changes in repressilator: transition name + degradation reactions; change in plots

core/plots.jl

@@ -126,8 +126,6 @@ function plot_periodic_trajectory(A::LHA, σ::SynchronizedTrajectory, sym_obs::S
     scatter!(p, times(σ)[idx_n], σ[sym_obs][idx_n], annotations = annots,
                              markershape = :utriangle, markersize = 3, label = "n")
     hline!(p, [A.constants[:L], A.constants[:H]], label = "L, H", color = :grey; linestyle = :dot)
-    @show values_n
-    @show values_tp    
     if filename == ""
         display(p)
     else

models/repressilator.jl

@@ -6,12 +6,12 @@ repressilator = @network_model begin
     trl1: (mRNA1 => mRNA1 + P1, β * mRNA1)
     trl2: (mRNA2 => mRNA2 + P2, β * mRNA2)
     trl3: (mRNA3 => mRNA3 + P3, β * mRNA3)
-    d1: (mRNA1 => 0, mRNA1)
-    d2: (mRNA2 => 0, mRNA2)
-    d3: (mRNA3 => 0, mRNA3)
-    d4: (P1 => 0, P1)
-    d5: (P2 => 0, P2)
-    d6: (P3 => 0, P3)
+    degr1: (mRNA1 => 0, mRNA1)
+    degr2: (mRNA2 => 0, mRNA2)
+    degr3: (mRNA3 => 0, mRNA3)
+    degr4: (P1 => 0, P1)
+    degr5: (P2 => 0, P2)
+    degr6: (P3 => 0, P3)
 end "Repressilator pkg"
 
 set_observed_var!(repressilator, [:mRNA1, :mRNA2, :mRNA3, :P1, :P2, :P3])