Gene Expression: Unknown

globals [genes gcolors grates genecount gnat promotercount promoters xstartloc bindings pbound xcoords preg KB Kd knockout]
turtles-own [gtype age bound]
breed [ rna ]
breed [ protein ]

to setup 
  ;; (for this model to work with NetLogo's new plotting features,
  ;; __clear-all-and-reset-ticks should be replaced with clear-all at
  ;; the beginning of your setup procedure and reset-ticks at the end
  ;; of the procedure.)
  __clear-all-and-reset-ticks
  ; bindings determines which proteins bind to which promoters
;
; Problem 1
;
  if (problem = 1) [
  set bindings ["E" "C" 
                "C" "D" 
                "A" "D" 
                "E" "B" 
                "C" "A"]
; gnat is the natural tendency of the gene to be transcribed
  set gnat [1 0 0 0 0]
; preg is the promoter regulatory function
  set preg [ 1 -2 
            -1  2 
             1 -2 
             1 -1 
             1 -1 ]
 ]
 ;
 ; Problem 2
 ;
   if (problem = 2) [
  set bindings ["D" "E" 
                "A" "C" 
                "B" "E" 
                "B" "E" 
                "E" "D"]
; gnat is the natural tendency of the gene to be transcribed
  set gnat [0 0 -1 0 0]
; preg is the promoter regulatory function
  set preg [ -1 -1 
             1   -1 
             1   1 
             1  1 
             1  1 ]
 ]
 ;
 ; Problem 3
 ;
   if (problem = 3) [
  set bindings ["D" "E" 
                "D" "E" 
                "D" "B" 
                "A" "B" 
                "A" "B"]
; gnat is the natural tendency of the gene to be transcribed
  set gnat [1 1 0 1 1]
; preg is the promoter regulatory function
  set preg [ -1 -1 
             -1 -1 
             1 1 
             -1 -1 
             -1 -1 ]
 ]
   if (problem = 4) [
  set bindings ["B" "C" 
                "C" "D" 
                "B" "D" 
                "C" "E" 
                "C" "A"]
; gnat is the natural tendency of the gene to be transcribed
  set gnat [0 1 0 0 0]
; preg is the promoter regulatory function
  set preg [ 1 -2 
             -1 1 
             1 -2 
             1 -1 
             -1 2 ]
 ]
   if (problem = 5) [
  set bindings ["D" "E" 
                "D" "E" 
                "A" "E" 
                "A" "B" 
                "A" "B"]
; gnat is the natural tendency of the gene to be transcribed
  set gnat [1 1 -1 1 1]
; preg is the promoter regulatory function
  set preg [ -1 -1 
             -1 -1 
              1 1 
             -1 -1 
             -1 -1 ]
 ]
   if (problem = 6) [
  set bindings ["A" "C" 
                "A" "E" 
                "D" "A" 
                "C" "D" 
                "C" "D"]
; gnat is the natural tendency of the gene to be transcribed
  set gnat [0 0 0 1 0]
; preg is the promoter regulatory function
  set preg [ 1 1 
             -1 1 
             1 1 
             -1 -1 
             -1 1 ]
 ]
   if (problem = 7) [
  set bindings ["C" "B" 
                "D" "A" 
                "D" "A" 
                "C" "B" 
                "D" "B"]
; gnat is the natural tendency of the gene to be transcribed
  set gnat [1 1 1 1 0]
; preg is the promoter regulatory function
  set preg [ -2 -1 
             -1 -1 
             -1 -1 
             -2 -1 
             1 1 ]
 ]
   if (problem = 8) [
  set bindings ["B" "A" 
                "D" "A" 
                "A" "B" 
                "B" "E" 
                "B" "D"]
; gnat is the natural tendency of the gene to be transcribed
  set gnat [1 0 1 -2 0]
; preg is the promoter regulatory function
  set preg [ 1  1 
             1  1 
            -2  0 
             1  1 
            1 -1 ]
 ]

; normally you won't change anything down here

  set KB 100 ; binding coefficient
  set Kd 4 ; dissociation coefficient
  set genes ["A" "B" "C" "D" "E" ]
  set promoters 2
  set knockout [0 1 1 1 1 1]
  set gcolors [red blue green magenta yellow ]
  set grates [ 10 10 10 10 10 ]
  set promoters 2
  set pbound [0 0 0 0 0 0 0 0 0 0]
  set xcoords [0 0 0 0 0 0 0 0 0 0]

  set xstartloc (max-pxcor * -1) + 1
  set promotercount 0
  (foreach genes gcolors [
  ; create promoters
    repeat promoters [
      set promotercount promotercount + 1
      ask patches with [(pxcor = (xstartloc)) and (pycor = 0)] [ set pcolor gray set plabel promotercount ]
      set xcoords replace-item (promotercount - 1) xcoords xstartloc
      set xstartloc xstartloc + 1
    ]
    ; create gene
    ask patches with [(pxcor = xstartloc) and (pycor = 0)] [ set pcolor ?2 set plabel ?1 ]
    set xstartloc xstartloc + 1
    ; create white region
    repeat 4 [
      ask patches with [(pxcor = xstartloc) and (pycor = 0)] [ set pcolor white ]
      set xstartloc xstartloc + 1
    ]
    set genecount genecount + 1
  ])
  ; create ribosomes
  ask patches with [ ((pycor < -3) or (pycor > 3))] [ if random 10 = 1 [set pcolor cyan] ]

; create initial population of turtles
;  cct 5 [
;        set breed protein
;        set shape "repressor"
;        set bound false
;        set color red
;        set gtype "A"
;        set age random 25
;        set heading random 360
;        fd random 50
;      ]
end 

to go 
 let cnt 0
  
  ;set time time + 1
; set knockouts
ifelse (GENE-A) [set knockout replace-item 1 knockout 1] [set knockout replace-item 1 knockout 0]
ifelse (GENE-B) [set knockout replace-item 2 knockout 1] [set knockout replace-item 2 knockout 0]
ifelse (GENE-C) [set knockout replace-item 3 knockout 1] [set knockout replace-item 3 knockout 0]
ifelse (GENE-D) [set knockout replace-item 4 knockout 1] [set knockout replace-item 4 knockout 0]
ifelse (GENE-E) [set knockout replace-item 5 knockout 1] [set knockout replace-item 5 knockout 0]
; do gene transcription
ask patches [
 without-interruption [
  set cnt 0
  (foreach genes gcolors [
  set cnt cnt + 1
  if (plabel = ?1 and item cnt knockout = 1) [
    if ( random 100 <  item (cnt - 1) grates) [
      if ( ((item ((promoters * cnt) - 1) preg) * (item ((promoters * cnt) - 1) pbound)  + (item ((promoters * cnt) - 2) preg) * (item ((promoters * cnt) - 2) pbound) + item (cnt - 1) gnat) > 0) [
      sprout 1 [
       set breed rna
       set shape "rna"
       set gtype ?1
       set color ?2
       set bound false
       set age random 30
       set heading random 360
       fd 2
      ] ]
    ]
  ]
])
]
]
;; this determines which gate the system emulates
; if (plabel = "C" ) [
;   if (gate = "NAND" ) [if (not (rbound-A = true and rbound-B = true) ) [ express-c] ]
;   if (gate = "NOR" ) [if (rbound-A = false and rbound-B = false) [ express-c]]
;   if (gate = "AND" ) [if (rbound-A = true and rbound-B = true) [ express-c]]
;   if (gate = "OR" ) [if (rbound-A = true or rbound-B = true) [ express-c]]
;   if (gate = "XOR" ) [if ((rbound-A = true or rbound-B = true) and not (rbound-A = true and rbound-B = true)) [ express-c]]
; ]
;]

; this was a bit tricky to get the order of events right
ask protein [
    without-interruption [bind-site]
    ]
ask turtles 
    [wander ;; both rnas and proteins check to see if they bind and otherwise move around
     grow-old] ;; both also are recycled by the cell machinery after a while.
plot-history
plot-levels
end 

to bind-site
  let cnt 0
  
  if (bound = false) [
    if (random 100 < Kb and breed = protein) [
      set cnt 0
      (foreach bindings pbound [
        if (gtype = ?1 and ?2 = 0) [
          set bound cnt 
          set pbound replace-item cnt pbound 1 
          setxy item cnt xcoords 0  
          set heading 180
          stop
        ]
        set cnt cnt + 1
      ])
    ]
  ]
end 

to unbind-site
  if (random 100 < Kd and bound != false) [
    set pbound replace-item bound pbound 0
    set bound false
    setxy random world-width random world-height
]
end 

to grow-old ;; cells break down rnas and proteins after a while.  
   set age age + 1
   if (age > (50 + random 150))  [
     without-interruption[if (bound = false) [die] ]]
end 

to wander
  if (pcolor = cyan and shape = "rna") [  ;; this is the ribosome translating
;    set breed protein 
;    set shape "repressor"
;    set age 0 
     hatch 1 [
         set breed protein
         set shape "repressor"
         set bound false
        set age 0
        set heading random 360
      ]
  ] 
  ifelse (bound = false) [rt random 180 - random 180 fd 1 ] [without-interruption [unbind-site]] 
end 

to plot-levels ;; this creates creates the bar graph 
  let cnt 0
  
    set-current-plot "Protein Concentrations"
    clear-plot
    set cnt 0
    (foreach genes gcolors [
    set-current-plot-pen ?1
    plot-pen-down
    set cnt cnt + 1
    plotxy cnt count protein with [color = ?2] 
    ])
end 

to plot-history ;; this creates the line graph
  set-current-plot "Concentration History"
      (foreach genes  gcolors [
    set-current-plot-pen ?1
  plot ( count protein with [color = ?2]  )
])
end 

;; red blue green magenta yellow

to insert-A
     crt 30 [
         set breed protein
         setxy random-xcor random-ycor
         set color red
         set gtype "A"
         set shape "repressor"
         set bound false
         set age 0
         set heading random 360
      ]
end 

to insert-B
     crt 30 [
         set breed protein
         setxy random-xcor random-ycor
         set color blue
         set gtype "B"
         set shape "repressor"
         set bound false
         set age 0
         set heading random 360
      ]
end 

to insert-C
     crt 30 [
         set breed protein
         setxy random-xcor random-ycor
         set color green
         set gtype "C"
         set shape "repressor"
         set bound false
         set age 0
         set heading random 360
      ]
end 

to insert-D
     crt 30 [
         set breed protein
         setxy random-xcor random-ycor
         set color magenta
         set gtype "D"
         set shape "repressor"
         set bound false
         set age 0
         set heading random 360
      ]
end 

to insert-E
     crt 30 [
         set breed protein
         setxy random-xcor random-ycor
         set gtype "E"
         set color yellow
         set shape "repressor"
         set bound false
         set age 0
         set heading random 360
      ]
end