Merge pull request #223 from AlgebraicJulia/cm/canon-oncology

Cm/canon oncology

examples/oncology/tumor_proliferation_invasion.jl

@@ -0,0 +1,88 @@
+# Load Dependencies
+using Catlab
+using Catlab.Graphics
+using CombinatorialSpaces
+using Decapodes
+using DiagrammaticEquations, DiagrammaticEquations.Deca
+using Distributions
+using MLStyle
+using OrdinaryDiffEq
+using LinearAlgebra
+using ComponentArrays
+using CairoMakie
+using GeometryBasics: Point2, Point3
+Point2D = Point2{Float64}
+Point3D = Point3{Float64}
+
+# Load in our Decapodes models
+using Decapodes.Canon.Oncology
+
+# Examine our models
+# Note that the implementation is entirely specified by its documentation
+@doc invasion
+
+@doc logistic
+
+@doc gompertz
+
+# Load in a mesh, initial conditions, and a plotting function
+function show_heatmap(Cdata)
+  heatmap(reshape(Cdata, (floor(Int64, sqrt(length(Cdata))), floor(Int64, sqrt(length(Cdata))))))
+end
+
+s = triangulated_grid(50,50,0.2,0.2,Point2D);
+sd = EmbeddedDeltaDualComplex2D{Bool, Float64, Point2D}(s);
+subdivide_duals!(sd, Circumcenter());
+
+constants_and_parameters = (
+  invasion_Dif = 0.005,
+  invasion_Kd = 0.5,
+  Cmax = 10)
+
+# "The model ... considers an equivalent radially symmetric tumour"
+# - Murray J.D., Glioblastoma brain tumours
+c_dist  = MvNormal([25, 25], 2)
+C = 100 * [pdf(c_dist, [p[1], p[2]]) for p in sd[:point]]
+
+u₀ = ComponentArray(C=C)
+
+# Compose our Proliferation-Invasion models
+proliferation_invasion_composition_diagram = @relation () begin
+  proliferation(C, fC, Cmax)
+  invasion(C, fC, Cmax)
+end
+
+logistic_proliferation_invasion_cospan = oapply(proliferation_invasion_composition_diagram,
+  [Open(logistic, [:C, :fC, :Cmax]),
+   Open(invasion, [:C, :fC, :Cmax])])
+
+logistic_proliferation_invasion = apex(logistic_proliferation_invasion_cospan)
+
+gompertz_proliferation_invasion_cospan = oapply(proliferation_invasion_composition_diagram,
+  [Open(gompertz, [:C, :fC, :Cmax]),
+   Open(invasion, [:C, :fC, :Cmax])])
+
+gompertz_proliferation_invasion = apex(gompertz_proliferation_invasion_cospan)
+
+# Generate the logistic simulation
+logistic_sim = evalsim(logistic_proliferation_invasion)
+
+lₘ = logistic_sim(sd, default_dec_generate, DiagonalHodge())
+
+# Execute the logistic simulation
+tₑ = 15.0
+
+prob = ODEProblem(lₘ, u₀, (0, tₑ), constants_and_parameters)
+logistic_soln = solve(prob, Tsit5())
+
+show_heatmap(logistic_soln(tₑ).C)
+
+# Generate the Gompertz simulation
+gompertz_sim = evalsim(gompertz_proliferation_invasion)
+gₘ = gompertz_sim(sd, default_dec_generate, DiagonalHodge())
+
+# Execute the Gompertz simulation
+prob = ODEProblem(gₘ, u₀, (0, tₑ), constants_and_parameters)
+gompertz_soln = solve(prob, Tsit5())
+
+show_heatmap(gompertz_soln(tₑ).C)

src/canon/Canon.jl

@@ -45,5 +45,6 @@ include("Physics.jl")
 include("Chemistry.jl")
 include("Biology.jl")
 include("Environment.jl")
+include("Oncology.jl")
 
 end

src/canon/Oncology.jl

@@ -0,0 +1,58 @@
+module Oncology 
+
+using DiagrammaticEquations
+using DiagrammaticEquations.Deca
+
+# for testing
+using Decapodes
+using ComponentArrays
+using CombinatorialSpaces
+
+using ..Canon 
+using Markdown
+
+@docapode("TumorInvasion"
+  ,"https://en.wikipedia.org/wiki/Cancer_cell#Causes"
+  ,"Eq. 35 from Yi et al.
+  A Review of Mathematical Models for Tumor Dynamics and Treatment Resistance
+  Evolution of Solid Tumors"
+  ,invasion
+  ,begin
+    (C,fC)::Form0
+    (Dif, Kd, Cmax)::Constant
+
+    ∂ₜ(C) == Dif * Δ(C) + fC - Kd * C
+end)
+
+@docapode("Logistic"
+  ,"https://en.wikipedia.org/wiki/Logistic_function"
+  ,"Eq. 5 from Yi et al.
+  A Review of Mathematical Models for Tumor Dynamics and Treatment Resistance
+  Evolution of Solid Tumors"
+  ,logistic
+  ,begin
+    (C,fC)::Form0
+    Cmax::Constant
+
+    fC == C * (1 - C / Cmax)
+  end)
+
+@docapode("Gompertz"
+  ,"https://en.wikipedia.org/wiki/Gompertz_function"
+  ,"Eq. 6 from Yi et al.
+  A Review of Mathematical Models for Tumor Dynamics and Treatment Resistance
+  Evolution of Solid Tumors"
+  ,gompertz
+  ,begin
+    (C,fC)::Form0
+    Cmax::Constant
+
+    fC == C * ln(Cmax / C)
+end)
+
+## Another way to account for angiogenesis effect on tumor
+## growth is by assuming the carrying capacity of the tumor is
+## determined by the effective tumor vascular support that is
+## in turn affected by the tumor volume (Eqs. 15 and 16). -Review of...
+
+end

src/canon/Physics.jl

@@ -101,7 +101,7 @@ end)
   end
 )
 
-@docapode("Schoedinger"
+@docapode("Schroedinger"
   ,"https://en.wikipedia.org/wiki/Schrodinger_equation"
   ,"The evolution of the wave function over time."
   ,schroedinger

src/operators.jl

@@ -136,6 +136,7 @@ function default_dec_generate(sd, my_symbol, hodge=GeometricHodge())
 
     :plus => (+)
     :(-) || :neg => x -> -1 .* x
+    :ln => (x -> log.(x))
 
     _ => error("Unmatched operator $my_symbol")
   end

src/simulation.jl

@@ -333,17 +333,20 @@ end =#
           end
         end
 
+        # TODO: Clean this in another PR (with a @match maybe).
         if(operator == :(*))
           operator = promote_arithmetic_map[operator]
         end
         if(operator == :(-))
           operator = promote_arithmetic_map[operator]
         end
+        if(operator == :(/))
+          operator = promote_arithmetic_map[operator]
+        end
         if(operator == :(^))
           operator = promote_arithmetic_map[operator]
         end
 
-
         visited_2[op] = true
         visited_Var[r] = true
         c = BinaryCall(operator, equality, a1name, a2name, rname)