Repressilator_Synthetic_Biology

globals [
  promoter-color-list                                                                                                 ; color list to set promoter colors based on their sequences
  gRNA-color-list                                                                                                     ; color list to set gRNA colors based on their sequences
  gene-color                                                                                                          ; color of the gene
  promoter-transcribed?                                                                                               ; a boolean to see if the promoter is transcribed
  cas9-number                                                                                                         ; number of cas9 molecules
  RNAPs-number                                                                                                        ; number of RNA polymerase molecules
  gRNA-number                                                                                                         ; number of gRNA molecules
  non-dna                                                                                                             ; agentset excluding the patches that are DNA

  dna                                                                                                                 ; agentset containing the patches that are Gene1/Tet
  CDS                                                                                                                 ; agentset containing the patches that are CDS for Gene1/Tet
  promoter                                                                                                            ; agentset containing the patches that are for the promoter for Gene1/Tet
  terminator                                                                                                          ; agentset containing the patches that are for the terminator for Gene1/Tet
  pro_seq_1                                                                                                           ; agentset containing the user-defined sequence for promoter_1
  pro-1-transcribed?                                                                                                  ; boolean for whether or not Gene2/Tet is transcribed
  inhibited-pro1?                                                                                                     ; boolean for whether or not the promoter is inhibited

  dna_2                                                                                                               ; agentset containing the patches that are Gene2/LacI
  CDS_2                                                                                                               ; agentset containing the patches that are CDS for Gene2/LacI
  promoter_2                                                                                                          ; agentset containing the patches that are for the promoter_2 for Gene2/LacI
  pro_seq_2                                                                                                           ; agentset containing the user-defined sequence for promoter_2
  terminator_2                                                                                                        ; agentset containing the patches that are for the terminator_2
  pro-2-transcribed?                                                                                                  ; boolean for whether or not Gene2/LacI is transcribed
  inhibited-pro2?                                                                                                     ; boolean for whether or not the promoter for Gene2/LacI is inhibited

  dna_3                                                                                                               ; agentset containing the patches that are DNA_3
  CDS_3                                                                                                               ; agentset containing the patches that are mRNA gene_3
  promoter_3                                                                                                          ; agentset containing the patches that are for the promoter_3
  pro_seq_3                                                                                                           ; agentset containing the user-defined sequence for promoter_3
  terminator_3                                                                                                        ; agentset containing the patches that are for the terminator_3
  pro-3-transcribed?                                                                                                  ; boolean for whether or not Gene3/Lam is transcribed
  inhibited-pro3?                                                                                                     ; boolean for whether or not the promoter for Gene3/Lam is inhibited

  temp_Tet                                                                                                            ; temporary boolean for whether or not the RNAP is physically on a promoter
  Tet_count                                                                                                           ; boolean for whether or not the RNAP is physically on the promoter for Tet
  temp_LacI                                                                                                           ; temporary  boolean for whether or not the RNAP is physically on the promoter for LacI
  LacI_count                                                                                                          ; boolean for whether or not the RNAP is physically on the promoter for LacI
  Lam_count                                                                                                           ; temporary  boolean for whether or not the RNAP is physically on the promoter for Lam
  temp_Lam                                                                                                            ; boolean for whether or not the RNAP is physically on the promoter for LacI

  cas9-bound-1?
  cas9-bound-2?
  cas9-bound-3?

]

breed [ cas9s cas9 ]                                                                                                  ; cas9 repressor protein (violet pentagon proteins)
breed [ mRNAs mRNA ]                                                                                                  ; mRNA  ( red circle proteins)
breed [ gRNAs gRNA ]                                                                                                  ; gRNA molecule (cyan triangle molecules) that bind to Cas9 to direct it to promoter.
breed [ RNAPs RNAP ]                                                                                                  ; RNA Polymerases (brown proteins) that bind to promoter part of DNA and synthesize mRNA from the downstream DNA
breed [ Tetrs Tetr ]                                                                                                  ; Tetrocycline signal produced by gene 1
breed [ LacIs LacI ]                                                                                                  ; LacI signal produced by gene 2
breed [ Lams Lam ]                                                                                                    ; LacI signal produced by gene 2

cas9s-own [
  partner                                                                                                             ; a partner is an gRNA molecule with which a cas9 molecule binds to form a complex
  on-promoter?                                                                                                        ; a boolean to track if a cas9 is bound to DNA as an inhibitor of transcription
  life
]

RNAPs-own [                                                                                                           ; a boolean to track if a RNAPs is transcribing on the DNA
  on-dna?
]

Tetrs-own [
  on-promoter?                                                                                                        ; a boolean to track if Tetr is near promoter_3
  life
]

LacIs-own [
  on-promoter?                                                                                                        ; a boolean to track if Tetr is near promoter_3
  life
]

Lams-own [
  on-promoter?                                                                                                        ; a boolean to track if Tetr is near promoter_3
  life
]



;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;;;;;;;;;;;;;;;;;;;;;;;; Setup Procedures ;;;;;;;;;;;;;;;;;;;;;;;;
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;

to setup
  clear-all
  set-global-variables
  set-DNA-patches
  set-DNA-patches_2
  set-DNA-patches_3
  add-proteins
  reset-ticks
end 

to set-global-variables
  set promoter-color-list [ 42 44 45 48 ]
  set gene-color 115
  set cas9-number 10
  set RNAPs-number number-of-RNAPs
  set promoter-transcribed? false
  set pro-1-transcribed? false
  set pro-2-transcribed? false
  set pro-3-transcribed? false
  set temp_tet false
  set temp_LacI false
  set temp_Lam false
  set Lam_count count Lams
  set Tet_count count Tetrs
  set LacI_count count LacIs
  set inhibited-pro1? false
  set inhibited-pro2? false
  set inhibited-pro3? false
  set cas9-bound-1? false
  set cas9-bound-2? false
  set cas9-bound-3? false
end 

to set-DNA-patches                                                                                                   ; a procedure to set the DNA patches in the cell and assign appropriate colors based on their sequences
  ask patches [set pcolor white]

  set dna patches with [
    pxcor >= Tet-X-Axis and pxcor < Tet-X-Axis + 50 and pycor > Tet-Y-Axis and pycor < Tet-Y-Axis + 4
  ]
  set promoter patches with [
    pxcor >= Tet-X-Axis and pxcor < Tet-X-Axis + 10 and pycor > Tet-Y-Axis and pycor < Tet-Y-Axis + 4
   ]
  set CDS patches with [
    pxcor >= Tet-X-Axis + 10 and pxcor < Tet-X-Axis + 45 and pycor > Tet-Y-Axis and pycor < Tet-Y-Axis + 4
  ]
  set terminator patches with [
    pxcor >= Tet-X-Axis + 45 and pxcor < Tet-X-Axis + 50 and pycor > Tet-Y-Axis and pycor < Tet-Y-Axis + 4
  ]

  ask dna [ set pcolor gray ]
  ask promoter [ set pcolor orange + 2 ]
  ask CDS [ set pcolor orange ]
  ask terminator [ set pcolor gray ]

  ask promoter [
    set pro_seq_1 Tet-promoter-sequence
  ]
end 

to set-DNA-patches_2                                                                                                   ; a procedure to set the DNA patches in the cell and assign appropriate colors based on their sequences

  set dna_2 patches with [
    pxcor >= LacI-X-Axis and pxcor < LacI-X-Axis + 50 and pycor > LacI-Y-Axis and pycor < LacI-Y-Axis + 4
  ]
  set promoter_2 patches with [
    pxcor >= LacI-X-Axis and pxcor < LacI-X-Axis + 10 and pycor > LacI-Y-Axis and pycor < LacI-Y-Axis + 4
  ]
  set CDS_2 patches with [
    pxcor >= LacI-X-Axis + 10 and pxcor < LacI-X-Axis + 45 and pycor > LacI-Y-Axis and pycor < LacI-Y-Axis + 4
  ]
  set terminator_2 patches with [
    pxcor >= LacI-X-Axis + 45 and pxcor < LacI-X-Axis + 50 and pycor > LacI-Y-Axis and pycor < LacI-Y-Axis + 4
 ]

  ask dna_2 [ set pcolor gray ]
  ask promoter_2 [ set pcolor blue + 2 ]
  ask CDS_2 [ set pcolor blue ]
  ask terminator_2 [ set pcolor gray ]

  ask promoter_2 [
    set pro_seq_2 LacI-promoter-sequence
  ]
end 

to set-DNA-patches_3                                                                                                   ; a procedure to set the DNA patches in the cell and assign appropriate colors based on their sequences

  set dna_3 patches with [
    pxcor >= Lam-X-Axis and pxcor < Lam-X-Axis + 50 and pycor > Lam-Y-Axis and pycor < Lam-Y-Axis + 4
  ]
  set promoter_3 patches with [
    pxcor >= Lam-X-Axis and pxcor < Lam-X-Axis + 10 and pycor > Lam-Y-Axis and pycor < Lam-Y-Axis + 4
  ]
  set CDS_3 patches with [
    pxcor >= Lam-X-Axis + 10 and pxcor < Lam-X-Axis + 45 and pycor > Lam-Y-Axis and pycor < Lam-Y-Axis + 4
  ]
  set terminator_3 patches with [
    pxcor >= Lam-X-Axis + 45 and pxcor < Lam-X-Axis + 50 and pycor > Lam-Y-Axis and pycor < Lam-Y-Axis + 4
 ]

  ask dna_3 [ set pcolor gray ]
  ask promoter_3 [ set pcolor green + 2 ]
  ask CDS_3 [ set pcolor green ]
  ask terminator_3 [ set pcolor gray ]

  ask promoter_3 [
    set pro_seq_3 Lambda-promoter-sequence
  ]

  set non-dna patches with [ pcolor = white ]
end 

;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;;;;;;;;;;;;;;;;; RUNTIME PROCEDURES ;;;;;;;;;;;;;;;;;;;;;;;;;
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;

to go
  go-cas9s
  go-RNAPs
  go-Tetrs
  go-LacIs
  go-Lams
  check-transcription
  tick
end 

to move                                    ; a random walk procedure for the proteins and gRNA molecules in the cell
  rt random-float 360
  fd 1
end 

to setshape                                ; a procedure to set shapes of the molecules
  if breed = cas9s [
    set size 10
    ifelse partner = nobody
    [ set shape "Cas9"]
    [ set shape "cas9-gRNA-complex" set size 6 ]
  ]
  if breed = RNAPs [
    set size 6
    set shape "circle"
    set color brown]

  if breed = Tetrs [
    set shape "pentagon"
    set color orange
    set size 3]

  if breed = LacIs [
    set shape "pentagon"
    set color blue
    set size 3]

    if breed = Lams [
    set shape "pentagon"
    set color green
    set size 3]
end 

to go-RNAPs                                ; If an RNAPs is close or on the promoter (green) and the promoter is open and is not inhibited,
                                           ; start-transcription and change heading and move on the DNA towards the terminator.
  if (inhibited-pro1? = false) and (not any? Lams-on promoter)[
    ask RNAPs [
      start-transcription
    ]
  ]
  if (inhibited-pro2? = false) and (not any? Tetrs-on promoter_2) [
    ask RNAPs [
      start-transcription
    ]
  ]
  if (inhibited-pro3? = false) and (not any? LacIs-on promoter_3) [
    ask RNAPs [
      start-transcription
    ]
  ]

  if any? RNAPs with [ on-dna? ] [
    ask RNAPs with [ on-dna? ] [
      set heading 90
      fd 1
      if member? patch-here terminator [
        set promoter-transcribed? true
        set on-dna? false
        rt random-float 360
        set pro-1-transcribed? true
      ]

      if member? patch-here terminator_2 [
        set promoter-transcribed? true
        set on-dna? false
        rt random-float 360
        set pro-2-transcribed? true
      ]

      if member? patch-here terminator_3 [
        set promoter-transcribed? true
        set on-dna? false
        rt random-float 360
        set pro-3-transcribed? true
        ]
      ]
    ]

  ask RNAPs with [ not on-dna? ] [
    move
  ]
end 

to produce-Cas9s                                ; procedure to synthesize Cas9 proteins
  create-cas9s cas9-number [
    set on-promoter? false
    setxy random-xcor random-ycor
    set partner nobody
    setshape
  ]
end 

to add-proteins                                 ; procedure to add RNAPs for set-up
  create-RNAPs RNAPs-number [
    setxy random-xcor random-ycor
    set on-dna? false
    setshape
  ]
end 

to produce-Tetrs                                ; procedure to synthesize Tet molecules
  create-Tetrs 1 [
    setshape
;    setxy -11 17
    setxy Tet-X-Axis + 45 Tet-Y-Axis + 3
    set on-promoter? false
  ]
end 

to produce-LacIs                                ; procedure to synthesize LacI molecules
  create-LacIs 1 [
    setshape
;    setxy -11 3
    setxy LacI-X-Axis + 45 LacI-Y-Axis + 3
    set on-promoter? false
  ]
end 

to produce-Lams                                 ; procedure to synthesize Lam molecules
  create-Lams 1 [
    setshape
    setxy Lam-X-Axis + 45 Lam-Y-Axis + 3
    set on-promoter? false
  ]
end 

to produce-RNAPs                                ; procedure to synthesize RNAP proteins
    create-RNAPs 1 [
    setxy random-xcor random-ycor
    set on-dna? false
    setshape
  ]
end 

to start-transcription                           ; a turtle procedure for RNAPs that checks if inhibitory signal molecules are on each promoter;
  if (member? patch-here promoter or member? patch-ahead 9 promoter) and (not any? cas9s-on promoter) [
      ask Lams [
        if on-promoter? = true [
          set temp_Lam True
        ]
      ]
      if temp_Lam = False [
       set on-dna? true
      ]
      if on-dna? = true [
        if Lam_count < 50 [
          setxy xcor Tet-Y-Axis + 1
          set heading 90
          set on-dna? True
        ]
      ]
    ]
  if (member? patch-here promoter_2 or member? patch-ahead 9 promoter_2) and (not any? cas9s-on promoter_2) [
      ask Tetrs [
        if on-promoter? = true [
          set temp_Tet True
        ]
      ]
      if temp_Tet = False [
       set on-dna? true
      ]
      if on-dna? = true [
        if Tet_count < 80 [
          setxy xcor LacI-Y-Axis + 1
          set heading 90
          set on-dna? True
        ]
      ]
    ]
  if (member? patch-here promoter_3 or member? patch-ahead 9 promoter_3) and (not any? cas9s-on promoter_3) [
    ask LacIs [
      if on-promoter? = true [
       set temp_LacI True
      ]
    ]
    if temp_LacI = False [
     set on-dna? true
    ]
    if on-dna? = true [
      if LacI_count < 100 [
        setxy xcor Lam-Y-Axis + 1
        set heading 90
        set on-dna? True
      ]
    ]
  ]
end 

to go-Tetrs                           ; a turtle procedure for Tetrs that checks if they're near promoter_2 and binds if true
  set Tet_count count Tetrs
  ask Tetrs [
    set life life + 1
    ask one-of Tetrs-here [
      if life >= Tet-max [
        die
      ]
      set Tet_count count Tetrs
    ]
      if member? patch-here promoter_2 or member? patch-ahead 15 promoter_2[
        setxy LacI-X-Axis + 1 LacI-Y-Axis + 3
        set on-promoter? true
    ]
  ]

  ask Tetrs with [ not on-promoter? ] [
    move
  ]
end 

to go-LacIs                           ; a turtle procedure for LacIs that checks if they're near promoter_3 and binds if true
  set LacI_count count LacIs
  ask LacIs [
    set life life + 1
    ask one-of LacIs-here [
      if life >= LacI-max [
        die
        ]
      set LacI_count count LacIs
    ]
    if member? patch-here promoter_3 or member? patch-ahead 15 promoter_3[
      setxy Lam-X-Axis + 1 Lam-Y-Axis + 3
      set on-promoter? true
    ]
  ]

  ask LacIs with [ not on-promoter? ] [
    move
  ]
end 

to go-Lams                           ; a turtle procedure for Lams that checks if they're near promoter_1 and binds if true
  set Lam_count count Lams
  ask Lams [
    set life life + 1
    ask one-of Lams-here [
      if life >= Lam-max [
        die
      ]
      set Lam_count count Lams
    ]
    if member? patch-here promoter or member? patch-ahead 15 promoter [
      setxy Tet-X-Axis + 1 Tet-Y-Axis + 3
      set on-promoter? true
    ]
  ]
  ask Lams with [ not on-promoter? ] [
    move
  ]
end 

to go-cas9s                           ; a turtle procedure for Cas9s that checks if they're near a promoter with similar sequence to the user-defined gRNA and binds if true
  ask cas9s [
    set life life + 1
    ask one-of Cas9s-here [
      if life >= Cas9s-max [
        die
      ]
    ]
    if (member? patch-here promoter or member? patch-ahead 9 promoter) and pro_seq_1 = gRNA-sequence [
;      check-promoter
      if cas9-bound-1? = false [
        setxy Tet-X-Axis + 1 Tet-Y-Axis + 3
        set on-promoter? true
        set heading 0
        set inhibited-pro1? true
      ]
    ]
    if (member? patch-here promoter_2 or member? patch-ahead 9 promoter_2) and pro_seq_2 = gRNA-sequence [
      if cas9-bound-2? = false [
        setxy LacI-X-Axis + 1 LacI-Y-Axis + 3
        set on-promoter? true
        set heading 0
        set inhibited-pro2? true
      ]
    ]
    if (member? patch-here promoter_3 or member? patch-ahead 9 promoter_3) and pro_seq_3 = gRNA-sequence [
      if cas9-bound-3? = false [
        setxy Lam-X-Axis + 1 Lam-Y-Axis + 3
        set on-promoter? true
        set heading 0
        set inhibited-pro3? true
      ]
    ]
  ]
  ask Cas9s with [ not on-promoter? ] [
    move
  ]
  ask promoter_3 [
    set pro_seq_3 Lambda-promoter-sequence
  ]
  ask promoter_2 [
    set pro_seq_2 LacI-promoter-sequence
  ]
  ask promoter [
    set pro_seq_1 Tet-promoter-sequence
  ]
end 

to check-transcription                           ; a patch procedure that checks if the CDS was transcribed and produces the corresponding inhibitory signal protein
  if pro-1-transcribed? [
    produce-Tetrs
    set pro-1-transcribed? false
    ]
  if pro-2-transcribed? [
    produce-LacIs
    set pro-2-transcribed? false
  ]
   if pro-3-transcribed? [
      produce-Lams
    set pro-3-transcribed? false
    ]
   ask promoter_3 [
     if any? LacIs-on promoter_3 [
        set temp_LacI False
      ]
    ]
    ask promoter_2 [
      if any? Tetrs-on promoter_2 [
        set temp_Tet False
      ]
    ]
    ask promoter [
      if any? Lams-on promoter [
        set temp_Lam False
      ]
  ]
end 

to add-tet                           ; a procedure to add tet in a user-defined location
  while [mouse-down?] [
    create-Tetrs 1 [
      setshape
      setxy mouse-xcor mouse-ycor
      set on-promoter? false
    ]
    print ""
  ]
end 

to add-LacI                          ; a procedure to add LacI in a user-defined location
  while [mouse-down?] [
    create-LacIs 1 [
      setshape
      setxy mouse-xcor mouse-ycor
      set on-promoter? false
    ]
    print ""
  ]
end 

to add-Lambda                         ; a procedure to add Lam in a user-defined location
  while [mouse-down?] [
    create-Lams 1 [
      setshape
      setxy mouse-xcor mouse-ycor
      set on-promoter? false
    ]
    print ""
  ]
end 

to add-dCas9-gRNA                       ; a procedure to add Cas9-gRNA complexes at a user-defined location
  while [mouse-down?] [
    create-Cas9s 1 [
      setxy mouse-xcor mouse-ycor
      set on-promoter? false
      set partner nobody
      setshape
    ]
    print ""
  ]
end 

to add-RNAP                             ; a procedure to add RNAPs complexes at a user-defined location
  while [mouse-down?] [
    create-RNAPs 1 [
    setxy mouse-xcor mouse-ycor
    set on-dna? false
    setshape
    ]
    print ""
  ]
end 

; Acknowledgements to Uri Wilensky's 2016 Genetic Switch Synthetic Biology Extension and Farzaneh Moghadam's CRISPR repression Model