# command line: # KaDE n_phos_sites_5.ka -print-efficiency -ode-backend DOTNET -with-symmetries Backward -dotnet-output network_n_phos_sites_5_with_bsym.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 ku6 235298 5 kp5 9375 6 n_k5 5 7 ku5 33614 8 kp4 1875 9 n_k4 4 10 ku4 4802 11 kp3 375 12 n_k3 3 13 ku3 686 14 kp2 75 15 n_k2 2 16 ku2 98 17 kp1 15 18 n_k1 1 19 ku1 14 20 kp0 3 21 n_k0 0 end parameters begin species 1 A(s1~u,s2~u,s3~u,s4~u,s5~u) 100 2 A(s1~u,s2~u,s3~u,s4~u,s5~p) 0 3 A(s1~u,s2~u,s3~u,s4~p,s5~p) 0 4 A(s1~u,s2~u,s3~p,s4~p,s5~p) 0 5 A(s1~u,s2~p,s3~p,s4~p,s5~p) 0 6 A(s1~p,s2~p,s3~p,s4~p,s5~p) 0 end species begin reactions # rule : A(s1~p,s2~p,s3~p,s4~p,s5~p) -> A(s1~u,s2~p,s3~p,s4~p,s5~p) # A(s1~p, s2~p, s3~p, s4~p, s5~p) -> A(s1~u, s2~p, s3~p, s4~p, s5~p) 1 6 5 ku5 # rule : A(s1~p,s2~p,s3~p,s4~p,s5~p) -> A(s1~p,s2~u,s3~p,s4~p,s5~p) # A(s1~p, s2~p, s3~p, s4~p, s5~p) -> A(s1~u, s2~p, s3~p, s4~p, s5~p) 2 6 5 ku5 # rule : A(s1~p,s2~p,s3~p,s4~p,s5~p) -> A(s1~p,s2~p,s3~u,s4~p,s5~p) # A(s1~p, s2~p, s3~p, s4~p, s5~p) -> A(s1~u, s2~p, s3~p, s4~p, s5~p) 3 6 5 ku5 # rule : A(s1~p,s2~p,s3~p,s4~p,s5~p) -> A(s1~p,s2~p,s3~p,s4~u,s5~p) # A(s1~p, s2~p, s3~p, s4~p, s5~p) -> A(s1~u, s2~p, s3~p, s4~p, s5~p) 4 6 5 ku5 # rule : A(s1~p,s2~p,s3~p,s4~p,s5~p) -> A(s1~p,s2~p,s3~p,s4~p,s5~u) # A(s1~p, s2~p, s3~p, s4~p, s5~p) -> A(s1~u, s2~p, s3~p, s4~p, s5~p) 5 6 5 ku5 # rule : A(s1~u,s2~p,s3~p,s4~p,s5~p) -> A(s1~p,s2~p,s3~p,s4~p,s5~p) # A(s1~u, s2~p, s3~p, s4~p, s5~p) -> A(s1~p, s2~p, s3~p, s4~p, s5~p) 6 5 6 kp4 # rule : A(s1~u,s2~p,s3~p,s4~p,s5~p) -> A(s1~u,s2~u,s3~p,s4~p,s5~p) # A(s1~u, s2~p, s3~p, s4~p, s5~p) -> A(s1~u, s2~u, s3~p, s4~p, s5~p) 7 5 4 ku4 # rule : A(s1~u,s2~p,s3~p,s4~p,s5~p) -> A(s1~u,s2~p,s3~u,s4~p,s5~p) # A(s1~u, s2~p, s3~p, s4~p, s5~p) -> A(s1~u, s2~u, s3~p, s4~p, s5~p) 8 5 4 ku4 # rule : A(s1~u,s2~p,s3~p,s4~p,s5~p) -> A(s1~u,s2~p,s3~p,s4~u,s5~p) # A(s1~u, s2~p, s3~p, s4~p, s5~p) -> A(s1~u, s2~u, s3~p, s4~p, s5~p) 9 5 4 ku4 # rule : A(s1~u,s2~p,s3~p,s4~p,s5~p) -> A(s1~u,s2~p,s3~p,s4~p,s5~u) # A(s1~u, s2~p, s3~p, s4~p, s5~p) -> A(s1~u, s2~u, s3~p, s4~p, s5~p) 10 5 4 ku4 # rule : A(s1~u,s2~u,s3~p,s4~p,s5~p) -> A(s1~p,s2~u,s3~p,s4~p,s5~p) # A(s1~u, s2~u, s3~p, s4~p, s5~p) -> A(s1~u, s2~p, s3~p, s4~p, s5~p) 11 4 5 kp3 # rule : A(s1~u,s2~u,s3~p,s4~p,s5~p) -> A(s1~u,s2~p,s3~p,s4~p,s5~p) # A(s1~u, s2~u, s3~p, s4~p, s5~p) -> A(s1~u, s2~p, s3~p, s4~p, s5~p) 12 4 5 kp3 # rule : A(s1~u,s2~u,s3~p,s4~p,s5~p) -> A(s1~u,s2~u,s3~u,s4~p,s5~p) # A(s1~u, s2~u, s3~p, s4~p, s5~p) -> A(s1~u, s2~u, s3~u, s4~p, s5~p) 13 4 3 ku3 # rule : A(s1~u,s2~u,s3~p,s4~p,s5~p) -> A(s1~u,s2~u,s3~p,s4~u,s5~p) # A(s1~u, s2~u, s3~p, s4~p, s5~p) -> A(s1~u, s2~u, s3~u, s4~p, s5~p) 14 4 3 ku3 # rule : A(s1~u,s2~u,s3~p,s4~p,s5~p) -> A(s1~u,s2~u,s3~p,s4~p,s5~u) # A(s1~u, s2~u, s3~p, s4~p, s5~p) -> A(s1~u, s2~u, s3~u, s4~p, s5~p) 15 4 3 ku3 # rule : A(s1~u,s2~u,s3~u,s4~p,s5~p) -> A(s1~p,s2~u,s3~u,s4~p,s5~p) # A(s1~u, s2~u, s3~u, s4~p, s5~p) -> A(s1~u, s2~u, s3~p, s4~p, s5~p) 16 3 4 kp2 # rule : A(s1~u,s2~u,s3~u,s4~p,s5~p) -> A(s1~u,s2~p,s3~u,s4~p,s5~p) # A(s1~u, s2~u, s3~u, s4~p, s5~p) -> A(s1~u, s2~u, s3~p, s4~p, s5~p) 17 3 4 kp2 # rule : A(s1~u,s2~u,s3~u,s4~p,s5~p) -> A(s1~u,s2~u,s3~p,s4~p,s5~p) # A(s1~u, s2~u, s3~u, s4~p, s5~p) -> A(s1~u, s2~u, s3~p, s4~p, s5~p) 18 3 4 kp2 # rule : A(s1~u,s2~u,s3~u,s4~p,s5~p) -> A(s1~u,s2~u,s3~u,s4~u,s5~p) # A(s1~u, s2~u, s3~u, s4~p, s5~p) -> A(s1~u, s2~u, s3~u, s4~u, s5~p) 19 3 2 ku2 # rule : A(s1~u,s2~u,s3~u,s4~p,s5~p) -> A(s1~u,s2~u,s3~u,s4~p,s5~u) # A(s1~u, s2~u, s3~u, s4~p, s5~p) -> A(s1~u, s2~u, s3~u, s4~u, s5~p) 20 3 2 ku2 # rule : A(s1~u,s2~u,s3~u,s4~u,s5~p) -> A(s1~p,s2~u,s3~u,s4~u,s5~p) # A(s1~u, s2~u, s3~u, s4~u, s5~p) -> A(s1~u, s2~u, s3~u, s4~p, s5~p) 21 2 3 kp1 # rule : A(s1~u,s2~u,s3~u,s4~u,s5~p) -> A(s1~u,s2~p,s3~u,s4~u,s5~p) # A(s1~u, s2~u, s3~u, s4~u, s5~p) -> A(s1~u, s2~u, s3~u, s4~p, s5~p) 22 2 3 kp1 # rule : A(s1~u,s2~u,s3~u,s4~u,s5~p) -> A(s1~u,s2~u,s3~p,s4~u,s5~p) # A(s1~u, s2~u, s3~u, s4~u, s5~p) -> A(s1~u, s2~u, s3~u, s4~p, s5~p) 23 2 3 kp1 # rule : A(s1~u,s2~u,s3~u,s4~u,s5~p) -> A(s1~u,s2~u,s3~u,s4~p,s5~p) # A(s1~u, s2~u, s3~u, s4~u, s5~p) -> A(s1~u, s2~u, s3~u, s4~p, s5~p) 24 2 3 kp1 # rule : A(s1~u,s2~u,s3~u,s4~u,s5~p) -> A(s1~u,s2~u,s3~u,s4~u,s5~u) # A(s1~u, s2~u, s3~u, s4~u, s5~p) -> A(s1~u, s2~u, s3~u, s4~u, s5~u) 25 2 1 ku1 # rule : A(s1~u,s2~u,s3~u,s4~u,s5~u) -> A(s1~p,s2~u,s3~u,s4~u,s5~u) # A(s1~u, s2~u, s3~u, s4~u, s5~u) -> A(s1~u, s2~u, s3~u, s4~u, s5~p) 26 1 2 kp0 # rule : A(s1~u,s2~u,s3~u,s4~u,s5~u) -> A(s1~u,s2~p,s3~u,s4~u,s5~u) # A(s1~u, s2~u, s3~u, s4~u, s5~u) -> A(s1~u, s2~u, s3~u, s4~u, s5~p) 27 1 2 kp0 # rule : A(s1~u,s2~u,s3~u,s4~u,s5~u) -> A(s1~u,s2~u,s3~p,s4~u,s5~u) # A(s1~u, s2~u, s3~u, s4~u, s5~u) -> A(s1~u, s2~u, s3~u, s4~u, s5~p) 28 1 2 kp0 # rule : A(s1~u,s2~u,s3~u,s4~u,s5~u) -> A(s1~u,s2~u,s3~u,s4~p,s5~u) # A(s1~u, s2~u, s3~u, s4~u, s5~u) -> A(s1~u, s2~u, s3~u, s4~u, s5~p) 29 1 2 kp0 # rule : A(s1~u,s2~u,s3~u,s4~u,s5~u) -> A(s1~u,s2~u,s3~u,s4~u,s5~p) # A(s1~u, s2~u, s3~u, s4~u, s5~u) -> A(s1~u, s2~u, s3~u, s4~u, s5~p) 30 1 2 kp0 end reactions