Bio 14 Lab 2 model 1
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;; this is the most up-to-date version globals [ regions ; a list of regions definitions, where each region is a list of its min pxcor and max pxcor ] breed [ blue-strains blue-strain ] breed [ red-strains red-strain ] ;;red-strains-own [red-resistance-cost] ;;blue-strains-own [blue-resistance-cost] ; removing cost of resistance as a paramter for now turtles-own [ resistant? energy mutation-rate cost-of-repair benefit? benefit-gain] ;; some variables that apply to both strains, ;resistance-cost removed patches-own [ region ; the region that the patch is in, patches outside all regions have region = 0 antibiotic ; ] to setup ; this procedure sets up the "world" into 2 different regions. It contains a few subprocedures described next clear-all setup-regions 2 color-regions ; Finally, distribute the turtles in the different regions setup-turtles if (resistance + lethal + metabolic-benefit) > 100.00 [user-message ("Mutation rates should not sum to more than 100%")] ; this message appears to warn users about mutation rate settings reset-ticks end to color-regions ;this subprocedure colors the regions ; The patches with region = 0 act as dividers and are ; not part of any region. All other patches get colored ; according to the region they're in. ask patches with [ region != 0 ] [ set pcolor 1 ;; what color is this - started at times 10 set plabel-color pcolor + 0 ;set plabel region check-antibiotic ] end to setup-turtles ; this subprocedure creates the strains foreach n-values length regions [ [?1] -> ?1 + 1 ] [ [?1] -> let region-patches patches with [ region = ?1 ] create-blue-strains initial-blue-strain-population [ move-to one-of region-patches if (count other turtles-here > 1) [move-to one-of region-patches] set shape "circle" set size 0.15 set color blue set resistant? false ;; they all start not resistant ;;if ( show-resistance? ) [ show-resistance ] set energy random blue-life-span ;;they all start out with some amt of energy - a random value between 0 and blue-life-span set mutation-rate blue-mutation-rate set benefit? false ; they all start without beneficial mutations ] create-red-strains initial-red-strain-population [ move-to one-of region-patches set shape "circle" set size 0.15 set color red set resistant? false ;; they all start not resistant ;;if ( show-resistance? ) [ show-resistance ] set energy random red-life-span ;;they all start out with some amt of energy set mutation-rate red-mutation-rate set benefit? false ] ] end to go every 0.1 [ ; can be manipulated to make things happen faster ask turtles [ ; below are the things turtles do every half tick move ; see details under this procedure metabolize ; see details under this procedure mutate ; see details under this procedure if ( count other turtles-here > 20) [ die ] ;; this is where carrying capacity is specified at the moment if ( [antibiotic] of patch-here = true and not resistant? ) [ die ] ;; womp womp...notice antibiotic is 100% lethal if (energy <= 0) [die] ;; so tired... reproduce ;; see details under this procedure ;;if ( show-resistance? ) [ show-resistance ] ;if ( show-benefit?) [show-benefit] ;; obviously ;set-resistance-values ;] ; ifelse (resistant?) ; [ ; if cost-of-resistance = "high" [set resistance-cost 5] ; if cost-of-resistance = "low" [set resistance-cost 2] ; if cost-of-resistance = "none" [set resistance-cost 0] ; ] ; [set resistance-cost 0] show-resistance ] check-antibiotic ; this checks the status of the antibiotic so that it can be changed mid run check-mutation-rates ; this checks to see if the mutation rate has been changed mid-run if ( count turtles = 0 ) [ stop ] ; the simulation stops if all the turtles die update-plots display ;if vid:recorder-status = "recording" [ vid:record-interface ] tick ] end to move ; turtle procedure ; First, save the region that the turtle is currently in: let current-region region ; Then, after saving the region, we can move the turtle: right random 30 left random 30 forward 0.25 ; Finally, after moving, make sure the turtle ; stays in the region it was in before: keep-in-region current-region end to check-mutation-rates ask red-strains [if red-mutation-rate != mutation-rate [user-message ("You cannot change the mutation rate in the middle of a run. Restart the model!")]] ask blue-strains [if blue-mutation-rate != mutation-rate [user-message ("You cannot change the mutation rate in the middle of a run. Restart the model!")]] end to show-resistance ;; turtle procedure that colors bacteria to show resistance ifelse resistant? [ifelse (breed = red-strains) [ set color red + 3] [set color blue + 3]] ; if resistant set to lighter colors [ifelse (breed = red-strains) [ set color red ] [set color blue]] ; otherwise keep original colors end to show-benefit ;; turtle procedure that colors bacteria to show resistance ifelse benefit? [ifelse (breed = red-strains) [ set color yellow] [set color green]] ; if resistant set to lighter colors [ifelse (breed = red-strains) [ set color red ] [set color blue]] ; otherwise keep original colors end to mutate ;; turtle procedure if random-float 100 < mutation-rate [ ;; random float chooses a number between 0-100. If that number is less than mutation-rate (set by a slider on the interface) then... if random-float 100 < resistance ;; roll the resistant dice (this used to be ifelse for some reason) [ ;; this is the if part if ( not resistant? ) [ ;; toggle the resistance set resistant? true ] ;; YOUR POISON IS FUTILE!! ;[set resistant? false] ;[ if random-float 100 < 20 [set resistant? false ] ;] ;; back mutations set to 20% ] ;this is the else part if random-float 100 < lethal [ ;; roll the lethal dice...switch the greater than to less than die ;; end of the line :( ] ifelse benefit? [set benefit-gain random 2] [set benefit-gain 0] ; make this a random value - this specifies the value of benefit from beneficial mutation if random-float 100 > ( 100 - metabolic-benefit) [if ( not benefit?) [set benefit? true] ] ] end to metabolize ;; turtle procedure that sucks your life away let total-cost ( cost-of-repair + 1) ;; metabolic cost is sum of all costs, + resistance-cost removed set energy (energy - total-cost + benefit-gain) end to reproduce ;; turtle procedure ;; i guess we'll make all the bacteria reproduce all the time. set energy energy / 2 ;; takes money to make money - but what is the point of this? sets effective lifespan to half so changed it to same energy as parents hatch 1 [ ;; they're cloning, so inherits any mutation including resistance (or not) and they are the same strain as parent rt random 360 let current-region region fd random-float .5 ;; move a bit keep-in-region current-region ifelse breed = red-strains [set energy red-life-span] [set energy blue-life-span] ;; so lively ] end to check-antibiotic ifelse antibiotic? [ ask patches with [pxcor >= 0] [set pcolor grey set antibiotic true] ask patches with [pxcor < 0] [set antibiotic false] ] [ ask patches with [pxcor >= 0] [set pcolor 22 set antibiotic false] ask patches with [pxcor < 0] [set antibiotic false] ] end ;;to plate-on-agar ;; let blue-plated-cells round concentration / 100 * count blue-strains ;;set blue-plated-cells count blue-strains - blue-plated-cells ;; ask n-of blue-plated-cells blue-strains [ ;; die] ;; let red-plated-cells round concentration / 100 * count red-strains ;; set red-plated-cells count red-strains - red-plated-cells ;; ask n-of red-plated-cells red-strains [ ;; die] ;;end ;;to plate-on-antibiotic ;; let blue-plated-cells round concentration / 100 * count blue-strains ;; set blue-plated-cells count blue-strains - blue-plated-cells ;; ask n-of blue-plated-cells blue-strains [ ;; die ;; ] ;; ask blue-strains [ ;; if not resistant? [die]] ;; let red-plated-cells round concentration / 100 * count red-strains ;; set red-plated-cells count red-strains - red-plated-cells ;; ask n-of red-plated-cells red-strains [ ;; die] ;; ask red-strains [ ;; if not resistant? [die]] ;;end to setup-regions [ n ] ; First, draw some dividers at the intervals reported by `region-divisions`: foreach region-divisions n draw-region-division ; Store our region definitions globally for faster access: set regions region-definitions n ; Set the `region` variable for all patches included in regions: (foreach regions (n-values n [ [?1] -> ?1 + 1 ]) [ [?1 ?2] -> ; We're looping through region definitions (?1) and region numbers (?2) ask patches with [ pxcor >= first ?1 and pxcor <= last ?1 ] [ set region ?2 ] ]) end to-report region-definitions [ n ] ; The region definitions are built from the region divisions: let divisions region-divisions n ; Each region definition lists the min-pxcor and max-pxcor of the region. ; To get those, we use `map` on two "shifted" copies of the division list, ; which allow us to scan through all pairs of dividers ; and built our list of definitions from those pairs: report (map [ [?1 ?2] -> list (?1 + 1) (?2 - 1) ] (but-last divisions) (but-first divisions)) end to-report region-divisions [ n ] ; This procedure reports a list of pxcor that should be outside every region. ; Patches with these pxcor will act as "dividers" between regions. report n-values (n + 1) [ [?1] -> [ pxcor ] of patch (min-pxcor + (?1 * ((max-pxcor - min-pxcor) / n))) 0 ] end to draw-region-division [ x ] ; This procedure makes the division patches grey ; and draw a vertical line in the middle. This is ; arbitrary and could be modified to your liking. ask patches with [ pxcor = x ] [ set pcolor grey + 1.5 ] create-turtles 1 [ ; use a temporary turtle to draw a line in the middle of our division setxy x max-pycor + 0.5 set heading 0 set color grey - 3 pen-down forward world-height set xcor xcor + 1 / patch-size right 180 set color grey + 3 forward world-height die ; our turtle has done its job and is no longer needed ] end to keep-in-region [ which-region ] ; turtle procedure ; This is the procedure that make sure that turtles don't leave the region they're ; supposed to be in. It is your responsability to call this whenever a turtle moves. if region != which-region [ ; Get our region boundaries from the global region list: let region-min-pxcor first item (which-region - 1) regions let region-max-pxcor last item (which-region - 1) regions ; The total width is (min - max) + 1 because `pxcor`s are in the middle of patches: let region-width (region-max-pxcor - region-min-pxcor) + 1 ifelse xcor < region-min-pxcor [ ; if we crossed to the left, set xcor xcor + region-width ; jump to the right boundary ] [ if xcor > region-max-pxcor [ ; if we crossed to the right, set xcor xcor - region-width ; jump to the left boundary ] ] ] end ; Public Domain: ; To the extent possible under law, Uri Wilensky has waived all ; copyright and related or neighboring rights to this model.
There is only one version of this model, created almost 3 years ago by James Johnson.
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Bio 14 Lab 2 model 1.png | preview | Preview for 'Bio 14 Lab 2 model 1' | almost 3 years ago, by James Johnson | Download |
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