From aeecb05b6b304b2364945157b798d5b2144cf9d9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Zo=C3=AB=20Humphries?= Date: Sat, 12 Sep 2015 22:31:49 -0400 Subject: [PATCH] SAR Spread fixes & Virion time requirements - SAR spread is now concurrent, fixing the overload - Viral founder population now has a realistic range - Ticks are set to be ~one minute - Virus requires 16h before it spreads to the next cell (960 ticks) - Altered SAR molecule levels so the viral spread matches the SAR spread - Vasculature can now be infected WARNING: the initiation of systemic infection is not exactly working, as the "in--neighbors" doesn't seem to be working for the phloem... Would love help on this one :) --- .../viralspread/netlogo/ODEViralSpread.nlogo | 1052 +++++++++++++++++ 1 file changed, 1052 insertions(+) create mode 100644 models/viralspread/netlogo/ODEViralSpread.nlogo diff --git a/models/viralspread/netlogo/ODEViralSpread.nlogo b/models/viralspread/netlogo/ODEViralSpread.nlogo new file mode 100644 index 0000000..dbcdd79 --- /dev/null +++ b/models/viralspread/netlogo/ODEViralSpread.nlogo @@ -0,0 +1,1052 @@ +;; ----- DECLARATIONS ----- +;; Add extension enabling use of arrays +extensions [array] + +;; Create "breed" of 'turtle' called cell +breed [cells cell] ;; eventually separate mesophyll? +breed [vasculars vascular] ;; phloem vascular bundles + +;; Create "breed" of 'link' called phloem +directed-link-breed [phloems phloem] +;; Note: I know there shouldn't be an s, but it wanted a different plural :( +undirected-link-breed [plasmodesmata plasmodesma] + +;; Declare global variables +globals +[ + num-infected ;; keep track of number infected + num-viruses ;; keep track of the viral particles + mod-num-viruses ;; keep track of the modified viral particles + lysed-cells ;; keep track of apoptotic cells + infect-per-leaf ;; array of infection counts +] + +;; Declare the cell-specific (turtle breed) variables +cells-own +[ + infected? ;; if true, the cell is infectious + resistant? ;; if true, cell can't be infected + num-plasmodesmata ;; number of connections with other cells + dna-gap ;; track the number of genomes in the nucleus + dna-ccc ;; track the number of pregenomes in the cell + mod-dna-gap ;; + mod-dna-ccc ;; + rna-19s ;; + rna-35s ;; + mod-rna-35s ;; + protein-one ;; + protein-two ;; + protein-three ;; + protein-four ;; + protein-four-sub ;; + protein-five ;; + protein-six ;; track functional P6 + int-virions ;; + viral-count ;; keeps track of the virions produced by the cell + mod-int-virions ;; + mod-viral-count ;; + sar-level ;; amount of "salicylic acid" present in the cell + time-infected ;; the time since the cell was infected +] + + + + +;; ----- SETUP ----- + +;; This marshalls the setup processes - activated when the user clicks "setup" +to setup + + ;; Reset from previous runs + clear-all ;; remove anything from previous runs + reset-ticks ;; reset timer + if file-exists? "netlogo_sim.csv" [file-delete "netlogo_sim.csv"] ;; delete file + + ;random-seed 1;; ensures consistent setup (when other parameters constant) + setup-stem ;; make a stem structure to connect the leaves + setup-cells ;; set up the cells + setup-leaf ;; set up the connections between cells + + set infect-per-leaf array:from-list n-values 4 [0] ;; initialize 1xn array of 0s + ask n-of initial-infection-sites cells ;; infect this number of cells + [ + become-infected + set dna-gap founder-population-viruses ;; start with x genomes per infected cell + ] + ask links [ set color white ] ;; make the symplastic connections white + ask phloems + [ + set color green ;; make the vascular bundles green and thicker + set thickness 0.3 + ] +end + + +to setup-stem + set-default-shape vasculars "plant" ;; uses stem-looking shape for vasculature + ;; Create and position vascular cells + create-vasculars 1 [ setxy 0 -16 ] + create-vasculars 1 + [ + setxy 0 -6 + create-phloem-from vascular 0 ;; directed stem connection + ] + create-vasculars 1 + [ + setxy 0 6 + create-phloem-from vascular 1 ;; directed stem connection + ] + create-vasculars 1 + [ + setxy 0 16 + create-phloem-from vascular 2 ;; directed stem connection + ] + ask vasculars ;; make the vasculature stand out from the leaf cells + [ + set color green + set size 2.5 + ] +end + + +to setup-cells + set-default-shape cells "circle" ;; uses circle shape for displayed cells + create-cells num-cells + [ + let xguess random-pxcor + while [abs xguess < 0.1 * max-pxcor or abs xguess > 0.95 * max-pxcor] + [set xguess random-pxcor] + + let yguess random-pycor + while [abs yguess < 0.1 * max-pycor or abs yguess > 0.95 * max-pycor] + [set yguess random-pycor] + + setxy xguess yguess ;; no nodes too close to edges + become-susceptible + ask cells [ set size 0.5 ] ;; makes the circles smaller for larger scale + ] +end + + +to setup-leaf + ask cells + [ + ;; using random-possion to give a more realistic distribution of links per cell + while [ count my-links < random-poisson avg-num-plasmodesmata ] + [ + let choice (min-one-of (other cells with [not link-neighbor? myself]) + [distance myself]) + if choice != nobody [ create-plasmodesma-with choice ] + ] + ] + ;; to make the network look nicer + repeat 10 [ layout-spring turtles links 0.3 (world-width / (sqrt num-cells)) 1 ] + ;; connect leaves to the vasculature + ask vascular 0 + [ + let choice ( one-of (cells with [pxcor < 0 and pycor < 0]) ) + if choice != nobody [ create-phloem-from choice ] + ] + ask vascular 1 + [ + let choice ( one-of (cells with [pxcor > 0 and pycor < 0]) ) + if choice != nobody [ create-phloem-from choice ] + ] + ask vascular 2 + [ + let choice ( one-of (cells with [pxcor < 0 and pycor > 0]) ) + if choice != nobody [ create-phloem-from choice ] + ] + ask vascular 3 + [ + let choice ( one-of (cells with [pxcor > 0 and pycor > 0]) ) + if choice != nobody [ create-phloem-from choice ] + ] +end + + + + +to-report random-radius [rmin rmax] + ;; picks a radius at random such that points will be uniform in a circle + ;; pdf is r/const ; use inverse transform method + let u random-float 1 + let r sqrt(u * (rmax ^ 2 - rmin ^ 2) + rmin ^ 2 ) + report r +end + + + + + +;; ----- MAIN ----- + +;; This is the main process - what is activated when the user clicks "go" +to go + ;; if the user specified a duration, stop after that + if specified-duration + [ + if ticks > num-ticks [ stop ] + ] + ;; otherwise, check if all cells are infected + if all? cells [ infected? ] + [ + ;; if they are, run 40 more times (make the graph look nice) + let i 0 + while [i <= 40] + [ + spread-virus + set i i + 1 + tick + ] + stop ;; stop model completely + ] + + ;; otherwise, continue to spread the virus + assemble-virus + spread-virus + + ;; implement cell defences + spread-sar + do-apoptosis-checks + + ;; print data about the infected cells + record-data + + ;; one tick is approximately equivalent to one minute + tick +end + + + + +;; ----- DATA OUTPUT ----- + +;; Create a csv file containing the ID number of infected cells +to record-data + file-open "netlogo_sim.csv" + let leaf-infect-list array:to-list infect-per-leaf + foreach leaf-infect-list + [ + file-write ? ;; print the number + file-type "," ;; print a comma + ] + file-type "\n" ;; newline + file-close +end + + + + + +;; ----- CELL PROCEDURES ----- + +;; When cells are infected by natural CaMV +to become-infected + set infected? true + set resistant? false + set color red + ;; determine number of viruses entering the susceptible cell + ;let new-viruses ( sum [viral-count] of link-neighbors ) + ;set viral-count 0 ; new-viruses + set dna-gap dna-gap + 1 + set num-viruses num-viruses + 1 +end + +;; When cells are infected by modified CaMV +to mod-become-infected + set infected? true + set resistant? false + set color orange + set mod-dna-gap mod-dna-gap + 1 + set mod-num-viruses mod-num-viruses + 1 +end + +;; Generated cells are vulnerable to the virus +to become-susceptible + set infected? false + set resistant? false + set color green + set dna-gap 0 ;; track the number of genomes in the nucleus + set dna-ccc 0 + set mod-dna-gap 0 + set mod-dna-ccc 0 + set rna-19s 0 + set rna-35s 0 + set mod-rna-35s 0 + set protein-one 0 + set protein-two 0 + set protein-three 0 + set protein-four 0 + set protein-four-sub 0 + set protein-five 0 + set protein-six 0 + set int-virions 0 + set viral-count 0 + set mod-int-virions 0 + set mod-viral-count 0 + set time-infected 0 +end + +to become-resistant + set resistant? true + set color blue +end + + + + +;; ---- SAR Molecule Spread & Apoptosis ---- + +;; Increase levels of signalling molecule based on neighbours' levels +to spread-sar + ;; Initial generation of sar + ;; small initial amount based on infection state of neighbouring cells + ask-concurrent cells + [ + let neighboured false ;; remember if a neighbour is infected + ask link-neighbors + [ + if (infected? and time-infected >= 1000) [ set neighboured true ] + ] + ;; if a neighbour has been infected for 500 minutes, increase sar signalling molecule + if (neighboured) [ set sar-level sar-level + 1 ] + ] + + ;; Spread of existing sar + ;; assume the resistant cells are better able to spread the sar molecule + ask-concurrent cells with [resistant?] + [ + let shared-sar sar-level / 1000 ;; fifth of the molecules will be shared + ask link-neighbors + [ + set sar-level sar-level + shared-sar + if sar-level >= resistance-threshold [ become-resistant ] + ] + ;; portion of the shared sar molecules are retained in the cell + set sar-level sar-level + shared-sar / (avg-num-plasmodesmata + 1) + ] + ;; assume the susceptible cells can produce an okay amount of sar molecule + ask-concurrent cells with [not infected? and not resistant?] + [ + let shared-sar sar-level / 2500 ;; tenth of the molecules will be shared + ask link-neighbors + [ + set sar-level sar-level + shared-sar + if sar-level >= resistance-threshold [ become-resistant ] + ] + set sar-level sar-level + shared-sar / avg-num-plasmodesmata + ] + ;; assume the infected cells are unable to produce sar signal molecules +end + + +;; Determine whether the cell can destroy itself to help prevent viral spread +to do-apoptosis-checks + ;; if the cell is infected and can still lyse, check + ask cells with [infected?] + [ + if (sar-level >= lysis-threshold) + [ + set color violet + set lysed-cells lysed-cells + 1 + die + set num-viruses num-viruses - viral-count + set mod-num-viruses mod-num-viruses - mod-viral-count + ] + ] +end + + + + +;; ----- VIRUS PROCEDURES ----- + +;; Procedure governing spread to neighbouring cells +to spread-virus + ask cells with [infected?] + [ + ;; allow the spread to occur only once the cells have been infected for 16 hours + if (time-infected >= 960) + [ + ask link-neighbors with [not resistant? and not infected?] + [ + become-infected ;; If chance has it, infect the cell + set num-infected num-infected + 1 ;; increase the count for infected cells + ] + ] + ;; determine whether the cells are connected to the vasculature + if (any? my-in-links) + [ + ;; infect the other leaves + ask vasculars [ set color red ] + ask phloems [ set color red ] + ask phloem-neighbors [ become-infected ] + ] + ] +end + + +;; Assembly of the virus before it can spread +to assemble-virus +;; Genome parameters + let max-genomes-in-nucleus 100 + let intracellular-reinfection-rate 0.01 + let gapped-dna-repair-rate 0.1 + let dna-modification-rate 0.01 + let dna-degradation-rate 0.00001 + + ;; RNA parameters + let transcription-rate-19s 0.05 + let degradation-rate-19s 0.001155 + let transcription-rate-35s 0.0653 + let degradation-rate-35s 0.001155 + let packaging-rate 0.1 + let frac-unspliced 0.3 + + ;; Protein parameters + let translation-rate 0.1 + let degradation-rate 0.0001 + let p4-splicing-rate 1 + + ;; Virion parameters + let anchoring-rate 1 + let virion-degradation-rate 0.01 + let virion-exit-rate 0.1 + + ;; Time step + let delta-t 0.001 + + ask cells with [infected?] + [ + set dna-gap dna-gap + delta-t * ( intracellular-reinfection-rate * viral-count * ( max-genomes-in-nucleus - dna-gap - mod-dna-gap ) - gapped-dna-repair-rate * dna-gap - dna-modification-rate * dna-gap ) + set dna-ccc dna-ccc + delta-t * ( gapped-dna-repair-rate * dna-gap - dna-degradation-rate * dna-ccc - dna-modification-rate * dna-ccc ) + set mod-dna-gap mod-dna-gap + delta-t * ( intracellular-reinfection-rate * mod-viral-count * ( max-genomes-in-nucleus - dna-gap - mod-dna-gap ) - gapped-dna-repair-rate * mod-dna-gap + dna-modification-rate * dna-gap ) + set mod-dna-ccc mod-dna-ccc + delta-t * ( gapped-dna-repair-rate * mod-dna-gap - dna-degradation-rate * mod-dna-ccc + dna-modification-rate * dna-ccc ) + set rna-19s rna-19s + delta-t * ( transcription-rate-19s * dna-ccc - degradation-rate-19s * rna-19s ) + set rna-35s rna-35s + delta-t * ( transcription-rate-35s * dna-ccc - degradation-rate-35s * rna-35s - packaging-rate * protein-four-sub * protein-five * rna-35s * frac-unspliced ) + set mod-rna-35s mod-rna-35s + delta-t * ( transcription-rate-35s * mod-dna-ccc - degradation-rate-35s * mod-rna-35s - packaging-rate * protein-four-sub * protein-five * mod-rna-35s * frac-unspliced ) + set protein-one protein-one + delta-t * ( translation-rate * ( rna-35s + mod-rna-35s ) * frac-unspliced - degradation-rate * protein-one ) + set protein-two protein-two + delta-t * ( translation-rate * ( rna-35s + mod-rna-35s ) * frac-unspliced - degradation-rate * protein-two ) + set protein-three protein-three + delta-t * ( translation-rate * ( rna-35s + mod-rna-35s ) - degradation-rate * protein-three - anchoring-rate * protein-three * ( int-virions + mod-int-virions ) ) + set protein-four protein-four + delta-t * ( translation-rate * ( rna-35s + mod-rna-35s ) - degradation-rate * protein-four - p4-splicing-rate * protein-four ) + set protein-four-sub protein-four-sub + delta-t * ( p4-splicing-rate * protein-four - degradation-rate * protein-four-sub - packaging-rate * protein-four-sub * protein-five * ( rna-35s + mod-rna-35s ) * frac-unspliced ) + set protein-five protein-five + delta-t * ( translation-rate * ( rna-35s + mod-rna-35s ) - degradation-rate * protein-five - packaging-rate * protein-four-sub * protein-five * ( rna-35s + mod-rna-35s ) * frac-unspliced ) + set protein-six protein-six + delta-t * ( translation-rate * rna-19s - degradation-rate * protein-six ) + set int-virions int-virions + delta-t * ( packaging-rate * protein-four-sub * protein-five * rna-35s * frac-unspliced - anchoring-rate * protein-three * int-virions ) + set viral-count viral-count + delta-t * ( anchoring-rate * protein-three * int-virions - intracellular-reinfection-rate * viral-count - virion-degradation-rate * viral-count - virion-exit-rate * viral-count ) + set mod-int-virions mod-int-virions + delta-t * ( packaging-rate * protein-four-sub * protein-five * mod-rna-35s * frac-unspliced - anchoring-rate * protein-three * mod-int-virions ) + set mod-viral-count mod-viral-count + delta-t * ( anchoring-rate * protein-three * mod-int-virions - intracellular-reinfection-rate * mod-viral-count - virion-degradation-rate * mod-viral-count - virion-exit-rate * mod-viral-count ) + set time-infected time-infected + 1 + + set num-viruses num-viruses + viral-count + set mod-num-viruses mod-num-viruses + mod-viral-count + ] +end +@#$#@#$#@ +GRAPHICS-WINDOW +238 +10 +672 +465 +16 +16 +12.85 +1 +10 +1 +1 +1 +0 +0 +0 +1 +-16 +16 +-16 +16 +0 +0 +1 +ticks +30.0 + +BUTTON +116 +288 +179 +321 +go +go +T +1 +T +OBSERVER +NIL +NIL +NIL +NIL +1 + +SLIDER +22 +102 +196 +135 +initial-infection-sites +initial-infection-sites +1 +4 +4 +1 +1 +NIL +HORIZONTAL + +SLIDER +20 +10 +192 +43 +num-cells +num-cells +1 +1000 +599 +1 +1 +NIL +HORIZONTAL + +SLIDER +20 +49 +208 +82 +avg-num-plasmodesmata +avg-num-plasmodesmata +1 +10 +6 +1 +1 +NIL +HORIZONTAL + +PLOT +231 +475 +454 +672 +#infected over time +ticks +#infected cells +0.0 +50.0 +0.0 +50.0 +true +false +"set-plot-x-range 0 num-ticks\nset-plot-y-range 0 num-cells" "" +PENS +"infected" 1.0 0 -13791810 true "" "plot num-infected" + +BUTTON +38 +289 +101 +322 +setup +setup +NIL +1 +T +OBSERVER +NIL +NIL +NIL +NIL +1 + +SLIDER +21 +227 +193 +260 +num-ticks +num-ticks +0 +500 +167 +1 +1 +NIL +HORIZONTAL + +SWITCH +22 +190 +177 +223 +specified-duration +specified-duration +1 +1 +-1000 + +PLOT +466 +485 +666 +635 +Number of Viruses +ticks +#viruses +0.0 +10.0 +1.0 +1000.0 +true +false +"set-plot-x-range 0 num-ticks\nset-plot-y-range 0 num-cells" "" +PENS +"default" 1.0 0 -16777216 true "" "plot (num-viruses + mod-num-viruses)" + +SLIDER +22 +141 +268 +174 +founder-population-viruses +founder-population-viruses +2 +13 +8 +1 +1 +genomes +HORIZONTAL + +SLIDER +28 +375 +200 +408 +lysis-threshold +lysis-threshold +1 +10000 +10000 +1 +1 +NIL +HORIZONTAL + +PLOT +19 +490 +219 +640 +Lysed Cells +ticks +#cells +0.0 +10.0 +0.0 +10.0 +true +false +"set-plot-x-range 0 num-ticks\nset-plot-y-range 0 10" "" +PENS +"default" 1.0 0 -16777216 true "" "plot lysed-cells" + +SLIDER +27 +339 +199 +372 +resistance-threshold +resistance-threshold +100 +1000 +1000 +5 +1 +NIL +HORIZONTAL + +@#$#@#$#@ +## WHAT IS IT? + +This is a model tracking viral spread in a plant-structure made of leaf cells and vascular cells. The spatial locations of the cells are divided into "leaves", and individual cells are connected by plasmodesmata. + + +## HOW IT WORKS + +The model begins by creating all of the cells - it places them in space (in 4 leaves separated by the coodrinate axes) and iteratively goes through the cells, giving each a random number of connections. + +All the cells start as susceptible, except for some small initial infection. Then the virus spreads along the plasmodesmata connections as time progresses. + +In this model there's also a chance of cells becoming resistant. This is triggered by either proximity to infected cells, or by spreading among + + +## HOW TO USE IT + +Set the sliders as you see fit and click setup. Hit go to see what happens! + + +## THINGS TO NOTICE + +How does the viral infection curve change as # of connections is increased and viral spread chance is decreased? + + +## THINGS TO TRY + +Move the sliders! And note the variations in the random setup, especially as it concerns connections between different leaves. + + +## EXTENDING THE MODEL + +Giving appropriate parameters for the viral spread chance. + + +## 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 + +UWaterloo's 2015 iGEM team +@#$#@#$#@ +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 + +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 -16777216 false 150 135 15 75 +Line -16777216 false 150 135 285 75 + +bug +true +0 +Circle -7500403 true true 96 182 108 +Circle -7500403 true true 110 127 80 +Circle -7500403 true true 110 75 80 +Line -7500403 true 150 100 80 30 +Line -7500403 true 150 100 220 30 + +butterfly +true +0 +Polygon -7500403 true true 150 165 209 199 225 225 225 255 195 270 165 255 150 240 +Polygon -7500403 true true 150 165 89 198 75 225 75 255 105 270 135 255 150 240 +Polygon -7500403 true true 139 148 100 105 55 90 25 90 10 105 10 135 25 180 40 195 85 194 139 163 +Polygon -7500403 true true 162 150 200 105 245 90 275 90 290 105 290 135 275 180 260 195 215 195 162 165 +Polygon -16777216 true false 150 255 135 225 120 150 135 120 150 105 165 120 180 150 165 225 +Circle -16777216 true false 135 90 30 +Line -16777216 false 150 105 195 60 +Line 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