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Tagged by George Dombi about 7 years ago

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Collagen (Question)

Hi, I need some help. I have a series of questions, but 2 at a time. 1) I have a model with 2 breeds. Rod shaped collagen and circle shaped inhibitor. As set-up now, collagen rods interact. How do I get inhibitor circles to interact with collagen rods but not with each other. 2) If a inhibitor circle binds to a collagen rod, no other rod can bind to the circle, but another collagen rod can bind to the first. 3) if two or more inhibitor circles bind to a collagen rod, then it is out of action and nothing else can bind. 4) is there a way to plot the average number of collagen rods in a the various clusters?

Posted about 7 years ago

Clue (edited)

Hi, I only briefly looked at your code, but I have some ideas that might or might not help. 1) I don't see any inhibitors interacting with each other. Could you maybe give an example of where this happens? 2) and 3) Maybe you could specify a property for each breed which gives information on its linked status. Ex: inhibitor-own [bound] and collagen-own [blocked]. When you merge clusters in your ask collagen procedure, you could set the bound property of inhibitors to yes whenever collagen binds to inhibitor. For the blocked property of collagen, you could have a counter. +1 for each inhibitor that the collagen merges to, up to a max of 2. At the beginning of the ask collagen procedure, you would have to check and see if bound = yes, ignore that inhibitor. If blocked = 2, ignore that collagen rod. Otherwise, proceed with merge. 4) Isn't this count collagen/# leaders ? Hope any of this helps.

Posted about 7 years ago

Collagen model - inhibitors don't interact.

Hi Cecilia, I took your advice, as I could implement it and now the collagen binds only 2 inhibitors before no longer binding to self. This is a definite improvement. Now what to know how to change leader so that when single collagen binds to an existing group, the direction of the leader is in the group not the direction of the newly added collagen. Please take a look when you have time. Bye for now, George

Posted about 7 years ago

Click to Run Model

breed [collagen]
breed [inhibitor]

turtles-own [
  ;; The easiest way to handle the clusters is to designate one
  ;; node in the cluster as the "leader".  It doesn't really matter
  ;; which node it is; the choice is arbitrary, but it gives us a way
  ;; to identify the cluster.  Every node knows who the leader of
  ;; its cluster is.
  ;; This is used to make all of the nodes in a cluster turn by
  ;; the same number of degrees.  Each leader chooses a random
  ;; amount, then everyone else uses the amount from their leader.
  collagen-own [ blocked ]

to setup
  set-default-shape collagen "collagen"
  set-default-shape inhibitor "circle"
   create-collagen population
    [ set size 2.5  
      set color white
      setxy random-xcor random-ycor
      rt random-float 360
      ;; initially, every node leads its own cluster of one
      set leader self 
      set blocked 0]
   create-inhibitor Inhibitors ; number of inhibitors from slider
    [ set color green
      set size 0.5
      setxy random-xcor random-ycor
      rt random-float 360
       ;; initially, every node leads its own cluster of one
      set leader self] 

to go
  ;; All the leaders choose turn amounts
  ask collagen with [leader = self] [
    set turn-amount 0 ;random 10 - random 10
  ;; All nodes follow their leaders
  ask collagen [
    rt [turn-amount] of leader
    fd 0.1
  ask inhibitor with [leader = self] [
    set turn-amount random 10 - random 10
  ask inhibitor [
    rt [turn-amount] of leader
    fd 0.1
  ;; Here's the tricky part. We check whether any pairs
  ;; of clusters are touching, and if they are, we merge them.
  ask collagen [
     ifelse blocked < 3 
     [let candidates collagen in-radius 1 with [leader != [leader] of myself] 
      if any? candidates [
      create-links-with candidates [ hide-link ]
      ask candidates [ merge ] 
    ] ]
     [ stop ] 
     let binders inhibitor in-radius 1 with [leader != [leader] of myself]
    if any? binders [
      create-links-with binders [ hide-link ]
      set blocked  blocked + 1 
      ask binders [ merge ]
 ; do-plots

;to do-plots
 ; set-current-plot "Width"
 ; set-current-plot-pen "max group"
 ; plot count collagen
; end

;; This is a recursive procedure -- it calls itself.
;; That way the new leader propagates through the entire
;; cluster.

to merge  ;; node procedure
  ;; First this node merges.
  set leader [leader] of myself
  set heading [heading] of leader
  set color yellow
  ;; Then any neighboring nodes that haven't merged yet
  ;; merge.
  ask link-neighbors with [leader != [leader] of myself]
    [ merge ]

; Public Domain:
; To the extent possible under law, Uri Wilensky has waived all
; copyright and related or neighboring rights to this model.
; Modified March 4, 2014
; George Dombi 

There are 3 versions of this model.

Uploaded by When Description Download
George Dombi about 7 years ago Inhibitors don't bind each other Download this version
George Dombi about 7 years ago Binding inhibitors Download this version
George Dombi about 7 years ago Initial upload Download this version

Attached files

File Type Description Last updated
Collagen.png preview Collagen and inhibitors about 7 years ago, by George Dombi Download
Collagen02_5.1 view.png png Start-up image about 7 years ago, by George Dombi Download

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