On Designing Multicore-Aware Simulators for Systems Biology Endowed with OnLine Statistics

Table 2

Biological simulation tools comparison.

Tool	Calculus	Simulation schema	Parallelism	Data analysis
SCWC	CWC	Gillespie	FastFlow	Online statistics
SPiM	𝜋-calculus	Gillespie	None	None
Dizzy	Reaction model	Gillespie, Gibson-Bruck, Tau-Leap, ODE	None	None
BioPEPA	Process algebra	ODE, Gillespie	None	None
Cellware	Reaction model	Gillespie, Gibson-Bruck, ODE	None	None
DiVinE	Model checker	ODE	MPI	None
StochKit	Reaction model	Gillespie, Tau-leaping	MPI	Postprocessing
StochKit2	Reaction model	Gillespie, Tau-leaping	Multithread	Postprocessing
StochKit-FF	Reaction model	Gillespie, Tau-leaping	FastFlow	Online statistics
Hy3S	Reaction model	Gibson-Bruck, Hybrid	MPI	Postprocessing
Li and Petzold’s	Reaction model	Gillespie	GPGPU	None
StochSimGPU	Reaction model	Gillespie, Gibson-Bruck, Li	GPGPU	Postprocessing