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CourseworkforTissueGrowth.nlogo
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CourseworkforTissueGrowth.nlogo
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breed [children child];; creating a population of children to move around within the world
breed [copies copy] ;; creating copies of a child and hatch a copy
globals [AMPL big-list Expected-AMPL clustering coefficient CC Expected-Clustering-Coefficient generationstep Average-Degree degree] ; creating global variables for generationstep, ampl , CC and patch-count
copies-own [state]
extensions [nw]
;network extension
directed-link-breed [red-links red-link] ; this defines a directed-link-breed
to setup ; creates a function called setup
ca
nw:set-context turtles links
clear-output
set show-patch-color TRUE
set generationstep 1
crt 1
[
setxy (max-pxcor / 2) (max-pycor)
mark-and-breed
]
reset-ticks
end
to go-once ; creates a function to go-once
clear-all
if show-circle?
[
make-circle
]
compute-metrics
end
to mark-and-breed ; creates a function to mark-and-breed
ifelse (pcolor != green)
[set pcolor green replicate]
[set pcolor red]
die
end
to replicate ; to replicate function to move turtles
hatch-children 1
[
set size 0.75
set color orange
set shape "triangle"
if pcolor = green [make-copy]
]
end
to make-circle ; creates a make-circle function
layout-circle turtles (world-width / 2 - 20)
end
to make-copy ; creates a make-copy function
hatch-copies 2
[
set size 0.25
set shape "circle"
set color white
if who mod 2 = 0 [set state "L"]
]
end
to-report provisional-path ; created a report procedure called provisional-path (temp)
report nw:mean-path-length
end
to-report max-links ; created a report procedure called max-links
report min (list (#generations * (#generations - 1) / 2) 1000)
end
to go ; creates a go function
set generationstep generationstep + 1
ask copies
[
ifelse pcolor != red
[move mark-and-breed] [die]
]
if generationstep = #generations
[
ask copies [die]
stop
]
if show-patch-color = FALSE
[
clear-patches
]
tick
if not show-patch-color
[ cp
if show-circle?
[ layout-circle turtles (world-width / 2 - 20)
if #generations > 1 [ set #generations num-links ]
while [count links < #generations]
[ask one-of turtles
[ create-link-with one-of other turtles ]
]
]
]
compute-metrics ; CALLS compute-metrics function
end
to move ; creates a move function
ifelse state = "L"
[setxy (xcor - 1) (ycor - 1)]
[setxy (xcor + 1) (ycor - 1)]
end
to compute-metrics ; creates a compute-metrics function
set Average-Degree mean [degree] of turtles
nw:set-context turtles links
set AMPL nw:mean-path-length
set CC mean [nw:clustering-coefficient] of turtles
end
to make-scatterplot ; creates a procedure for scatterplot
set-current-plot "AMPL AND CC VS GENERATIONS "
clear-plot
ASK PATCHES [
plotxy AMPL CC
]
end
;---------------------------------------------------------------------
to make-links ; creates a make-link function
if pcolor != red [ create-links-with children-on neighbors with [pycor < [pycor] of myself]]
let a link-neighbors with [ycor < [ycor] of myself]
if count a > 1 [ask a [ create-link-with turtle item 0 [who] of other a]]
; ask turtles with [label = 0][create-links-with other turtles]
; ask turtles with [label = 1][create-link-with turtle 2]
; create-links-with turtles with [pcolor = green]
;; --------------------------------------------------
; ask turtle 0 [ create-links-with other turtles ]
; ask turtle 0 [ create-link-with turtle 1 ]
; ask turtle 2 [ create-link-with turtle 1 ]
;; -------------------------------------------------
; ask turtle 0 [ create-red-links-to other turtles with [pcolor = green] ]
; ask turtle 0 [ create-red-links-from other turtles with [pcolor = green]]
;; -----------------------------------------------------------------------
; ask turtles [
; if not any? turtles-on neighbors with [pcolor = green]
; [create-links-with other turtles]
; ]
end
@#$#@#$#@
GRAPHICS-WINDOW
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BUTTON
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NIL
setup
NIL
1
T
OBSERVER
NIL
NIL
NIL
NIL
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SLIDER
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133
144
166
#generations
#generations
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NIL
HORIZONTAL
BUTTON
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go-once
go\n\n
NIL
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T
OBSERVER
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NIL
NIL
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NIL
go
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OBSERVER
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SWITCH
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show-patch-color
show-patch-color
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SWITCH
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show-circle?
show-circle?
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PLOT
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coverage
generation
#cells
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10.0
0.0
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"" ""
PENS
"# reproductive cells" 1.0 0 -10899396 true "" "plot count patches with [pcolor = green]"
"# nonreproducing cells" 1.0 0 -2674135 true "" "plot count patches with [pcolor = red]"
"# children" 1.0 0 -3844592 true "" "plot count children"
MONITOR
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443
217
488
Average Minimal Path Length (AMPL)
AMPL
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1
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MONITOR
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177
536
Clustering Coefficient (CC)
CC
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1
11
MONITOR
0
390
90
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# nodes
count children
17
1
11
MONITOR
95
391
152
436
# links
count links
17
1
11
PLOT
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1510
367
AMPL AND CC VS GENERATIONS
AMPL
CC
0.0
26.0
0.0
1.0
false
true
"" ""
PENS
"AMPL " 1.0 2 -16777216 true "" "plotxy AMPL CC "
SLIDER
21
168
149
201
num-links
num-links
0
max-links
25.0
1
1
NIL
HORIZONTAL
BUTTON
112
35
176
70
NIL
make-links\n
NIL
1
T
TURTLE
NIL
NIL
NIL
NIL
1
MONITOR
1272
191
1377
236
Average-Degree
Average-Degree
17
1
11
MONITOR
1387
189
1574
234
Expected Clustering Coefficient
Average-Degree / #generations
17
1
11
MONITOR
2
340
102
385
Expected-AMPL
(((ln #generations) - 0.577) / ln Average-Degree) + 0.5
17
1
11
@#$#@#$#@
## WHAT IS IT?
This project shows the visual version of sierpinskis triangle which show population growth by cell division.
## HOW IT WORKS
The biological notion is that of growth and structure formation by a cell (containing a “nucleus”) that reproduces by splitting off daughter cells, which are formed at defined positions (lower left and lower right of the parent cell). After this, they behave as parent cells and repeat the cycle of separation and positioning. However, daughter cells that end up at the same location experience competition for space and resources and as a result become infertile. The outcome of the process is a tree-shaped “tissue” of green and red patches (respectively reproducing and non-reproducing cells). For more details, see the description of the first course work.
# Visulisation of the Network
Linking the essential agents in such a way that the flow of instructed actions becomes visible as a network.
# Characterisation of the network
Monitors The structure of the network is to be characterised by two parameters, the Average Minimal Path Length (AMPL) and the Clustering Coefficient (CC). Their computed values should show up in the monitors of that name (already on the Interface) during a run of the simulation.
## HOW TO USE IT
# Buttons:
Setup: When Setup is pressed then the model is initialised with a single cell in the center
# Go-Once:
When go-once is pressed then it displays a top-down pyramid shown in model 2 of the cw3 answer sheet on netlogo.
#Go:
When go is pressed then it begins running the model with the set rule for in this case is sierpinski triangle of the cw3 answer sheet on netlogo.
# Clear-All :
Clears the world of all turtles.
# Sliders
#Generations: Adjust generations to view changes to model.
# Switch
show-patch-color: The switch shows the patch color when switched on.
show-circle?: The switch shows the circle at the centre of the nucleus.
# Monitors
Patch-Count: Displays patch-count of number of turtles.
Count-Children: Displays patch-count of number of children.
Count-Copies: Displays patch-count of number of copies.
Plot:
Shows number of patches against number of generations.
## THINGS TO NOTICE
Adjust the #generations and num-links to collect data on the network.
#GENERATIONS: 5, 10 , 15 , 20 , 25
#num-links: 5 , 10 , 15 , 20 , 25
Adjust the values for #generations and num-links accordingly then press the go button which will automatically run the model. After, press make-links to link sibling to sibling and switch off patch-color to notice values changing in Monitor AMPL: Nodes, links and CC.
Adjust the values for #generations and num-links accordingly and press go to run the model then switch off patch-color , press go. Adjust num-links accordingly and notice changes to the model.
## THINGS TO TRY
Run the model once, then switch the show-patch-color off and have show-circle on to notice different results.
Second run:
Run the model once, then press the make-links button after switching the show-patch-color off and switch off the show-circle to notice different results that affect the main model.
(suggested things for the user to try to do (move sliders, switches, etc.) with the model)
## EXTENDING THE MODEL
try uncommenting the code and giving running the code below.
to make-links
; ask turtles with [label = 0][create-links-with other turtles]
; ask turtles with [label = 1][create-link-with turtle 2]
; create-links-with turtles with [pcolor = green]
;; --------------------------------------------------
; ask turtle 0 [ create-links-with other turtles ]
; ask turtle 0 [ create-link-with turtle 1 ]
; ask turtle 2 [ create-link-with turtle 1 ]
;; -------------------------------------------------
; ask turtle 0 [ create-red-links-to other turtles with [pcolor = green] ]
; ask turtle 0 [ create-red-links-from other turtles with [pcolor = green]]
;; -----------------------------------------------------------------------
; ask turtles [
; if not any? turtles-on neighbors with [pcolor = green]
; [create-links-with other turtles]
; ]
end
(suggested things to add or change in the Code tab to make the model more complicated, detailed, accurate, etc.)
## NETLOGO FEATURES
This model used breeds to implement the population of children and copies to form each model.
## RELATED MODELS
CA 1D Rule 90 - the basic rule 90 model
## CREDITS AND REFERENCES
Wilensky, U. (2002). NetLogo CA 1D Rule 90 model. http://ccl.northwestern.edu/netlogo/models/CA1DRule90. Center for Connected Learning and Computer-Based Modeling, Northwestern University, Evanston, IL.
Rene.2020. Practical 3 Population Growth by cell divison https://herts.instructure.com/courses/77620/files/2351766?module_item_id=1320622 Date Accessed: 10/11/2020
Rene.2020.Design Program Population Growth by cell divison.https://herts.instructure.com/courses/77620/files/2370872?module_item_id=1328164 Date Accessed : 10/11/2020
@#$#@#$#@
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Rectangle -7500403 true true 135 90 165 300
Polygon -7500403 true true 135 255 90 210 45 195 75 255 135 285
Polygon -7500403 true true 165 255 210 210 255 195 225 255 165 285
Polygon -7500403 true true 135 180 90 135 45 120 75 180 135 210
Polygon -7500403 true true 165 180 165 210 225 180 255 120 210 135
Polygon -7500403 true true 135 105 90 60 45 45 75 105 135 135
Polygon -7500403 true true 165 105 165 135 225 105 255 45 210 60
Polygon -7500403 true true 135 90 120 45 150 15 180 45 165 90
sheep
false
15
Circle -1 true true 203 65 88
Circle -1 true true 70 65 162
Circle -1 true true 150 105 120
Polygon -7500403 true false 218 120 240 165 255 165 278 120
Circle -7500403 true false 214 72 67
Rectangle -1 true true 164 223 179 298
Polygon -1 true true 45 285 30 285 30 240 15 195 45 210
Circle -1 true true 3 83 150
Rectangle -1 true true 65 221 80 296
Polygon -1 true true 195 285 210 285 210 240 240 210 195 210
Polygon -7500403 true false 276 85 285 105 302 99 294 83
Polygon -7500403 true false 219 85 210 105 193 99 201 83
square
false
0
Rectangle -7500403 true true 30 30 270 270
square 2
false
0
Rectangle -7500403 true true 30 30 270 270
Rectangle -16777216 true false 60 60 240 240
star
false
0
Polygon -7500403 true true 151 1 185 108 298 108 207 175 242 282 151 216 59 282 94 175 3 108 116 108
target
false
0
Circle -7500403 true true 0 0 300
Circle -16777216 true false 30 30 240
Circle -7500403 true true 60 60 180
Circle -16777216 true false 90 90 120
Circle -7500403 true true 120 120 60
tree
false
0
Circle -7500403 true true 118 3 94
Rectangle -6459832 true false 120 195 180 300
Circle -7500403 true true 65 21 108
Circle -7500403 true true 116 41 127
Circle -7500403 true true 45 90 120
Circle -7500403 true true 104 74 152
triangle
false
0
Polygon -7500403 true true 150 30 15 255 285 255
triangle 2
false
0
Polygon -7500403 true true 150 30 15 255 285 255
Polygon -16777216 true false 151 99 225 223 75 224
truck
false
0
Rectangle -7500403 true true 4 45 195 187
Polygon -7500403 true true 296 193 296 150 259 134 244 104 208 104 207 194
Rectangle -1 true false 195 60 195 105
Polygon -16777216 true false 238 112 252 141 219 141 218 112
Circle -16777216 true false 234 174 42
Rectangle -7500403 true true 181 185 214 194
Circle -16777216 true false 144 174 42
Circle -16777216 true false 24 174 42
Circle -7500403 false true 24 174 42
Circle -7500403 false true 144 174 42
Circle -7500403 false true 234 174 42
turtle
true
0
Polygon -10899396 true false 215 204 240 233 246 254 228 266 215 252 193 210
Polygon -10899396 true false 195 90 225 75 245 75 260 89 269 108 261 124 240 105 225 105 210 105
Polygon -10899396 true false 105 90 75 75 55 75 40 89 31 108 39 124 60 105 75 105 90 105
Polygon -10899396 true false 132 85 134 64 107 51 108 17 150 2 192 18 192 52 169 65 172 87
Polygon -10899396 true false 85 204 60 233 54 254 72 266 85 252 107 210
Polygon -7500403 true true 119 75 179 75 209 101 224 135 220 225 175 261 128 261 81 224 74 135 88 99
wheel
false
0
Circle -7500403 true true 3 3 294
Circle -16777216 true false 30 30 240
Line -7500403 true 150 285 150 15
Line -7500403 true 15 150 285 150
Circle -7500403 true true 120 120 60
Line -7500403 true 216 40 79 269
Line -7500403 true 40 84 269 221
Line -7500403 true 40 216 269 79
Line -7500403 true 84 40 221 269
wolf
false
0
Polygon -16777216 true false 253 133 245 131 245 133
Polygon -7500403 true true 2 194 13 197 30 191 38 193 38 205 20 226 20 257 27 265 38 266 40 260 31 253 31 230 60 206 68 198 75 209 66 228 65 243 82 261 84 268 100 267 103 261 77 239 79 231 100 207 98 196 119 201 143 202 160 195 166 210 172 213 173 238 167 251 160 248 154 265 169 264 178 247 186 240 198 260 200 271 217 271 219 262 207 258 195 230 192 198 210 184 227 164 242 144 259 145 284 151 277 141 293 140 299 134 297 127 273 119 270 105
Polygon -7500403 true true -1 195 14 180 36 166 40 153 53 140 82 131 134 133 159 126 188 115 227 108 236 102 238 98 268 86 269 92 281 87 269 103 269 113
x
false
0
Polygon -7500403 true true 270 75 225 30 30 225 75 270
Polygon -7500403 true true 30 75 75 30 270 225 225 270
@#$#@#$#@
NetLogo 6.1.1
@#$#@#$#@
@#$#@#$#@
@#$#@#$#@
<experiments>
<experiment name="experiment SierpinskyTurtle" repetitions="1" runMetricsEveryStep="true">
<setup>setup</setup>
<go>go</go>
<metric>generation</metric>
<metric>patch-count</metric>
<enumeratedValueSet variable="#generations">
<value value="25"/>
</enumeratedValueSet>
</experiment>
</experiments>
@#$#@#$#@
@#$#@#$#@
default
0.0
-0.2 0 0.0 1.0
0.0 1 1.0 0.0
0.2 0 0.0 1.0
link direction
true
0
Line -7500403 true 150 150 90 180
Line -7500403 true 150 150 210 180
@#$#@#$#@
0
@#$#@#$#@