StochKit2 is the rst major upgrade of the popular StochKit stochastic simulation software package. StochKit2 provides highly efcient implementations of several variants of Gillespie's stochastic simulation algorithm (SSA), and tau-leaping with automatic step size selection. StochKit2 features include automatic selection of the optimal SSA method based on model properties, event handling, and automatic parallelism on multicore architectures. The underlying structure of the code has been completely updated to provide a exible framework for extending its functionality.
Bibliographical noteFunding Information:
Funding: National Institute of Biomedical Imaging and Bioengineering (Grant No. R01EB007511); Institute for Collaborative Biotechnologies from the US Army Research Office (Grant No. DFR3A-8-447850-23002); DOE Contract No. DE-FG02-04ER25621; NSF Contract No. IGERT DG02-21715 and DMS-1001012; National Science Foundation Graduate Research Fellowships (to K.S. and R.K.L).