STOCKS swMATH ID: 10438 Software Authors: Andrzej M. Kierzek Description: STOCKS: STOChastic kinetic simulations of biochemical systems with Gillespie algorithm. STOCKS, software for the stochastic kinetic simulation of biochemical processes is presented. The program uses a rigorously derived Gillespie algorithm that has been shown to be applicable to the study of prokaryotic gene expression. Features dedicated to the study of cellular processes are implemented, such as the possibility to study a process in the range of several cell generations with the application of a simple cell division model. Taking expression of Escherichia coli beta-galactosidase as an example, it is shown that the program is able to simulate systems composed of reactions varying in several orders of magnitude by means of reaction rates and the numbers of molecules involved. Homepage: http://bioinformatics.oxfordjournals.org/content/18/3/470 Related Software: PROPhESY; PARAM; MRMC; Bio-PEPA; PRISM; SPPARKS; Virtual Cell; JigCell; YSMP; MEG; MetaModel; ODEPACK; E-CELL; GEPASI; SCAMP; IntelliGEN; KINSOLVER; J3DV; Dizzy; Chronux Cited in: 12 Publications all top 5 Cited by 38 Authors 1 Aleman-Meza, Boanerges 1 Andrecut, M. 1 Arampatzis, Georgios 1 Arnold, Jonathan 1 Bortolussi, Luca 1 Bruck, Jehoshua 1 Brunelli, Marcello 1 Carletti, Timoteo 1 Cataldo, Enrico 1 Charlebois, Daniel A. 1 Chatelain, Philippe 1 Cloud, David J. 1 Cook, Matthew 1 Degano, Pierpaolo 1 Dimitrova, Elena S. 1 Enright, Wayne H. 1 Filisetti, Alessandro 1 Fraser, Dawn 1 Ilie, Silvana 1 Intosalmi, Jukka 1 Jackson, Kenneth R. 1 Kærn, Mads 1 Kauffman, Stuart Alan 1 Koumoutsakos, Petros D. 1 Lipková, Jana 1 Menze, Bjoern H. 1 Milios, Dimitrios 1 Reif, John H. 1 Sahu, Sudheer 1 Sanguinetti, Guido 1 Schüttler, Heinz-Bernd 1 Soloveichik, David 1 Stigler, Brandilyn 1 Taha, Thiab R. 1 Wang, Bei 1 Wang, Yan 1 Winfree, Erik 1 Yu, Yihai all top 5 Cited in 10 Serials 1 Computers & Mathematics with Applications 1 Bulletin of Mathematical Biology 1 Theoretical Computer Science 1 Information and Computation 1 The Canadian Applied Mathematics Quarterly 1 Soft Computing 1 Natural Computing 1 Computational & Mathematical Methods in Medicine 1 Communications in Computational Physics 1 Journal of Theoretical Biology all top 5 Cited in 8 Fields 8 Biology and other natural sciences (92-XX) 5 Computer science (68-XX) 3 Probability theory and stochastic processes (60-XX) 2 Numerical analysis (65-XX) 2 Classical thermodynamics, heat transfer (80-XX) 1 Combinatorics (05-XX) 1 Partial differential equations (35-XX) 1 Statistical mechanics, structure of matter (82-XX) Citations by Year