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We note that the latest version of COPASI (version 4.19 build 140) considered in our benchmarks provides other two implementation cases of hybrid simulation algorithms (Hybrid LSODA and Hybrid RK45).
Algorithm Software Parameters DM HSimulator No parameters needed DM COPASI No parameters needed RSSA HSimulator [delta] = 0.1 LSODA COPASI Relative and absolute thresholds: [10.sup.-3] RK45 HSimulator Initial stepsize: 10-2 Error threshold: [10.sup.-3] Hybrid Runge-Kutta COPASI Maximum number of reactant molecules for slow reactions: 100 RK4 stepsize: [10.sup.-2] HRSSA HSimulator [delta] = 0.1; [[tau].sub.fast] = [10.sup.-2]; [gamma] = 100; [theta] = 10 Table 2: Simulation running times of HSimulator and of the state- of-the-art simulator COPASI.
The differential equations in the PFR model were solved using the subroutine LSODA of ODEPACK (17).