mtk cases added

cases/mtk/mm.jl

@@ -0,0 +1,66 @@
+#= 
+    This code was generated by heta-compiler 
+=#
+function get_MTKmodel()
+
+  ### Define independent and dependent variables
+
+  @variables t
+  __ruleVariables__ = @variables S(t) P(t) r1(t)
+  __dynamicVariables__ = @variables _S_(t) _P_(t)
+
+  ### Define potential algebraic variables
+
+  ### Define parameters (constants and statics)
+  __constParameters__ = @parameters Vmax Km
+  __staticParameters__ = @parameters default_comp
+
+  ### Define an operator for the differentiation w.r.t. time
+  __D__ = Differential(t)
+
+  ### ODE Equations ###
+  __eqs__ = [
+    # extended rules
+    S ~ _S_/ default_comp,
+    P ~ _P_/ default_comp,
+    r1 ~ Vmax * S / (Km + S) * default_comp,
+
+    # ODEs
+    __D__(_S_) ~ -r1, # dS/dt
+    __D__(_P_) ~ r1, # dP/dt
+  ]
+
+  ### Continious events ###
+
+  ### Discrete events ###
+
+  ### Initialization ###
+
+  __constValues__ = [
+    Vmax => 0.1,
+    Km => 2.5,
+  ]
+
+  __init__ = [
+    default_comp => 1e+0,
+    S => 1e+1,
+    P => 0e+0,
+    r1 => Vmax * S / (Km + S) * default_comp,
+  ]
+
+  __amountsInit__ = [
+      _S_ => S * default_comp,
+      _P_ => P * default_comp,
+  ]
+
+  ### ODESystem definition ###
+  __sys__ = ODESystem(__eqs__, t, [__dynamicVariables__; __ruleVariables__], [__constParameters__; __staticParameters__],
+    name = :mm,
+    discrete_events = [],
+    defaults = [__constValues__; __init__; __amountsInit__]
+  )
+
+  return structural_simplify(__sys__), __amountsInit__, __constValues__
+end
+
+__model__ = get_MTKmodel()

cases/mtk/nameless.jl

@@ -0,0 +1,109 @@
+#= 
+    This code was generated by heta-compiler 
+=#
+function get_MTKmodel()
+  ### Define independent and dependent variables
+
+  @variables t
+  __ruleVariables__ = @variables comp4(t) s1(t) s2(t) s3(t) s4(t) s5(t) r1(t) r2(t) r3(t) p1(t) s6(t) s7(t) s8(t) s9(t) s10(t) r4(t) r5(t)
+  __dynamicVariables__ = @variables comp3(t) _s1_(t) _s2_(t) _s6_(t) _s7_(t) _s8_(t)
+
+  ### Define potential algebraic variables
+
+  ### Define parameters (constants and statics)
+  __constParameters__ = @parameters k1 k2 k3 k4 k5 k6
+  __staticParameters__ = @parameters comp1 comp2 _s3_ _s4_ _s9_
+
+  ### Define an operator for the differentiation w.r.t. time
+  __D__ = Differential(t)
+
+  ### ODE Equations ###
+  __eqs__ = [
+    # extended rules
+    comp4 ~ 4e+0,
+    s1 ~ _s1_/ comp1,
+    s2 ~ _s2_/ comp1,
+    s3 ~ _s3_/ comp2,
+    s4 ~ _s4_/ comp2,
+    s5 ~ 0e+0,
+    r1 ~ k1 * s1 * comp1,
+    r2 ~ k2 * s3 * comp2,
+    r3 ~ k3 * s2 * comp1,
+    p1 ~ k4 * comp3,
+    s6 ~ _s6_,
+    s7 ~ _s7_/ comp1,
+    s8 ~ _s8_,
+    s9 ~ _s9_,
+    s10 ~ 0e+0,
+    r4 ~ k5 * s6,
+    r5 ~ k6 * s9,
+
+    # ODEs
+    __D__(comp3) ~ -p1, # dcomp3_/dt
+    __D__(_s1_) ~ -r1, # ds1_/dt
+    __D__(_s2_) ~ 2*r1-r3, # ds2_/dt
+    __D__(_s6_) ~ -r4, # ds6_/dt
+    __D__(_s7_) ~ r4, # ds7_/dt
+    __D__(_s8_) ~ r4, # ds8_/dt
+  ]
+
+  ### Continious events ###
+
+  ### Discrete events ###
+
+  ### Initialization ###
+
+  __constValues__ = [
+    k1 => 0.1,
+    k2 => 0.2,
+    k3 => 0.3,
+    k4 => 0.4,
+    k5 => 0.5,
+    k6 => 0.6,
+  ]
+
+  __init__ = [
+    comp1 => 1e+0,
+    comp2 => 2.1,
+    comp3 => 3e+0,
+    comp4 => 4e+0,
+    s1 => 1e+1,
+    s2 => 0e+0,
+    s3 => 1e+1,
+    s4 => 1.1,
+    s5 => 0e+0,
+    r1 => k1 * s1 * comp1,
+    r2 => k2 * s3 * comp2,
+    r3 => k3 * s2 * comp1,
+    p1 => k4 * comp3,
+    s6 => 1e+1,
+    s7 => 0e+0,
+    s8 => 0e+0,
+    s9 => 1e+0,
+    s10 => 0e+0,
+    r4 => k5 * s6,
+    r5 => k6 * s9,
+  ]
+
+  __amountsInit__ = [
+      _s1_ => s1 * comp1,
+      _s2_ => s2 * comp1,
+      _s3_ => s3 * comp2,
+      _s4_ => s4 * comp2,
+      _s6_ => s6,
+      _s7_ => s7 * comp1,
+      _s8_ => s8,
+      _s9_ => s9,
+  ]
+
+  ### ODESystem definition ###
+  __sys__ = ODESystem(__eqs__, t, [__dynamicVariables__; __ruleVariables__], [__constParameters__; __staticParameters__],
+    name = :nameless,
+    discrete_events = [],
+    defaults = [__constValues__; __init__; __amountsInit__]
+  )
+
+  return structural_simplify(__sys__), __amountsInit__, __constValues__
+end
+
+__model__ = get_MTKmodel()

cases/mtk/run_mm.jl

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+using HetaSimulator, Plots
+using DiffEqCallbacks
+
+m = load_mtkmodel("$HetaSimulatorDir/cases/mtk/mm.jl")
+observed(m.sys)
+equations(m.sys)
+
+prob = ODEProblem(m.sys, m.u0map, (0.,250.), m.parammap)
+
+obs = [:r1, :_S_, :Km]
+# check if obs are present in sys
+saved_values = SavedValues(Float64, Vector{Float64})
+saved_fun = (u,t,integrator) -> prob.f.observed(getproperty.((m.sys,), obs))(u, integrator.p, t)
+scb = SavingCallback(saved_fun, saved_values)
+
+s = solve(prob, Tsit5(), callback=scb, save_everystep=false, save_start=false, save_end = false)
+saved_values
+
+plot(HetaSimulator.DiffEqArray(saved_values.saveval, saved_values.t))

cases/mtk/run_nameless.jl

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+using HetaSimulator, Plots
+using DiffEqCallbacks
+
+m = load_mtkmodel("$HetaSimulatorDir/cases/mtk/nameless.jl")
+observed(m.sys)
+equations(m.sys)
+
+prob = ODEProblem(m.sys, m.u0map, (0.,60.), m.parammap)
+
+obs = [:r4, :_s1_, :comp1]
+# check if obs are present in sys
+saved_values = SavedValues(Float64, Vector{Float64})
+saved_fun = (u,t,integrator) -> prob.f.observed(getproperty.((m.sys,), obs))(u, integrator.p, t)
+scb = SavingCallback(saved_fun, saved_values)
+
+s = solve(prob, Tsit5(), callback=scb, save_everystep=false, save_start=false, save_end = false)
+saved_values
+
+plot(HetaSimulator.DiffEqArray(saved_values.saveval, saved_values.t))