Algorithms

Direct()

Gillespie's Direct Method.

References

• Gillespie, D.T. (1976) A general method for numerically simulating the stochastic time evolution of coupled chemical reactions. Journal of Computational Physics. https://doi.org/10.1016/0021-9991(76)90041-3

• Gillespie, D.T. (1977) Exact stochastic simulation of coupled chemical reactions. The Journal of Physical Chemistry. https://doi.org/10.1021/j100540a008

EnhancedDirect()

A Direct method that uses a dependency graph.

References

• Marchetti L., Priami C., Thanh V.H. (2017) Simulation Algorithms for Computational Systems Biology. Texts in Theoretical Computer Science.

SortingDirect()

The sorting direct method reorders reactions to identify frequently occurring events. This effectively reduces the search depth in selecting the next reaction.

References

• McCollum, J.M., Peterson, G.D., Cox, C.D., Simpson, M.L., Samatova, N.F. (2006). The sorting direct method for stochastic simulation of biochemical systems with varying reaction execution behavior. Computational Biology and Chemistry. https://doi.org/10.1016/j.compbiolchem.2005.10.007.

FirstReaction()

A first reaction method that samples reaction events and times jointly.

References

• Gillespie, D.T. (1976) A general method for numerically simulating the stochastic time evolution of coupled chemical reactions. Journal of Computational Physics. https://doi.org/10.1016/0021-9991(76)90041-3

NextReaction()

Gibson and Bruck's next reaction method. Uses a priority queue to select the next reaction event and time.

References

• Gibson, M.A., Bruck, J. (1999) Efficient exact stochastic simulation of chemical systems with many species and many channels. Journal of Physical Chemistry. https://doi.org/10.1021/jp993732q

RejectionSSA()

A rejection-based algorithm that operates on "virtual states" to accelerate simulation.

WARNING: This implementation is a work in progress.

References

• Thahn, V.H., Priami, C., Zunino, R. (2014) Efficient rejection-based simulation of biochemical reactions with stochastic noise and delays. Journal of Chemical Physics. https://doi.org/10.1063/1.4896985

TauLeapingDG2001()

A pure tau-leaping method using the Equation (26a) to select tau.

Optional Arguments

Work in progress.

References

• Gillespie, D.T. (2001) Approximate accelerated stochastic simulation of chemically reacting systems. Journal of Chemical Physics. https://doi.org/10.1063/1.1378322

TauLeapingDGLP2003()

A pure tau-leaping method using the Equation (6) to select tau.

Optional Arguments

Work in progress.

References

• Gillespie, D.T., Petzold, L.R. (2003) Improved leap-size selection for accelerated stochastic simulation. Journal of Chemical Physics. https://doi.org/10.1063/1.1613254

StepAnticipation()

A pure tau-leaping method using the Equation (15) to select tau.

Optional Arguments

Work in progress.

References

• Sehl, M.E., Alekseyenko, A.L., Lange, K.L. (2009) Accurate stochastic simulation via the step anticipation tau-leaping (SAL) algorithm. Journal of Computational Biology. https://dx.doi.org/10.1089/cmb.2008.0249

HybridSAL()

Same as StepAnticipation(), but defaults to Direct() depending on the cumulative intensity.

Optional Arguments

Work in progress.

References

• Sehl, M.E., Alekseyenko, A.L., Lange, K.L. (2009) Accurate stochastic simulation via the step anticipation tau-leaping (SAL) algorithm. Journal of Computational Biology. https://dx.doi.org/10.1089/cmb.2008.0249