HSimulator: Hybrid Stochastic/Deterministic Simulation of Biochemical Reaction Networks

Algorithm 2

Rejection-based Stochastic Simulation Algorithm (RSSA).

Input: The same as DM (Algorithm 1) together with a simulation parameter for

calculating the fluctuation interval of the system state.

Output: a time series of states , providing the dynamics of the system.

Pseudocode:

   ;

   while    do

     Define the fluctuation interval according to (8);

     For each reaction , compute propensity bounds , and

     the total propensity ;

     while    do

       Generate three random numbers in ;

       ;

       Select such that satisfies

               ;

       ;

       if    then

         ;

       else

         Compute according to (5);

         if    then  ;

       end  if

       if    then

         Compute by applying to ;

       end  if

       ;

     end  while

   end  while