEnv >= glucoseConcEnv and aspartateConcEnv >= phenolConcEnv)
    [
    ifelse (aspartateConcEnv > (item nextOff aspartateConc))
      [ifelse (random rMax > P_AspGt) [behaviorRun] [behaviorTumble]] ; default: 10
      [ifelse (aspartateConcEnv = (item nextOff aspartateConc))
        [ifelse (random rMax > P_AspEq) [behaviorRun] [behaviorTumble]] ; default: 40
        [ifelse (random rMax > P_AspLt) [behaviorRun] [behaviorTumble]] ; default: 70
      ]
    ]

  ; Glucose (food; move towards)
  [ifelse (glucoseConcEnv >= aspartateConcEnv and glucoseConcEnv >= phenolConcEnv)
    [
    ifelse (glucoseConcEnv > (item nextOff glucoseConc))
      [ifelse (random rMax > P_GluGt) [behaviorRun] [behaviorTumble]] ; default: 10
      [ifelse (glucoseConcEnv = (item nextOff glucoseConc))
        [ifelse (random rMax > P_GluEq) [behaviorRun] [behaviorTumble]] ; default: 40
        [ifelse (random rMax > P_GluLt) [behaviorRun] [behaviorTumble]] ; default: 70
      ]
    ]

  ; Phenol (move away)
  [if (phenolConcEnv >= aspartateConcEnv and phenolConcEnv >= glucoseConcEnv)
    [
    ifelse (phenolConcEnv > (item nextOff phenolConc))
      [ifelse (random rMax > P_PheGt) [behaviorRun] [behaviorTumble]] ; default: 90
      [ifelse (phenolConcEnv = (item nextOff phenolConc))
        [ifelse (random rMax > P_PheEq) [behaviorRun] [behaviorTumble]] ; default: 60
        [ifelse (random rMax > P_PheLt) [behaviorRun] [behaviorTumble]] ; default: 30
      ]
    ]
  ]]
  set nextOff (nextOff + 1) mod SlidingWindowSize
end

; Do the Running behavior
to behaviorRun ; eColi procedure
  internalize-environment
  set runCounter runCounter + 1
  fd 1
end

; Do the Tumbling behavior
to behaviorTumble ; eColi procedure
  set runList lput runCounter runList
  internalize-environment
  right random 360
  set runCounter 0
end
@#$#@#$#@
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BUTTON
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@#$#@#$#@
WHAT IS IT?
-----------
This section could give a general understanding of what the model is trying to show or explain.


HOW IT WORKS
------------
This section could explain what rules the agents use to create the overall behavior of the model.


HOW TO USE IT
-------------
This section could explain how to use the model, including a description of each of the items in the interface tab.


THINGS TO NOTICE
----------------
This section could give some ideas of things for the user to notice while running the model.


THINGS TO TRY
-------------
This section could give some ideas of things for the user to try to do (move sliders, switches, etc.) with the model.


EXTENDING THE MODEL
-------------------
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NETLOGO FEATURES
----------------
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RELATED MODELS
--------------
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CREDITS AND REFERENCES
----------------------
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@#$#@#$#@
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Polygon -6524078 true true 170 127 200 93 231 93 237 103 262 103 261 113 253 119 231 119 215 143 213 160 208 173 189 187 169 190 154 190 126 180 106 171 72 171 73 126 122 126 144 123 159 123
Polygon -6524078 true true 201 99 214 69 215 99
Polygon -6524078 true true 207 98 223 71 220 101
Polygon -6524078 true true 184 172 189 234 203 238 203 246 187 247 180 239 171 180
Polygon -6524078 true true 197 174 204 220 218 224 219 234 201 232 195 225 179 179
Polygon -6524078 true true 78 167 95 187 95 208 79 220 92 234 98 235 100 249 81 246 76 241 61 212 65 195 52 170 45 150 44 128 55 121 69 121 81 135
Polygon -6524078 true true 48 143 58 141
Polygon -6524078 true true 46 136 68 137
Polygon -6524078 true true 45 129 35 142 37 159 53 192 47 210 62 238 80 237
Line -16777216 false 74 237 59 213
Line -16777216 false 59 213 59 212
Line -16777216 false 58 211 67 192
Polygon -6524078 true true 38 138 66 149
Polygon -6524078 true true 46 128 33 120 21 118 11 123 3 138 5 160 13 178 9 192 0 199 20 196 25 179 24 161 25 148 45 140
Polygon -6524078 true true 67 122 96 126 63 144

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NetLogo 1.3.1
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