# command line: # KaDE n_phos_sites_1.ka -print-efficiency -ode-backend DOTNET -with-symmetries Backward -dotnet-output network_n_phos_sites_1_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 ku2 98 5 kp1 15 6 n_k1 1 7 ku1 14 8 kp0 3 9 n_k0 0 end parameters begin species 1 A(s1~u) 100 2 A(s1~p) 0 end species begin reactions # rule : A(s1~p) -> A(s1~u) # A(s1~p) -> A(s1~u) 1 2 1 ku1 # rule : A(s1~u) -> A(s1~p) # A(s1~u) -> A(s1~p) 2 1 2 kp0 end reactions