StochKit2 swMATH ID: 14081 Software Authors: Sanft KR, Wu S, Roh M, Fu J, Lim RK, Petzold LR Description: StochKit2: software for discrete stochastic simulation of biochemical systems with events. Summary: StochKit2 is the first major upgrade of the popular StochKit stochastic simulation software package. StochKit2 provides highly efficient 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 flexible framework for extending its functionality. Availability: StochKit2 runs on Linux/Unix, Mac OS X and Windows. It is freely available under GPL version 3 and can be downloaded from http://sourceforge.net/projects/stochkit/. Homepage: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3157925/ Related Software: StochKit; Python; GillesPy2; ppsim; libSBML; COPASI; BioNetGen; StochPy; GitHub; CERENA; iNA; NetworkX; ERODE; Jupyter; JuMP; DifferentialEquations.jl; Smoldyn; PySB; Gillespie.jl; GillespieSSA Cited in: 9 Publications all top 5 Cited by 24 Authors 2 Marr, Carsten 1 Ballarini, Paolo 1 Bentriou, Mahmoud 1 Cinquemani, Eugenio 1 Cournède, Paul-Henry 1 Dayar, Tugrul 1 Debusschere, Bert J. 1 Doty, David 1 Feigelman, Justin 1 Grima, Ramon 1 Hasenauer, Jan 1 Najm, Habib N. 1 Orhan, M. Can 1 Petrov, Tatjana 1 Popović, Nikola 1 Safta, Cosmin 1 Sanguinetti, Guido 1 Sargsyan, Khachik V. 1 Schnoerr, David 1 Severson, Eric E. 1 Swain, Peter S. 1 Theis, Fabian Joachim 1 Tognazzi, Stefano 1 Weindl, Daniel all top 5 Cited in 6 Serials 1 Journal of Computational Physics 1 Journal of Mathematical Biology 1 Automatica 1 Journal of Applied Probability 1 Theoretical Computer Science 1 Journal of Physics A: Mathematical and Theoretical all top 5 Cited in 9 Fields 7 Biology and other natural sciences (92-XX) 3 Probability theory and stochastic processes (60-XX) 2 Statistics (62-XX) 1 Ordinary differential equations (34-XX) 1 Dynamical systems and ergodic theory (37-XX) 1 Numerical analysis (65-XX) 1 Computer science (68-XX) 1 Classical thermodynamics, heat transfer (80-XX) 1 Systems theory; control (93-XX) Citations by Year