Simulating Biochemical Systems
- 1.8k Downloads
This chapter introduces the reader to the principles underlying Gillespie’s widely-used stochastic simulation algorithm (SSA), for the exact stochastic modeling of chemical reactions involving relatively small numbers of molecules. We also look at Gibson and Bruck’s improvements to the SSA, in order to support larger numbers of reactions, as well as the more recent variation by Slepoy, Thompson and Plimpton. All of these techniques are illustrated with Java implementations and a discussion of their complexity. We also introduce the Dizzy and SGNSim toolkits, which implement some of these approaches, along with tau-leap approximation and reaction delays.
KeywordsReaction Method Dependency Graph Stochastic Simulation Algorithm Java Implementation Delayed Reaction
- 15.Foundation, F.S.: Gnu general public license (2007). URL http://www.gnu.org/licenses/gpl.html
- 20.Gillespie, D.T.: A general method for numerically simulating the stochastic time evolution of coupled chemical reactions. Journal of Computational Physics 22(403) (1976) Google Scholar
- 33.Ramsey, S., Orrell, D., Bolouri, H.: Dizzy home page (2010). URL http://magnet.systemsbiology.net/software/Dizzy/