# command line: # KaDE n_phos_sites_3.ka -print-efficiency -ode-backend DOTNET -dotnet-output network_n_phos_sites_3_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 ku4 4802 5 kp3 375 6 n_k3 3 7 ku3 686 8 kp2 75 9 n_k2 2 10 ku2 98 11 kp1 15 12 n_k1 1 13 ku1 14 14 kp0 3 15 n_k0 0 end parameters begin species 1 A(s1~u,s2~u,s3~u) 100 2 A(s1~u,s2~u,s3~p) 0 3 A(s1~u,s2~p,s3~u) 0 4 A(s1~p,s2~u,s3~u) 0 5 A(s1~p,s2~u,s3~p) 0 6 A(s1~p,s2~p,s3~u) 0 7 A(s1~p,s2~p,s3~p) 0 8 A(s1~u,s2~p,s3~p) 0 end species begin reactions # rule : A(s1~u,s2~u,s3~p) -> A(s1~p,s2~u,s3~p) # A(s1~u, s2~u, s3~p) -> A(s1~p, s2~u, s3~p) 1 2 5 kp1 # rule : A(s1~u,s2~u,s3~p) -> A(s1~u,s2~p,s3~p) # A(s1~u, s2~u, s3~p) -> A(s1~u, s2~p, s3~p) 2 2 8 kp1 # rule : A(s1~u,s2~u,s3~p) -> A(s1~u,s2~u,s3~u) # A(s1~u, s2~u, s3~p) -> A(s1~u, s2~u, s3~u) 3 2 1 ku1 # rule : A(s1~u,s2~p,s3~u) -> A(s1~p,s2~p,s3~u) # A(s1~u, s2~p, s3~u) -> A(s1~p, s2~p, s3~u) 4 3 6 kp1 # rule : A(s1~u,s2~p,s3~u) -> A(s1~u,s2~u,s3~u) # A(s1~u, s2~p, s3~u) -> A(s1~u, s2~u, s3~u) 5 3 1 ku1 # rule : A(s1~u,s2~p,s3~u) -> A(s1~u,s2~p,s3~p) # A(s1~u, s2~p, s3~u) -> A(s1~u, s2~p, s3~p) 6 3 8 kp1 # rule : A(s1~p,s2~u,s3~p) -> A(s1~u,s2~u,s3~p) # A(s1~p, s2~u, s3~p) -> A(s1~u, s2~u, s3~p) 7 5 2 ku2 # rule : A(s1~p,s2~u,s3~p) -> A(s1~p,s2~p,s3~p) # A(s1~p, s2~u, s3~p) -> A(s1~p, s2~p, s3~p) 8 5 7 kp2 # rule : A(s1~p,s2~u,s3~p) -> A(s1~p,s2~u,s3~u) # A(s1~p, s2~u, s3~p) -> A(s1~p, s2~u, s3~u) 9 5 4 ku2 # rule : A(s1~u,s2~p,s3~p) -> A(s1~p,s2~p,s3~p) # A(s1~u, s2~p, s3~p) -> A(s1~p, s2~p, s3~p) 10 8 7 kp2 # rule : A(s1~u,s2~p,s3~p) -> A(s1~u,s2~u,s3~p) # A(s1~u, s2~p, s3~p) -> A(s1~u, s2~u, s3~p) 11 8 2 ku2 # rule : A(s1~u,s2~p,s3~p) -> A(s1~u,s2~p,s3~u) # A(s1~u, s2~p, s3~p) -> A(s1~u, s2~p, s3~u) 12 8 3 ku2 # rule : A(s1~p,s2~p,s3~p) -> A(s1~u,s2~p,s3~p) # A(s1~p, s2~p, s3~p) -> A(s1~u, s2~p, s3~p) 13 7 8 ku3 # rule : A(s1~p,s2~p,s3~p) -> A(s1~p,s2~u,s3~p) # A(s1~p, s2~p, s3~p) -> A(s1~p, s2~u, s3~p) 14 7 5 ku3 # rule : A(s1~p,s2~p,s3~p) -> A(s1~p,s2~p,s3~u) # A(s1~p, s2~p, s3~p) -> A(s1~p, s2~p, s3~u) 15 7 6 ku3 # rule : A(s1~p,s2~p,s3~u) -> A(s1~u,s2~p,s3~u) # A(s1~p, s2~p, s3~u) -> A(s1~u, s2~p, s3~u) 16 6 3 ku2 # rule : A(s1~p,s2~p,s3~u) -> A(s1~p,s2~u,s3~u) # A(s1~p, s2~p, s3~u) -> A(s1~p, s2~u, s3~u) 17 6 4 ku2 # rule : A(s1~p,s2~p,s3~u) -> A(s1~p,s2~p,s3~p) # A(s1~p, s2~p, s3~u) -> A(s1~p, s2~p, s3~p) 18 6 7 kp2 # rule : A(s1~p,s2~u,s3~u) -> A(s1~u,s2~u,s3~u) # A(s1~p, s2~u, s3~u) -> A(s1~u, s2~u, s3~u) 19 4 1 ku1 # rule : A(s1~p,s2~u,s3~u) -> A(s1~p,s2~p,s3~u) # A(s1~p, s2~u, s3~u) -> A(s1~p, s2~p, s3~u) 20 4 6 kp1 # rule : A(s1~p,s2~u,s3~u) -> A(s1~p,s2~u,s3~p) # A(s1~p, s2~u, s3~u) -> A(s1~p, s2~u, s3~p) 21 4 5 kp1 # rule : A(s1~u,s2~u,s3~u) -> A(s1~p,s2~u,s3~u) # A(s1~u, s2~u, s3~u) -> A(s1~p, s2~u, s3~u) 22 1 4 kp0 # rule : A(s1~u,s2~u,s3~u) -> A(s1~u,s2~p,s3~u) # A(s1~u, s2~u, s3~u) -> A(s1~u, s2~p, s3~u) 23 1 3 kp0 # rule : A(s1~u,s2~u,s3~u) -> A(s1~u,s2~u,s3~p) # A(s1~u, s2~u, s3~u) -> A(s1~u, s2~u, s3~p) 24 1 2 kp0 end reactions