# command line: # KaDE n_phos_sites_6.ka -print-efficiency -ode-backend DOTNET -with-symmetries Backward -dotnet-output network_n_phos_sites_6_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 ku7 1647086 5 kp6 46875 6 n_k6 6 7 ku6 235298 8 kp5 9375 9 n_k5 5 10 ku5 33614 11 kp4 1875 12 n_k4 4 13 ku4 4802 14 kp3 375 15 n_k3 3 16 ku3 686 17 kp2 75 18 n_k2 2 19 ku2 98 20 kp1 15 21 n_k1 1 22 ku1 14 23 kp0 3 24 n_k0 0 end parameters begin species 1 A(s1~u,s2~u,s3~u,s4~u,s5~u,s6~u) 100 2 A(s1~u,s2~u,s3~u,s4~u,s5~u,s6~p) 0 3 A(s1~u,s2~u,s3~u,s4~u,s5~p,s6~p) 0 4 A(s1~u,s2~u,s3~u,s4~p,s5~p,s6~p) 0 5 A(s1~u,s2~u,s3~p,s4~p,s5~p,s6~p) 0 6 A(s1~u,s2~p,s3~p,s4~p,s5~p,s6~p) 0 7 A(s1~p,s2~p,s3~p,s4~p,s5~p,s6~p) 0 end species begin reactions # rule : A(s1~p,s2~p,s3~p,s4~p,s5~p,s6~p) -> A(s1~u,s2~p,s3~p,s4~p,s5~p,s6~p) # A(s1~p, s2~p, s3~p, s4~p, s5~p, s6~p) -> A(s1~u, s2~p, s3~p, s4~p, s5~p, s6~p) 1 7 6 ku6 # rule : A(s1~p,s2~p,s3~p,s4~p,s5~p,s6~p) -> A(s1~p,s2~u,s3~p,s4~p,s5~p,s6~p) # A(s1~p, s2~p, s3~p, s4~p, s5~p, s6~p) -> A(s1~u, s2~p, s3~p, s4~p, s5~p, s6~p) 2 7 6 ku6 # rule : A(s1~p,s2~p,s3~p,s4~p,s5~p,s6~p) -> A(s1~p,s2~p,s3~u,s4~p,s5~p,s6~p) # A(s1~p, s2~p, s3~p, s4~p, s5~p, s6~p) -> A(s1~u, s2~p, s3~p, s4~p, s5~p, s6~p) 3 7 6 ku6 # rule : A(s1~p,s2~p,s3~p,s4~p,s5~p,s6~p) -> A(s1~p,s2~p,s3~p,s4~u,s5~p,s6~p) # A(s1~p, s2~p, s3~p, s4~p, s5~p, s6~p) -> A(s1~u, s2~p, s3~p, s4~p, s5~p, s6~p) 4 7 6 ku6 # rule : A(s1~p,s2~p,s3~p,s4~p,s5~p,s6~p) -> A(s1~p,s2~p,s3~p,s4~p,s5~u,s6~p) # A(s1~p, s2~p, s3~p, s4~p, s5~p, s6~p) -> A(s1~u, s2~p, s3~p, s4~p, s5~p, s6~p) 5 7 6 ku6 # rule : A(s1~p,s2~p,s3~p,s4~p,s5~p,s6~p) -> A(s1~p,s2~p,s3~p,s4~p,s5~p,s6~u) # A(s1~p, s2~p, s3~p, s4~p, s5~p, s6~p) -> A(s1~u, s2~p, s3~p, s4~p, s5~p, s6~p) 6 7 6 ku6 # rule : A(s1~u,s2~p,s3~p,s4~p,s5~p,s6~p) -> A(s1~p,s2~p,s3~p,s4~p,s5~p,s6~p) # A(s1~u, s2~p, s3~p, s4~p, s5~p, s6~p) -> A(s1~p, s2~p, s3~p, s4~p, s5~p, s6~p) 7 6 7 kp5 # rule : A(s1~u,s2~p,s3~p,s4~p,s5~p,s6~p) -> A(s1~u,s2~u,s3~p,s4~p,s5~p,s6~p) # A(s1~u, s2~p, s3~p, s4~p, s5~p, s6~p) -> A(s1~u, s2~u, s3~p, s4~p, s5~p, s6~p) 8 6 5 ku5 # rule : A(s1~u,s2~p,s3~p,s4~p,s5~p,s6~p) -> A(s1~u,s2~p,s3~u,s4~p,s5~p,s6~p) # A(s1~u, s2~p, s3~p, s4~p, s5~p, s6~p) -> A(s1~u, s2~u, s3~p, s4~p, s5~p, s6~p) 9 6 5 ku5 # rule : A(s1~u,s2~p,s3~p,s4~p,s5~p,s6~p) -> A(s1~u,s2~p,s3~p,s4~u,s5~p,s6~p) # A(s1~u, s2~p, s3~p, s4~p, s5~p, s6~p) -> A(s1~u, s2~u, s3~p, s4~p, s5~p, s6~p) 10 6 5 ku5 # rule : A(s1~u,s2~p,s3~p,s4~p,s5~p,s6~p) -> A(s1~u,s2~p,s3~p,s4~p,s5~u,s6~p) # A(s1~u, s2~p, s3~p, s4~p, s5~p, s6~p) -> A(s1~u, s2~u, s3~p, s4~p, s5~p, s6~p) 11 6 5 ku5 # rule : A(s1~u,s2~p,s3~p,s4~p,s5~p,s6~p) -> A(s1~u,s2~p,s3~p,s4~p,s5~p,s6~u) # A(s1~u, s2~p, s3~p, s4~p, s5~p, s6~p) -> A(s1~u, s2~u, s3~p, s4~p, s5~p, s6~p) 12 6 5 ku5 # rule : A(s1~u,s2~u,s3~p,s4~p,s5~p,s6~p) -> A(s1~p,s2~u,s3~p,s4~p,s5~p,s6~p) # A(s1~u, s2~u, s3~p, s4~p, s5~p, s6~p) -> A(s1~u, s2~p, s3~p, s4~p, s5~p, s6~p) 13 5 6 kp4 # rule : A(s1~u,s2~u,s3~p,s4~p,s5~p,s6~p) -> A(s1~u,s2~p,s3~p,s4~p,s5~p,s6~p) # A(s1~u, s2~u, s3~p, s4~p, s5~p, s6~p) -> A(s1~u, s2~p, s3~p, s4~p, s5~p, s6~p) 14 5 6 kp4 # rule : A(s1~u,s2~u,s3~p,s4~p,s5~p,s6~p) -> A(s1~u,s2~u,s3~u,s4~p,s5~p,s6~p) # A(s1~u, s2~u, s3~p, s4~p, s5~p, s6~p) -> A(s1~u, s2~u, s3~u, s4~p, s5~p, s6~p) 15 5 4 ku4 # rule : A(s1~u,s2~u,s3~p,s4~p,s5~p,s6~p) -> A(s1~u,s2~u,s3~p,s4~u,s5~p,s6~p) # A(s1~u, s2~u, s3~p, s4~p, s5~p, s6~p) -> A(s1~u, s2~u, s3~u, s4~p, s5~p, s6~p) 16 5 4 ku4 # rule : A(s1~u,s2~u,s3~p,s4~p,s5~p,s6~p) -> A(s1~u,s2~u,s3~p,s4~p,s5~u,s6~p) # A(s1~u, s2~u, s3~p, s4~p, s5~p, s6~p) -> A(s1~u, s2~u, s3~u, s4~p, s5~p, s6~p) 17 5 4 ku4 # rule : A(s1~u,s2~u,s3~p,s4~p,s5~p,s6~p) -> A(s1~u,s2~u,s3~p,s4~p,s5~p,s6~u) # A(s1~u, s2~u, s3~p, s4~p, s5~p, s6~p) -> A(s1~u, s2~u, s3~u, s4~p, s5~p, s6~p) 18 5 4 ku4 # rule : A(s1~u,s2~u,s3~u,s4~p,s5~p,s6~p) -> A(s1~p,s2~u,s3~u,s4~p,s5~p,s6~p) # A(s1~u, s2~u, s3~u, s4~p, s5~p, s6~p) -> A(s1~u, s2~u, s3~p, s4~p, s5~p, s6~p) 19 4 5 kp3 # rule : A(s1~u,s2~u,s3~u,s4~p,s5~p,s6~p) -> A(s1~u,s2~p,s3~u,s4~p,s5~p,s6~p) # A(s1~u, s2~u, s3~u, s4~p, s5~p, s6~p) -> A(s1~u, s2~u, s3~p, s4~p, s5~p, s6~p) 20 4 5 kp3 # rule : A(s1~u,s2~u,s3~u,s4~p,s5~p,s6~p) -> A(s1~u,s2~u,s3~p,s4~p,s5~p,s6~p) # A(s1~u, s2~u, s3~u, s4~p, s5~p, s6~p) -> A(s1~u, s2~u, s3~p, s4~p, s5~p, s6~p) 21 4 5 kp3 # rule : A(s1~u,s2~u,s3~u,s4~p,s5~p,s6~p) -> A(s1~u,s2~u,s3~u,s4~u,s5~p,s6~p) # A(s1~u, s2~u, s3~u, s4~p, s5~p, s6~p) -> A(s1~u, s2~u, s3~u, s4~u, s5~p, s6~p) 22 4 3 ku3 # rule : A(s1~u,s2~u,s3~u,s4~p,s5~p,s6~p) -> A(s1~u,s2~u,s3~u,s4~p,s5~u,s6~p) # A(s1~u, s2~u, s3~u, s4~p, s5~p, s6~p) -> A(s1~u, s2~u, s3~u, s4~u, s5~p, s6~p) 23 4 3 ku3 # rule : A(s1~u,s2~u,s3~u,s4~p,s5~p,s6~p) -> A(s1~u,s2~u,s3~u,s4~p,s5~p,s6~u) # A(s1~u, s2~u, s3~u, s4~p, s5~p, s6~p) -> A(s1~u, s2~u, s3~u, s4~u, s5~p, s6~p) 24 4 3 ku3 # rule : A(s1~u,s2~u,s3~u,s4~u,s5~p,s6~p) -> A(s1~p,s2~u,s3~u,s4~u,s5~p,s6~p) # A(s1~u, s2~u, s3~u, s4~u, s5~p, s6~p) -> A(s1~u, s2~u, s3~u, s4~p, s5~p, s6~p) 25 3 4 kp2 # rule : A(s1~u,s2~u,s3~u,s4~u,s5~p,s6~p) -> A(s1~u,s2~p,s3~u,s4~u,s5~p,s6~p) # A(s1~u, s2~u, s3~u, s4~u, s5~p, s6~p) -> A(s1~u, s2~u, s3~u, s4~p, s5~p, s6~p) 26 3 4 kp2 # rule : A(s1~u,s2~u,s3~u,s4~u,s5~p,s6~p) -> A(s1~u,s2~u,s3~p,s4~u,s5~p,s6~p) # A(s1~u, s2~u, s3~u, s4~u, s5~p, s6~p) -> A(s1~u, s2~u, s3~u, s4~p, s5~p, s6~p) 27 3 4 kp2 # rule : A(s1~u,s2~u,s3~u,s4~u,s5~p,s6~p) -> A(s1~u,s2~u,s3~u,s4~p,s5~p,s6~p) # A(s1~u, s2~u, s3~u, s4~u, s5~p, s6~p) -> A(s1~u, s2~u, s3~u, s4~p, s5~p, s6~p) 28 3 4 kp2 # rule : A(s1~u,s2~u,s3~u,s4~u,s5~p,s6~p) -> A(s1~u,s2~u,s3~u,s4~u,s5~u,s6~p) # A(s1~u, s2~u, s3~u, s4~u, s5~p, s6~p) -> A(s1~u, s2~u, s3~u, s4~u, s5~u, s6~p) 29 3 2 ku2 # rule : A(s1~u,s2~u,s3~u,s4~u,s5~p,s6~p) -> A(s1~u,s2~u,s3~u,s4~u,s5~p,s6~u) # A(s1~u, s2~u, s3~u, s4~u, s5~p, s6~p) -> A(s1~u, s2~u, s3~u, s4~u, s5~u, s6~p) 30 3 2 ku2 # rule : A(s1~u,s2~u,s3~u,s4~u,s5~u,s6~p) -> A(s1~p,s2~u,s3~u,s4~u,s5~u,s6~p) # A(s1~u, s2~u, s3~u, s4~u, s5~u, s6~p) -> A(s1~u, s2~u, s3~u, s4~u, s5~p, s6~p) 31 2 3 kp1 # rule : A(s1~u,s2~u,s3~u,s4~u,s5~u,s6~p) -> A(s1~u,s2~p,s3~u,s4~u,s5~u,s6~p) # A(s1~u, s2~u, s3~u, s4~u, s5~u, s6~p) -> A(s1~u, s2~u, s3~u, s4~u, s5~p, s6~p) 32 2 3 kp1 # rule : A(s1~u,s2~u,s3~u,s4~u,s5~u,s6~p) -> A(s1~u,s2~u,s3~p,s4~u,s5~u,s6~p) # A(s1~u, s2~u, s3~u, s4~u, s5~u, s6~p) -> A(s1~u, s2~u, s3~u, s4~u, s5~p, s6~p) 33 2 3 kp1 # rule : A(s1~u,s2~u,s3~u,s4~u,s5~u,s6~p) -> A(s1~u,s2~u,s3~u,s4~p,s5~u,s6~p) # A(s1~u, s2~u, s3~u, s4~u, s5~u, s6~p) -> A(s1~u, s2~u, s3~u, s4~u, s5~p, s6~p) 34 2 3 kp1 # rule : A(s1~u,s2~u,s3~u,s4~u,s5~u,s6~p) -> A(s1~u,s2~u,s3~u,s4~u,s5~p,s6~p) # A(s1~u, s2~u, s3~u, s4~u, s5~u, s6~p) -> A(s1~u, s2~u, s3~u, s4~u, s5~p, s6~p) 35 2 3 kp1 # rule : A(s1~u,s2~u,s3~u,s4~u,s5~u,s6~p) -> A(s1~u,s2~u,s3~u,s4~u,s5~u,s6~u) # A(s1~u, s2~u, s3~u, s4~u, s5~u, s6~p) -> A(s1~u, s2~u, s3~u, s4~u, s5~u, s6~u) 36 2 1 ku1 # rule : A(s1~u,s2~u,s3~u,s4~u,s5~u,s6~u) -> A(s1~p,s2~u,s3~u,s4~u,s5~u,s6~u) # A(s1~u, s2~u, s3~u, s4~u, s5~u, s6~u) -> A(s1~u, s2~u, s3~u, s4~u, s5~u, s6~p) 37 1 2 kp0 # rule : A(s1~u,s2~u,s3~u,s4~u,s5~u,s6~u) -> A(s1~u,s2~p,s3~u,s4~u,s5~u,s6~u) # A(s1~u, s2~u, s3~u, s4~u, s5~u, s6~u) -> A(s1~u, s2~u, s3~u, s4~u, s5~u, s6~p) 38 1 2 kp0 # rule : A(s1~u,s2~u,s3~u,s4~u,s5~u,s6~u) -> A(s1~u,s2~u,s3~p,s4~u,s5~u,s6~u) # A(s1~u, s2~u, s3~u, s4~u, s5~u, s6~u) -> A(s1~u, s2~u, s3~u, s4~u, s5~u, s6~p) 39 1 2 kp0 # rule : A(s1~u,s2~u,s3~u,s4~u,s5~u,s6~u) -> A(s1~u,s2~u,s3~u,s4~p,s5~u,s6~u) # A(s1~u, s2~u, s3~u, s4~u, s5~u, s6~u) -> A(s1~u, s2~u, s3~u, s4~u, s5~u, s6~p) 40 1 2 kp0 # rule : A(s1~u,s2~u,s3~u,s4~u,s5~u,s6~u) -> A(s1~u,s2~u,s3~u,s4~u,s5~p,s6~u) # A(s1~u, s2~u, s3~u, s4~u, s5~u, s6~u) -> A(s1~u, s2~u, s3~u, s4~u, s5~u, s6~p) 41 1 2 kp0 # rule : A(s1~u,s2~u,s3~u,s4~u,s5~u,s6~u) -> A(s1~u,s2~u,s3~u,s4~u,s5~u,s6~p) # A(s1~u, s2~u, s3~u, s4~u, s5~u, s6~u) -> A(s1~u, s2~u, s3~u, s4~u, s5~u, s6~p) 42 1 2 kp0 end reactions