;1) Is simulation modelling the best approach for this? (yes, actually. According to Dr. Peck, Simulation modeling is on the verge of having its heyday and is much better than mathematical modelling for these types of questions) ;2) What advantage does simulation modeling provide over other types of models? ;3) Question first, or model first? (both, but really question first because the model get's too difficult to make without clear boundaries. You can add onto it later) ;4) How to manage tons of different "breeds" without losing too much speed? (i was thinking netlogo wouldnt be good for this, but he said coders using C++ make him nervous - it's a more complicated language with fewer safety nets; the one modelling graduate student said pretty much nobody uses netlogo anymore lol) ;5) How to manage differences in scale? ;6) Can I get two screens? (one for environmental patches, one for organism distribution) (didn't sound like it) ; ;What am I trying to model here? ; 1) Popoulation Dynamics of a complex soil community ; a) Create a stable, in silico copy of a real ecosystem ; b) given our (myriad) assumptions: ; c) what does the community structure look like in a typical mineral, arid soil after the model stabilizes? (what is interesting about community structure? i.e. why do we want to know what it looks like?) ; i) What are the most abundant consumers? ; ii) Is the community structure static or dynamic? ; iii) If it is dynamic, are these shifts related to environmental changes? ; 2) shifts in population dynamics given climate driven changes in the MDV environment ;6/10/2020 ;Sandona crashes faster with more bacteria. I think what's happening is that they age out before they can reproduce, so either the lifespan is too short for the resolution of the energy-gaining process, or the reproductive threshold is too high. ;Okay, I tested the hypothesis that it had to do with reproduction, and while they did survive longer (from ~50 ticks to ~80 ticks), they still crash every time and it isn't that longer. I think the REAL problem is that the bacteria drain their local resources very quickly and their is no new input into the system. ; Start with the most abundant or seemingly important organisms/trends from your metagenome paper. Sandonidae, Acanthamoeba, Rhogostoma, Chilodonellidae, Scottnema, etc. ; Start with a single representative sample (don't do the whole valley system - eventually you might have to break the valley into pieces that are represent different ecologies rather than trying to represent everything geographically) ; If you write a grant, you might have to include money for experiments to add information you don't have - specifically, in-depth targeted amplicon study of a single soil type; in vitro cultivation of as many organisms as possible globals [ ;BacteriaStart ;Starting abundance for all Bacteria (sets each individual phylum to the input value) ActinoStart ;Starting abundance for Actinobacteria AcidoStart ;Starting abundance for Acidobacteria ProteoStart ;Starting abundance for Proteobacteria ChloroStart ;Starting abundance for Chlorobacteria CyanoStart ;Starting abundance for Cyanobacteria BacStartList ;List of all Bacteria phyla for general bacterial work DeadOld_Nematodes ;Mortality (dead from old age) tracker for Nematodes DeadOld_Ciliate ;Mortality (dead from old age) tracker for Ciliates DeadOld_Amoeba ;Mortality (dead from old age) tracker for Amoeba DeadOld_Flagellates ;Mortality (dead from old age) tracker for Flagellates DeadOld_TestateAmoeba ;Mortality (dead from old age) tracker for TestateAmoeba DeadOld_Bacteria ;Mortality (dead from old age) tracker for Bacteria Starved_Nematodes ;Mortality (dead from old age) tracker for Nematodes Starved_Ciliate ;Mortality (dead from old age) tracker for Ciliates Starved_Amoeba ;Mortality (dead from old age) tracker for Amoeba Starved_Flagellates ;Mortality (dead from old age) tracker for Flagellates Starved_TestateAmoeba ;Mortality (dead from old age) tracker for TestateAmoeba Starved_Bacteria ;Mortality (dead from old age) tracker for Bacteria Eaten ;counter to see how many bacteria have been consumed ] ;Cercozoa breed [Sandonas Sandona] breed [Rhogostomas Rhogostoma] ;Nematoda breed [Scottnemas Scottnema] breed [Eudorylaimuses Eudorylaimus] ;Bacteria breed [Actinobacteria Actinobacterium] breed [Acidobacteria Acidobacterium] breed [Proteobacteria Proteobacterium] breed [Chloroflexi Chloroflexum] breed [Cyanobacteria Cyanobacterium] turtles-own [ Org_Type trophic_preference ;Temperature_Tolerance ;Excysted ;Boolean movement ;Type speed ;Vertical_Position ;C:N_ratio reproduction_threshold ;Energy and/or time needed before offspring are born lifespan ;How long individuals in a species lives (in ticks) age ;Current age Energy ] patches-own[ Moisture ;0.001 to 100% Total_Carbon ;Equal to Legacy_Carbon + Carbon_Production + Carbon_Decomposition. Carbon_Production comes from phototrophs, Carbon_Decomposition comes from heterotrophs and the death rate. Legacy_Carbon ;Randomly decided at model start, always decreases over the lifespan of the model ] to setup ca ;Setup Environment ;patches each have: moisture, salinity, pH, OM, irradiation level ask patches [ set Moisture random-float 0.1 set Legacy_Carbon random 501 + 500 ;set Carbon_Production random [200 300] ;set Carbon_Decomposition random [100 200] set Total_Carbon Legacy_Carbon; + Carbon_Production + Carbon_Decomposition if Show_moisture = true [set pcolor scale-color blue Moisture 0 0.1] if Show_L-Carbon = true [set pcolor scale-color red Legacy_Carbon 1 1000] if Show_T-Carbon = true [set pcolor scale-color green Total_Carbon 1 2000] ] set Eaten 0 ;Setup Species Distribution ;patches each have: #of each species from above. ;Cercozoa create-Sandonas 21 [SpeciesSpecs "Flagellate" "Bacteria" "crcz" 2 80 120 25 "default" 85 1] ;Organism type, Trophic preference, movement type, movement speed, Energy, reproduction threshold, lifespan, shape, color, turtle size ;create-Rhogostomas 20 [SpeciesSpecs "Testate Amoeba" "Bacteria" "amba" 0.5 130 195 25 "balloon" 55 1.5] ;Reproduction threshold is set as 1.5 energy (what does energy actually mean here? Starting energy?) ;Nematoda ;create-Scottnemas 5 [SpeciesSpecs "Nematode" "Bacteria" "nmtd" 8 2000 3000 100 "caterpillar" 105 3.5] ;Age tracker will need to incorporate active aging vs inactive aging (so that scottnema's relatively shorter metabolic lifespan will result in a longer real-time lifespan than Eudorylaimus; I am assuming that as a smaller organism lower on the trophic ladder Scottnema has a shorter metabolic lifespan (metabolic lifespan meaning the lifespan of the organism's physiology, regardless of the environment's modulation of its real-time activity and resulting lifespan) ; create-Eudorylaimuses 1 [SpeciesSpecs "Nematode" "Omni" "nmtd" 5 5000 7500 120 "caterpillar" 15 5] set BacStartList ["ActinoStart" "AcidoStart" "ProteoStart" "ChloroStart" "CyanoStart"] foreach BacStartList [n -> set n BacteriaStart] ;Bacteria create-Actinobacteria BacteriaStart [SpeciesSpecs "Bacteria" "hetero" "bctra" 0 25 30 10 "dot" 44 0.5] create-Acidobacteria BacteriaStart [SpeciesSpecs "Bacteria" "hetero" "bctra" 0 25 30 10 "dot" 24 0.5] create-Proteobacteria BacteriaStart [SpeciesSpecs "Bacteria" "hetero" "bctra" 0 25 30 10 "dot" 94 0.5] create-Chloroflexi BacteriaStart [SpeciesSpecs "Bacteria" "hetero" "bctra" 0 25 30 10 "dot" 134 0.5] create-Cyanobacteria BacteriaStart [SpeciesSpecs "Bacteria" "hetero" "bctra" 0 25 30 10 "dot" 64 0.5] reset-ticks end to go ;;Environment ask patches [ if Show_moisture = true [set pcolor scale-color blue Moisture 0 0.1] if Show_L-Carbon = true [set pcolor scale-color red Legacy_Carbon 1 1000] if Show_T-Carbon = true [set pcolor scale-color green Total_Carbon 1 2000] ] ;;Biota ;Model search for food ask turtles [ Move Hunt if Energy >= reproduction_threshold [Reproduce] Senesce ] ;Model feeding ;Model reproduction ;Model starvation if (count turtles with [Org_Type = "Flagellate"] = 0) [STOP] tick end ;SPECIESSPECS ;Defines attributes for all species; group-specific characteristics are passed with function call in setup. ;Called by SETUP ;******************************************************************************** to SpeciesSpecs [Otype TrPr Mvm Spd Enrgy RepThr Lfspn shp clr sz] set Org_Type Otype set trophic_preference trPr set movement mvm ;Type set speed spd ;Vertical_Position set Energy Enrgy set reproduction_threshold repThr ;Energy and/or time needed before offspring are born set lifespan lfspn ;How long individuals in a species lives (in ticks) set age random lifespan ;Temperature_Tolerance ;Excysted ;Boolean set shape shp set color clr set size sz show-turtle setxy random-xcor random-ycor if Show_Turtles = false [hide-turtle] end ;MOVE ;Wrapper that sorts soil consumers into movement types. ;Called by Go. Calls Squirm, Wiggle, Swim, Ooze, and Crawl. ;******************************************************************************** to Move if Org_type = "Nematode" [Squirm] ;if Org_type = "Bacteria" [Wiggle] ;if Org_type = "Ciliate" [Swim] if (Org_type = "Testate Amoeba" or Org_type = "Amoeba") [Ooze] if Org_type = "Flagellate" [Crawl] end ;HUNT (Copied from CompBase5.0peck3_art4 6/2/2020, then modified) ;Manages the feeding behavior of soil consumers. (Will eventually be individualized and moved in with each type's movement) ;Soil consumers search for prey in a radius of 10, then move to prey's patch and consume it if their energy is not full (i.e. hungry). ;Called by Go. Calls ConsumeFood. ;******************************************************************************** to Hunt ifelse Org_type = "Bacteria" [ let Consume (size * 10) let HowMuch? 0 ask patch-here [set HowMuch? Total_Carbon] if Total_Carbon > Consume [ set Energy Energy + Consume ask patch-here [set Total_Carbon Total_Carbon - Consume ] ] ] [let fdpref trophic_preference let Nutrients 0 if any? turtles with [Org_type = fdpref] in-radius 1 ;; If the prey organism type matches the hunting organism's trophic preference, then the prey is consumed [ask one-of turtles with [Org_type = fdpref] in-radius 1 [ set Nutrients Energy set Eaten Eaten + 1 die ] set Energy Energy + Nutrients ;; Increases predator energy by a the conusmed prey's biomass ; set PreyDeadPredation PreyDeadPredation + 1 ]];] end ;SQUIRM (Movement Type) ;Defines movement for organisms with movement type "nmtd" (nematode). ;Called by GO ;******************************************************************************** to Reproduce if Org_Type = "Bacteria" [hatch 1 [set Energy 15 set age 0 rt 360 fd 1] set Energy 15] ; assumes reproduction takes half of the energy available to the parent cell if Org_type = "Nematode" [hatch 1] if Org_type = "Flagellate" or Org_type = "Amoeba" [hatch 1 [set Energy 60 set age 0] set Energy 60] ; assumes reproduction takes half of the energy available to the parent cell end ;BIN_FISS ;Defines reproduction for bacteria ;Called by REPRODUCE ;******************************************************************************** to Bin_Fiss [type_] end to Senesce set age age + 1 if (age >= lifespan) [ if (Org_Type = "Nematode") [set DeadOld_Nematodes DeadOld_Nematodes + 1] if (Org_Type = "Ciliate") [set DeadOld_Ciliate DeadOld_Ciliate + 1] if (Org_Type = "Amoeba") [set DeadOld_Amoeba DeadOld_Amoeba + 1] if (Org_Type = "Flagellate") [set DeadOld_Flagellates DeadOld_Flagellates + 1] if (Org_Type = "Testate Amoeba") [set DeadOld_TestateAmoeba DeadOld_TestateAmoeba + 1] if (Org_Type = "Bacteria") [set DeadOld_Bacteria DeadOld_Bacteria + 1] die] set Energy Energy - size ;expending energy (there must be a formula for how much there is of this) if (Energy <= 0) [ if (Org_Type = "Nematode") [set Starved_Nematodes Starved_Nematodes + 1] if (Org_Type = "Ciliate") [set Starved_Ciliate Starved_Ciliate + 1] if (Org_Type = "Amoeba") [set Starved_Amoeba Starved_Amoeba + 1] if (Org_Type = "Flagellate") [set Starved_Flagellates Starved_Flagellates + 1] if (Org_Type = "Testate Amoeba") [set Starved_TestateAmoeba Starved_TestateAmoeba + 1] if (Org_Type = "Bacteria") [set Starved_Bacteria Starved_Bacteria + 1] die] end ;SQUIRM (Movement Type) ;Defines movement for organisms with movement type "nmtd" (nematode). ;Called by GO ;******************************************************************************** to Squirm rt random 90 fd (speed / 2) lt random 90 fd (speed / 2) end ;OOZE (Movement Type) ;Defines movement for organisms with movement type "amba" (amoeba). ;Called by GO ;******************************************************************************** to Ooze fd speed let turn random 10 if turn = 5 [rt random 90 lt random 180] end ;CRAWL (Movement Type) ;Defines movement for organisms with movement type "crcz" (cercozoa). ;Called by GO ;******************************************************************************** to Crawl rt random 90 lt random 180 if (random 3 = 1) [fd speed] end @#$#@#$#@ GRAPHICS-WINDOW 210 10 647 448 -1 -1 13.0 1 10 1 1 1 0 1 1 1 -16 16 -16 16 0 0 1 ticks 30.0 BUTTON 75 11 138 44 NIL Go T 1 T OBSERVER NIL NIL NIL NIL 1 BUTTON 8 10 72 43 NIL Setup NIL 1 T OBSERVER NIL NIL NIL NIL 1 PLOT 674 12 1032 261 Eukaryote Ticks Abundance 0.0 10.0 0.0 10.0 true true "" "" PENS "Scottnema" 1.0 0 -13345367 true "" "plot count Scottnemas" "Eudorylaimus" 1.0 0 -2674135 true "" "plot count Eudorylaimuses" "Sandonas" 1.0 0 -11221820 true "" "plot count Sandonas" "Rhogostoma" 1.0 0 -13840069 true "" "plot count Rhogostomas" PLOT 1043 10 1374 261 Bacteria Ticks Abundance 0.0 10.0 0.0 10.0 true true "" "" PENS "Proteobacteria" 1.0 0 -14454117 true "" "plot count Proteobacteria" "Actinobacteria" 1.0 0 -4079321 true "" "plot count Actinobacteria" "Acidobacteria" 1.0 0 -3844592 true "" "plot count Acidobacteria" "Chloroflexi" 1.0 0 -4757638 true "" "plot count Chloroflexi" "Cyanobacteria" 1.0 0 -14439633 true "" "plot count Cyanobacteria" PLOT 673 266 1030 453 Energy (Euk) Ticks Energy 0.0 10.0 0.0 10.0 true true "" "" PENS "Scottnema" 1.0 0 -13345367 true "" "plot mean [Energy] of Scottnemas" "Eudorylaimus" 1.0 0 -2674135 true "" "plot mean [Energy] of Eudorylaimuses" "Sandona" 1.0 0 -11221820 true "" "plot mean [Energy] of Sandonas" "Rhogostoma" 1.0 0 -13840069 true "" "plot mean [Energy] of Rhogostomas" PLOT 1043 267 1374 453 Energy (Bac) Ticks Energy 0.0 10.0 0.0 10.0 true true "" "" PENS "Proteobacteria" 1.0 0 -14454117 true "" "plot mean [Energy] of Proteobacteria" "Actinobacteria" 1.0 0 -4079321 true "" "plot mean [Energy] of Actinobacteria" "Acidobacteria" 1.0 0 -3844592 true "" "plot mean [Energy] of Acidobacteria" "Chloroflexi" 1.0 0 -4757638 true "" "plot mean [Energy] of Chloroflexi" "Cyanobacteria" 1.0 0 -14439633 true "" "plot mean [Energy] of Cyanobacteria" PLOT 678 462 1029 663 Mortality-Starved Ticks Dead 0.0 10.0 0.0 10.0 true true "" "" PENS "Nematodes" 1.0 0 -13345367 true "" "plot Starved_Nematodes" "Amoeba" 1.0 0 -6459832 true "" "plot Starved_Amoeba" "TestateAmoeba" 1.0 0 -8630108 true "" "plot Starved_TestateAmoeba" "Flagellates" 1.0 0 -5825686 true "" "plot Starved_Flagellates" "Bacteria" 1.0 0 -14835848 true "" "plot Starved_Bacteria" SWITCH 35 65 166 98 Show_Turtles Show_Turtles 0 1 -1000 SWITCH 30 101 170 134 Show_moisture Show_moisture 1 1 -1000 SWITCH 28 137 171 170 Show_L-Carbon Show_L-Carbon 1 1 -1000 SWITCH 28 172 172 205 Show_T-Carbon Show_T-Carbon 0 1 -1000 MONITOR 472 478 593 523 Total_Carbon (avg) mean [Total_Carbon] of patches 1 1 11 PLOT 12 293 212 443 Total_Carbon NIL NIL -100.0 1000.0 0.0 5.0 false false "" "" PENS "default" 1.0 0 -16777216 true "" "histogram [Total_Carbon] of patches" MONITOR 475 527 606 572 Bacterial Generations ticks / (mean [lifespan] of turtles with [Org_Type = \"Bacteria\"]) 0 1 11 MONITOR 500 596 557 641 NIL Eaten 0 1 11 INPUTBOX 69 504 224 564 BacteriaStart 100.0 1 0 Number PLOT 1045 462 1363 663 Mortality-Age NIL NIL 0.0 10.0 0.0 10.0 true true "" "" PENS "Nematodes" 1.0 0 -13345367 true "" "plot DeadOld_Nematodes" "Amoeba" 1.0 0 -8431303 true "" "plot DeadOld_Amoeba" "TestateAmoeba" 1.0 0 -10141563 true "" "plot DeadOld_TestateAmoeba" "Flagellates" 1.0 0 -7858858 true "" "plot DeadOld_Flagellates" "Bacteria" 1.0 0 -15302303 true "" ";plot DeadOld_Bacteria" @#$#@#$#@ ## WHAT IS IT? (a general understanding of what the model is trying to show or explain) ## HOW IT WORKS (what rules the agents use to create the overall behavior of the model) ## HOW TO USE IT (how to use the model, including a description of each of the items in the Interface tab) ## THINGS TO NOTICE (suggested things for the user to notice while running the model) ## THINGS TO TRY (suggested things for the user to try to do (move sliders, switches, etc.) with the model) ## EXTENDING THE MODEL (suggested things to add or change in the Code tab to make the model more complicated, detailed, accurate, etc.) ## NETLOGO FEATURES (interesting or unusual features of NetLogo that the model uses, particularly in the Code tab; or where workarounds were needed for missing features) ## 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) @#$#@#$#@ default true 0 Polygon -7500403 true true 150 5 40 250 150 205 260 250 airplane true 0 Polygon -7500403 true true 150 0 135 15 120 60 120 105 15 165 15 195 120 180 135 240 105 270 120 285 150 270 180 285 210 270 165 240 180 180 285 195 285 165 180 105 180 60 165 15 arrow true 0 Polygon -7500403 true true 150 0 0 150 105 150 105 293 195 293 195 150 300 150 balloon false 0 Circle -7500403 true true 73 0 152 Polygon -7500403 true true 219 104 205 133 185 165 174 190 165 210 165 225 150 225 147 119 Polygon -7500403 true true 79 103 95 133 115 165 126 190 135 210 135 225 150 225 154 120 Rectangle -6459832 true false 129 241 173 273 Line -16777216 false 135 225 135 240 Line -16777216 false 165 225 165 240 Line -16777216 false 150 225 150 240 box false 0 Polygon -7500403 true true 150 285 285 225 285 75 150 135 Polygon -7500403 true true 150 135 15 75 150 15 285 75 Polygon -7500403 true true 15 75 15 225 150 285 150 135 Line -16777216 false 150 285 150 135 Line 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