# command line: # KaDE n_phos_sites_4.ka -print-efficiency -ode-backend DOTNET -dotnet-output network_n_phos_sites_4_wo_sym.net # THINGS THAT ARE KNOWN FROM KAPPA FILE AND KaSim OPTIONS: # # init - the initial abundances of each species and token # tinit - the initial simulation time (likely 0) # tend - the final simulation time # initialstep - initial time step at the beginning of numerical integration # maxstep - maximal time step for numerical integration # reltol - relative error tolerance; # abstol - absolute error tolerance; # period - the time period between points to return # # variables (init(i),y(i)) denote numbers of embeddings # rule rates are corrected by the number of automorphisms in the lhs of rules begin parameters 1 tinit 0 2 tend 1 3 period 0.01 4 ku5 33614 5 kp4 1875 6 n_k4 4 7 ku4 4802 8 kp3 375 9 n_k3 3 10 ku3 686 11 kp2 75 12 n_k2 2 13 ku2 98 14 kp1 15 15 n_k1 1 16 ku1 14 17 kp0 3 18 n_k0 0 end parameters begin species 1 A(s1~u,s2~u,s3~u,s4~u) 100 2 A(s1~u,s2~u,s3~u,s4~p) 0 3 A(s1~u,s2~u,s3~p,s4~u) 0 4 A(s1~u,s2~p,s3~u,s4~u) 0 5 A(s1~p,s2~u,s3~u,s4~u) 0 6 A(s1~p,s2~u,s3~u,s4~p) 0 7 A(s1~p,s2~u,s3~p,s4~u) 0 8 A(s1~p,s2~p,s3~u,s4~u) 0 9 A(s1~p,s2~p,s3~u,s4~p) 0 10 A(s1~p,s2~p,s3~p,s4~u) 0 11 A(s1~p,s2~p,s3~p,s4~p) 0 12 A(s1~u,s2~p,s3~p,s4~u) 0 13 A(s1~u,s2~p,s3~p,s4~p) 0 14 A(s1~u,s2~p,s3~u,s4~p) 0 15 A(s1~u,s2~u,s3~p,s4~p) 0 16 A(s1~p,s2~u,s3~p,s4~p) 0 end species begin reactions # rule : A(s1~u,s2~u,s3~u,s4~p) -> A(s1~p,s2~u,s3~u,s4~p) # A(s1~u, s2~u, s3~u, s4~p) -> A(s1~p, s2~u, s3~u, s4~p) 1 2 6 kp1 # rule : A(s1~u,s2~u,s3~u,s4~p) -> A(s1~u,s2~p,s3~u,s4~p) # A(s1~u, s2~u, s3~u, s4~p) -> A(s1~u, s2~p, s3~u, s4~p) 2 2 14 kp1 # rule : A(s1~u,s2~u,s3~u,s4~p) -> A(s1~u,s2~u,s3~p,s4~p) # A(s1~u, s2~u, s3~u, s4~p) -> A(s1~u, s2~u, s3~p, s4~p) 3 2 15 kp1 # rule : A(s1~u,s2~u,s3~u,s4~p) -> A(s1~u,s2~u,s3~u,s4~u) # A(s1~u, s2~u, s3~u, s4~p) -> A(s1~u, s2~u, s3~u, s4~u) 4 2 1 ku1 # rule : A(s1~u,s2~u,s3~p,s4~u) -> A(s1~p,s2~u,s3~p,s4~u) # A(s1~u, s2~u, s3~p, s4~u) -> A(s1~p, s2~u, s3~p, s4~u) 5 3 7 kp1 # rule : A(s1~u,s2~u,s3~p,s4~u) -> A(s1~u,s2~p,s3~p,s4~u) # A(s1~u, s2~u, s3~p, s4~u) -> A(s1~u, s2~p, s3~p, s4~u) 6 3 12 kp1 # rule : A(s1~u,s2~u,s3~p,s4~u) -> A(s1~u,s2~u,s3~u,s4~u) # A(s1~u, s2~u, s3~p, s4~u) -> A(s1~u, s2~u, s3~u, s4~u) 7 3 1 ku1 # rule : A(s1~u,s2~u,s3~p,s4~u) -> A(s1~u,s2~u,s3~p,s4~p) # A(s1~u, s2~u, s3~p, s4~u) -> A(s1~u, s2~u, s3~p, s4~p) 8 3 15 kp1 # rule : A(s1~u,s2~p,s3~u,s4~u) -> A(s1~p,s2~p,s3~u,s4~u) # A(s1~u, s2~p, s3~u, s4~u) -> A(s1~p, s2~p, s3~u, s4~u) 9 4 8 kp1 # rule : A(s1~u,s2~p,s3~u,s4~u) -> A(s1~u,s2~u,s3~u,s4~u) # A(s1~u, s2~p, s3~u, s4~u) -> A(s1~u, s2~u, s3~u, s4~u) 10 4 1 ku1 # rule : A(s1~u,s2~p,s3~u,s4~u) -> A(s1~u,s2~p,s3~p,s4~u) # A(s1~u, s2~p, s3~u, s4~u) -> A(s1~u, s2~p, s3~p, s4~u) 11 4 12 kp1 # rule : A(s1~u,s2~p,s3~u,s4~u) -> A(s1~u,s2~p,s3~u,s4~p) # A(s1~u, s2~p, s3~u, s4~u) -> A(s1~u, s2~p, s3~u, s4~p) 12 4 14 kp1 # rule : A(s1~p,s2~u,s3~u,s4~p) -> A(s1~u,s2~u,s3~u,s4~p) # A(s1~p, s2~u, s3~u, s4~p) -> A(s1~u, s2~u, s3~u, s4~p) 13 6 2 ku2 # rule : A(s1~p,s2~u,s3~u,s4~p) -> A(s1~p,s2~p,s3~u,s4~p) # A(s1~p, s2~u, s3~u, s4~p) -> A(s1~p, s2~p, s3~u, s4~p) 14 6 9 kp2 # rule : A(s1~p,s2~u,s3~u,s4~p) -> A(s1~p,s2~u,s3~p,s4~p) # A(s1~p, s2~u, s3~u, s4~p) -> A(s1~p, s2~u, s3~p, s4~p) 15 6 16 kp2 # rule : A(s1~p,s2~u,s3~u,s4~p) -> A(s1~p,s2~u,s3~u,s4~u) # A(s1~p, s2~u, s3~u, s4~p) -> A(s1~p, s2~u, s3~u, s4~u) 16 6 5 ku2 # rule : A(s1~p,s2~u,s3~p,s4~u) -> A(s1~u,s2~u,s3~p,s4~u) # A(s1~p, s2~u, s3~p, s4~u) -> A(s1~u, s2~u, s3~p, s4~u) 17 7 3 ku2 # rule : A(s1~p,s2~u,s3~p,s4~u) -> A(s1~p,s2~p,s3~p,s4~u) # A(s1~p, s2~u, s3~p, s4~u) -> A(s1~p, s2~p, s3~p, s4~u) 18 7 10 kp2 # rule : A(s1~p,s2~u,s3~p,s4~u) -> A(s1~p,s2~u,s3~u,s4~u) # A(s1~p, s2~u, s3~p, s4~u) -> A(s1~p, s2~u, s3~u, s4~u) 19 7 5 ku2 # rule : A(s1~p,s2~u,s3~p,s4~u) -> A(s1~p,s2~u,s3~p,s4~p) # A(s1~p, s2~u, s3~p, s4~u) -> A(s1~p, s2~u, s3~p, s4~p) 20 7 16 kp2 # rule : A(s1~p,s2~p,s3~u,s4~p) -> A(s1~u,s2~p,s3~u,s4~p) # A(s1~p, s2~p, s3~u, s4~p) -> A(s1~u, s2~p, s3~u, s4~p) 21 9 14 ku3 # rule : A(s1~p,s2~p,s3~u,s4~p) -> A(s1~p,s2~u,s3~u,s4~p) # A(s1~p, s2~p, s3~u, s4~p) -> A(s1~p, s2~u, s3~u, s4~p) 22 9 6 ku3 # rule : A(s1~p,s2~p,s3~u,s4~p) -> A(s1~p,s2~p,s3~p,s4~p) # A(s1~p, s2~p, s3~u, s4~p) -> A(s1~p, s2~p, s3~p, s4~p) 23 9 11 kp3 # rule : A(s1~p,s2~p,s3~u,s4~p) -> A(s1~p,s2~p,s3~u,s4~u) # A(s1~p, s2~p, s3~u, s4~p) -> A(s1~p, s2~p, s3~u, s4~u) 24 9 8 ku3 # rule : A(s1~p,s2~p,s3~p,s4~p) -> A(s1~u,s2~p,s3~p,s4~p) # A(s1~p, s2~p, s3~p, s4~p) -> A(s1~u, s2~p, s3~p, s4~p) 25 11 13 ku4 # rule : A(s1~p,s2~p,s3~p,s4~p) -> A(s1~p,s2~u,s3~p,s4~p) # A(s1~p, s2~p, s3~p, s4~p) -> A(s1~p, s2~u, s3~p, s4~p) 26 11 16 ku4 # rule : A(s1~p,s2~p,s3~p,s4~p) -> A(s1~p,s2~p,s3~u,s4~p) # A(s1~p, s2~p, s3~p, s4~p) -> A(s1~p, s2~p, s3~u, s4~p) 27 11 9 ku4 # rule : A(s1~p,s2~p,s3~p,s4~p) -> A(s1~p,s2~p,s3~p,s4~u) # A(s1~p, s2~p, s3~p, s4~p) -> A(s1~p, s2~p, s3~p, s4~u) 28 11 10 ku4 # rule : A(s1~u,s2~p,s3~u,s4~p) -> A(s1~p,s2~p,s3~u,s4~p) # A(s1~u, s2~p, s3~u, s4~p) -> A(s1~p, s2~p, s3~u, s4~p) 29 14 9 kp2 # rule : A(s1~u,s2~p,s3~u,s4~p) -> A(s1~u,s2~u,s3~u,s4~p) # A(s1~u, s2~p, s3~u, s4~p) -> A(s1~u, s2~u, s3~u, s4~p) 30 14 2 ku2 # rule : A(s1~u,s2~p,s3~u,s4~p) -> A(s1~u,s2~p,s3~p,s4~p) # A(s1~u, s2~p, s3~u, s4~p) -> A(s1~u, s2~p, s3~p, s4~p) 31 14 13 kp2 # rule : A(s1~u,s2~p,s3~u,s4~p) -> A(s1~u,s2~p,s3~u,s4~u) # A(s1~u, s2~p, s3~u, s4~p) -> A(s1~u, s2~p, s3~u, s4~u) 32 14 4 ku2 # rule : A(s1~p,s2~u,s3~p,s4~p) -> A(s1~u,s2~u,s3~p,s4~p) # A(s1~p, s2~u, s3~p, s4~p) -> A(s1~u, s2~u, s3~p, s4~p) 33 16 15 ku3 # rule : A(s1~p,s2~u,s3~p,s4~p) -> A(s1~p,s2~p,s3~p,s4~p) # A(s1~p, s2~u, s3~p, s4~p) -> A(s1~p, s2~p, s3~p, s4~p) 34 16 11 kp3 # rule : A(s1~p,s2~u,s3~p,s4~p) -> A(s1~p,s2~u,s3~u,s4~p) # A(s1~p, s2~u, s3~p, s4~p) -> A(s1~p, s2~u, s3~u, s4~p) 35 16 6 ku3 # rule : A(s1~p,s2~u,s3~p,s4~p) -> A(s1~p,s2~u,s3~p,s4~u) # A(s1~p, s2~u, s3~p, s4~p) -> A(s1~p, s2~u, s3~p, s4~u) 36 16 7 ku3 # rule : A(s1~u,s2~u,s3~p,s4~p) -> A(s1~p,s2~u,s3~p,s4~p) # A(s1~u, s2~u, s3~p, s4~p) -> A(s1~p, s2~u, s3~p, s4~p) 37 15 16 kp2 # rule : A(s1~u,s2~u,s3~p,s4~p) -> A(s1~u,s2~p,s3~p,s4~p) # A(s1~u, s2~u, s3~p, s4~p) -> A(s1~u, s2~p, s3~p, s4~p) 38 15 13 kp2 # rule : A(s1~u,s2~u,s3~p,s4~p) -> A(s1~u,s2~u,s3~u,s4~p) # A(s1~u, s2~u, s3~p, s4~p) -> A(s1~u, s2~u, s3~u, s4~p) 39 15 2 ku2 # rule : A(s1~u,s2~u,s3~p,s4~p) -> A(s1~u,s2~u,s3~p,s4~u) # A(s1~u, s2~u, s3~p, s4~p) -> A(s1~u, s2~u, s3~p, s4~u) 40 15 3 ku2 # rule : A(s1~u,s2~p,s3~p,s4~p) -> A(s1~p,s2~p,s3~p,s4~p) # A(s1~u, s2~p, s3~p, s4~p) -> A(s1~p, s2~p, s3~p, s4~p) 41 13 11 kp3 # rule : A(s1~u,s2~p,s3~p,s4~p) -> A(s1~u,s2~u,s3~p,s4~p) # A(s1~u, s2~p, s3~p, s4~p) -> A(s1~u, s2~u, s3~p, s4~p) 42 13 15 ku3 # rule : A(s1~u,s2~p,s3~p,s4~p) -> A(s1~u,s2~p,s3~u,s4~p) # A(s1~u, s2~p, s3~p, s4~p) -> A(s1~u, s2~p, s3~u, s4~p) 43 13 14 ku3 # rule : A(s1~u,s2~p,s3~p,s4~p) -> A(s1~u,s2~p,s3~p,s4~u) # A(s1~u, s2~p, s3~p, s4~p) -> A(s1~u, s2~p, s3~p, s4~u) 44 13 12 ku3 # rule : A(s1~u,s2~p,s3~p,s4~u) -> A(s1~p,s2~p,s3~p,s4~u) # A(s1~u, s2~p, s3~p, s4~u) -> A(s1~p, s2~p, s3~p, s4~u) 45 12 10 kp2 # rule : A(s1~u,s2~p,s3~p,s4~u) -> A(s1~u,s2~u,s3~p,s4~u) # A(s1~u, s2~p, s3~p, s4~u) -> A(s1~u, s2~u, s3~p, s4~u) 46 12 3 ku2 # rule : A(s1~u,s2~p,s3~p,s4~u) -> A(s1~u,s2~p,s3~u,s4~u) # A(s1~u, s2~p, s3~p, s4~u) -> A(s1~u, s2~p, s3~u, s4~u) 47 12 4 ku2 # rule : A(s1~u,s2~p,s3~p,s4~u) -> A(s1~u,s2~p,s3~p,s4~p) # A(s1~u, s2~p, s3~p, s4~u) -> A(s1~u, s2~p, s3~p, s4~p) 48 12 13 kp2 # rule : A(s1~p,s2~p,s3~p,s4~u) -> A(s1~u,s2~p,s3~p,s4~u) # A(s1~p, s2~p, s3~p, s4~u) -> A(s1~u, s2~p, s3~p, s4~u) 49 10 12 ku3 # rule : A(s1~p,s2~p,s3~p,s4~u) -> A(s1~p,s2~u,s3~p,s4~u) # A(s1~p, s2~p, s3~p, s4~u) -> A(s1~p, s2~u, s3~p, s4~u) 50 10 7 ku3 # rule : A(s1~p,s2~p,s3~p,s4~u) -> A(s1~p,s2~p,s3~u,s4~u) # A(s1~p, s2~p, s3~p, s4~u) -> A(s1~p, s2~p, s3~u, s4~u) 51 10 8 ku3 # rule : A(s1~p,s2~p,s3~p,s4~u) -> A(s1~p,s2~p,s3~p,s4~p) # A(s1~p, s2~p, s3~p, s4~u) -> A(s1~p, s2~p, s3~p, s4~p) 52 10 11 kp3 # rule : A(s1~p,s2~p,s3~u,s4~u) -> A(s1~u,s2~p,s3~u,s4~u) # A(s1~p, s2~p, s3~u, s4~u) -> A(s1~u, s2~p, s3~u, s4~u) 53 8 4 ku2 # rule : A(s1~p,s2~p,s3~u,s4~u) -> A(s1~p,s2~u,s3~u,s4~u) # A(s1~p, s2~p, s3~u, s4~u) -> A(s1~p, s2~u, s3~u, s4~u) 54 8 5 ku2 # rule : A(s1~p,s2~p,s3~u,s4~u) -> A(s1~p,s2~p,s3~p,s4~u) # A(s1~p, s2~p, s3~u, s4~u) -> A(s1~p, s2~p, s3~p, s4~u) 55 8 10 kp2 # rule : A(s1~p,s2~p,s3~u,s4~u) -> A(s1~p,s2~p,s3~u,s4~p) # A(s1~p, s2~p, s3~u, s4~u) -> A(s1~p, s2~p, s3~u, s4~p) 56 8 9 kp2 # rule : A(s1~p,s2~u,s3~u,s4~u) -> A(s1~u,s2~u,s3~u,s4~u) # A(s1~p, s2~u, s3~u, s4~u) -> A(s1~u, s2~u, s3~u, s4~u) 57 5 1 ku1 # rule : A(s1~p,s2~u,s3~u,s4~u) -> A(s1~p,s2~p,s3~u,s4~u) # A(s1~p, s2~u, s3~u, s4~u) -> A(s1~p, s2~p, s3~u, s4~u) 58 5 8 kp1 # rule : A(s1~p,s2~u,s3~u,s4~u) -> A(s1~p,s2~u,s3~p,s4~u) # A(s1~p, s2~u, s3~u, s4~u) -> A(s1~p, s2~u, s3~p, s4~u) 59 5 7 kp1 # rule : A(s1~p,s2~u,s3~u,s4~u) -> A(s1~p,s2~u,s3~u,s4~p) # A(s1~p, s2~u, s3~u, s4~u) -> A(s1~p, s2~u, s3~u, s4~p) 60 5 6 kp1 # rule : A(s1~u,s2~u,s3~u,s4~u) -> A(s1~p,s2~u,s3~u,s4~u) # A(s1~u, s2~u, s3~u, s4~u) -> A(s1~p, s2~u, s3~u, s4~u) 61 1 5 kp0 # rule : A(s1~u,s2~u,s3~u,s4~u) -> A(s1~u,s2~p,s3~u,s4~u) # A(s1~u, s2~u, s3~u, s4~u) -> A(s1~u, s2~p, s3~u, s4~u) 62 1 4 kp0 # rule : A(s1~u,s2~u,s3~u,s4~u) -> A(s1~u,s2~u,s3~p,s4~u) # A(s1~u, s2~u, s3~u, s4~u) -> A(s1~u, s2~u, s3~p, s4~u) 63 1 3 kp0 # rule : A(s1~u,s2~u,s3~u,s4~u) -> A(s1~u,s2~u,s3~u,s4~p) # A(s1~u, s2~u, s3~u, s4~u) -> A(s1~u, s2~u, s3~u, s4~p) 64 1 2 kp0 end reactions