main_commented.nlogo

; Melisa Saichi & Thomas Bersez
; M2 GENIOHME, fall semester 2018
;-----------------------------------------------------------------------

;variables definition:

patches-own [
  act-c     ; activator concentration at the current stage
  inh-c     ; inhibitor concentration at the current stage
  act-n     ; activator concentration at the next stage
  inh-n     ; activator concentration at the next stage
]


;----------------------------------------------------------------------
; Procedures , activator is set up on green

to show-concentration
  ask patches [
    set pcolor scale-color
    green act-c
    2 ; residual
    80 ; maximum
  ]
end

;----------------------------------------------------------------------

;to allow reproducibility, random seed is manually fixed
; random activator & inibitor concentrations are set. both in the range [0,50] as described in the article

to setup
  clear-all
  random-seed 137 
  ask patches [ set act-c random-float 50.0
    set inh-c random-float 50.0 ] 
end

;----------------------------------------------------------------------

to copy-concentration
  ask patches [
    set act-n ( act-c )
    set inh-n ( inh-c )
  ]
end

;-----------------------------------------------------------------------------------------

; Objective: determine the act & inh concentrations at the next stage 
; Procedure: consider the autonomous synthesis (autocatalysis) and decay for act & inh
;input:current act-c or inh-c   ;output: act-n or inh-n after production decay

to production-decay   
  ask patches [		
    set act-n ( act-c + ActivatorProduction - ( ActivatorDecayRate * act-c ) )
    set inh-n ( inh-c + InhibitorProduction - ( InhibitorDecayRate * inh-c ) )
  ]
end  


;----------------------------------------------------------------------------------------

;Aim:calculate the dependant production for either activator or inhibitor
;‘dependant’:concentrations depend on :interaction rate & activator autocatalysis term (act-c^2)
;if clauses : avoid both negative and huge positive concentrations 
;input:current act-c or inh-c  ;output: act-n or inh-n after production dependant

to act-inh-dependent-production
    ask patches [
    if act-c < 100
    [
      ifelse inh-c > 0
      [ set act-n ( act-n + ( InteractionRate * ( ( act-c * act-c ) / inh-c ) ) ) ]
      [ set act-n ( act-n + ( InteractionRate * ( ( act-c * act-c ) ) ) ) ]
    ]
    if inh-c < 100
    [ set inh-n ( inh-n + ( InteractionRate * ( act-c * act-c ) ) ) ]
  ]
end


;--------------------------------------------------------------------------------------------

;aim: simulate act & inh diffusion for each patch using one or two dimensions or homogeneous variation of parameters
; input:act-c or inh-c  ;output:act-n or inh-n after considering the diffusion mode


to diffusion
    ask patches [

    let ACT ( act-c )
    let INH ( inh-c )

    ; define activator diffusion coefficient according to mode

    if Mode = "OneDim"
    [ let onedim ( abs  ( cos ( Multact * pxcor ) ) )
    set act-n ( act-n - ( onedim * act-n ) )
    set inh-n ( inh-n - ( InhibitorDiffusionRate * act-n ) )
      ask neighbors [
        set act-n ( act-n + ( ( onedim * ACT ) / 8  ) )
        set inh-n ( inh-n + ( ( InhibitorDiffusionRate * INH ) / 8 ) )
      ]
    ]

    if Mode = "TwoDim"
    [ let twodim ( abs ( 0.5 * ( cos ( Multact * pxcor ) + cos ( Multact * pycor) ) ) )
      set act-n ( act-n - ( twodim * act-n ) )
      set inh-n ( inh-n - ( InhibitorDiffusionRate * act-n ) )
        ask neighbors [
        set act-n ( act-n + ( ( twodim * ACT ) / 8  ) )
        set inh-n ( inh-n + ( ( InhibitorDiffusionRate * INH ) / 8 ) )
      ]
    ]

    if Mode = "Homogenous"
    [ set act-n ( act-n - ( ActivatorDiffusionRate * act-n ) )
    set inh-n ( inh-n - ( InhibitorDiffusionRate * act-n ) )
        ask neighbors [
        set act-n ( act-n + ( ( ActivatorDiffusionRate * ACT ) / 8  ) )
        set inh-n ( inh-n + ( ( InhibitorDiffusionRate * INH ) / 8 ) )
      ]
    ]
  ]
end


;----------------------------------------------------------------------------------


;aim: show act-n & inh-n concentrations
;show the final concentrations after all the calculations
to next-turn
    ask patches [
    ifelse act-n < 0
    [ set act-c ( 0 ) ]
    [ set act-c ( act-n ) ]
    ifelse inh-n < 0
    [ set inh-c ( 0 ) ]
    [ set inh-c ( inh-n ) ]
  ]
  show-concentration
end

;---------------------------------------------------------------------------------
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