Test Model 12321

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1 collaborator

WHAT IS IT?

This model is attempting to explain how a generalized cell signaling pathway works.

HOW IT WORKS

The ligand, represented by the small white sphere, first bounces around in a certain defined area above the receptor (which is the blue object located near the top of the cell). Once the ligand hits a certain point on the receptor, the receptor sends a signal into the cell. (Note that when this occurs the switch titled "cellresponsetrigger" turns on, this is because we coded the program so that it understand to create relay molecules whenever a ligand binds to the receptor). This signal, which is represented by the orange colored arrow-like shape, causes the creation of relay molecules. Within this program, we have created three relay molecules to showcase the different stages of this generic cell-signaling pathway. (As a note, the first relay molecule is grey, the second is red, and the third is of a coral color). What occurs is that the first relay moelcule aids in the creation of the second relay molecule, and then the second relay molecule aids in the creation of the third relay molecule. The third relay molecule is what finally causes the creation of the response proteins.

HOW TO USE IT

In order to use this model, you will have to first press the "setup" button. While doing this, you will want to turn the tick speed up a bit so that the model will load faster. This will allow all parts of the model to set up so that they are ready to run. Then, in order to run the program, the button titled "start" must be pressed. Prior to pressing "start" you will want to decrease the tick speed so that the process does not occur so fast that you cannot see it happen. In order to stop the program at any time, simply press "clear".

THINGS TO NOTICE

Within the program, there are a few minor kinks. The background at the very top is partially black and partially blue, because we were unable to get the program to work unless we caused the background behind our picture to vary from the background color of the picture. This is because, the ligand is coded so that it stays within a specific area which is of a specific color; and, since the background of the picture is completely black, we were unable to use black as the background color of the entire screen. Additionally, we were unable to format our picture to be large enough to cover the partially blue background. There is also the slight implication that the viewer must adjust the tick speed during setup and start in order to be able to properly view the cell signaling pathway. Lastly, we understand that a real cell signaling pathway does not work so that the products within the cell form straight paths to the end response protein. However, with our limited coding skills, we were only able to format it as such.

THINGS TO TRY

There is a slider within the program that is labeled "intial-number-of-ligands", this slider allows a user to change the number of ligands that are created. This will, in turn, effect the amount of reponse proteins and relay molecules that are created. In order to use the slider, simply slide it to the desired number of ligands and then press setup before pressing play.

EXTENDING THE MODEL

It could be worthwhile and interesting to try adding code which creates seperate pathways within the cell so that all the products still look organized, though they are not being formed in a straight line.

NETLOGO FEATURES

Netlogo allows you to create groups of procedures into a function which performs a certain outcome. We used this feature in order to trigger the cell-response whenever a ligand binds to the cell receptor. Additionally, netlogo allows you to add additional variables to describe a turtle (in our case a ligand), which we used to determine when a was bound to the receptor.

RELATED MODELS

(models in the NetLogo Models Library and elsewhere which are of related interest)

CREDITS AND REFERENCES

(a reference to the model's URL on the web if it has one, as well as any other necessary credits, citations, and links)

Comments and Questions

Please start the discussion about this model! (You'll first need to log in.)

Click to Run Model

globals [redzone]
breed [ligands ligand]
breed [receptors receptor]
breed [signals signal]
breed [relaymolecules1 relaymolecule1]
breed [relaymolecules2 relaymolecule2]
breed [relaymolecules3 relaymolecule3]
breed [responseproteins responseprotein]
turtles-own [energy]

to setup
  clear-all

  ;;Set key variable values
  set cellresponsetrigger false  ;;tracks when the ligand binds to the receptor
 ;; import-drawing "IMG_1609.jpg"
  set-default-shape ligands "circle"

  ;;Create the number of ligands selected at start of simulation
  create-ligands initial-number-of-ligands [
    set size 1
    set color white
    set energy 1
  ]

  ;;Prepare the background color for the simulation
   ask ligands [setxy 10 13]
   ask patches [set pcolor black]
   ask patches with [pycor > 11] [set pcolor blue];; blue is above y=0
   ask patch 0 12 [set pcolor red]
   ask patch 0 13 [set pcolor red]
   ask patch 0 14 [set pcolor red]
   ask patch 0 15 [set pcolor red]

 ;;Reset the counter
  reset-ticks
  tick
end 

to go
  ask ligands [
    ;;check if ligand has bound to the receptor area
    ifelse [pcolor] of patch-ahead 1 = red AND energy = 1
        [ set cellresponsetrigger true set energy 0]
    [ ifelse [pcolor] of patch-ahead 1 = blue AND energy = 1
       [forward 1]
       [lt random-float 360 ] ;; moves randomly in only the blue area ; ifelse [pcolor] of patch-ahead 1 = blue
  ]
  ]

  if cellresponsetrigger = true
      [ cell-response ]
end 

to cell-response

  if cellresponsetrigger [
  ask ligands [
    if [pcolor] of patch-ahead 1 = red
        [ set size 0 forward 10]
  ]
  ]

  ifelse not cellresponsetrigger
      [ stop ]
      [ set cellresponsetrigger false]

  set-default-shape signals "pentagon" ;;"default"
  create-signals 8 [
    set size 2
    set xcor 0 set ycor 5
  ]
  ask signals [set xcor 0 set ycor 3]
  ask signals [
    set size 0
  ]

  set-default-shape relaymolecules1 "pentagon" ;;"relay molecule 1"
  create-relaymolecules1 1 [
  set size 2
  set color 13
  set xcor 0 set ycor 4
  ]
  ask relaymolecules1 [set xcor 0 set ycor 2]
  ask relaymolecules1 [
    set size 0
  ]

  set-default-shape relaymolecules2 "pentagon" ;;;;"relay molecule 2"
  create-relaymolecules2 1 [
    set size 2
    set color 15
    set xcor 0 set ycor 0
  ]
  ask relaymolecules2 [set xcor 0 set ycor -2]
  ask relaymolecules2 [
    set size 0
  ]

  set-default-shape relaymolecules3 "pentagon" ;;"relay molecule 3"
  create-relaymolecules3 1 [
    set size 2
    set color 17
    set xcor 0 set ycor -2]
  ask relaymolecules3 [set xcor 0 set ycor -4]
  ask relaymolecules3 [
    set size 0
  ]

  set-default-shape responseproteins "pentagon" ;;"response protein"
  create-responseproteins 3 [
  set size 3
  set color 115
  set xcor 0 set ycor -8
  ]
  ask responseproteins [set xcor 0 set ycor -10]
  ask responseproteins [
    set size 0
  ]

  stop
end 

to clear
  clear-all
end

There is only one version of this model, created almost 4 years ago by Sruthi Koneru.

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