Table 1:
Algorithm | Implementation / Reference | Class Name | Language | Advanced Features |
---|---|---|---|---|
SSA | Direct Method / Gillespie, 1977 | NumPySSASolver | Python | |
SSA | Direct Method / Gillespie, 1977 | SSACSolver | C++ | |
Tau-Leaping | Cao et al., 2006 | TauLeapingSolver | Python | |
Tau-Leaping | Cao et al., 2006 | TauLeapingCSolver | C++ | |
ODE | LSODA∗ / Petzold, 1983 | ODESolver | Python∗ | |
ODE | LSODA∗ / Petzold, 1983 | ODECSolver | C++∗ | |
CLE | Euler-Maruyama / McCauley, 2013 | CLESolver | Python | |
Tau-Hybrid | see Section 3 | TauHybridSolver | Python | Event, RateRule, AssignmentRule, FunctionDefinition |
Tau-Hybrid | see Section 3 | TauHybridCSolver | C++ | Event, RateRule |
The ODE solvers are wrappers to SciPy (Virtanen et al., 2020) (Python) and SUNDIALS (Hindmarsh et al., 2005) (C++) solvers. The ODE solvers use LSODA by default but other integrators can be chosen.