HSimulator: Hybrid Stochastic/Deterministic Simulation of Biochemical Reaction Networks

Algorithm 1

Gillespie’s Direct Method (DM).

Input: a reaction system with species and reactions as the one in (1), with a stochastic

reaction constant associated with each reaction ; an initial state defining molecule

abundances at time ; the last time instant to be simulated.

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

Pseudocode:

   ;

   while    do

     For each reaction , compute reaction propensities according

     to (5);

     Compute according to (4);

     Generate two random numbers in ;

     ;

     Select such that satisfies

               ;

     Compute by applying to ;

     ;

   end while