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.

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  1. Lipková, Jana; Arampatzis, Georgios; Chatelain, Philippe; Menze, Bjoern; Koumoutsakos, Petros: (S)-leaping: an adaptive, accelerated stochastic simulation algorithm, bridging (\tau)-leaping and (R)-leaping (2019)
  2. Bortolussi, Luca; Milios, Dimitrios; Sanguinetti, Guido: Smoothed model checking for uncertain continuous-time Markov chains (2016)
  3. Stigler, Brandilyn; Dimitrova, Elena: Inferring the topology of gene regulatory networks: an algebraic approach to reverse engineering (2013)
  4. Wang, Yan: Reliable kinetic Monte Carlo simulation based on random set sampling (2013)
  5. Carletti, T.; Filisetti, A.: The stochastic evolution of a protocell: the Gillespie algorithm in a dynamically varying volume (2012)
  6. Charlebois, Daniel A.; Intosalmi, Jukka; Fraser, Dawn; Kærn, Mads: An algorithm for the stochastic simulation of gene expression and heterogeneous population dynamics (2011)
  7. Sorathiya, Anil; Bracciali, Andrea; Liò, Pietro: Formal reasoning on qualitative models of coinfection of HIV and tuberculosis and HAART therapy (2010) ioport
  8. Aleman-Meza, Boanerges; Yu, Yihai; Schüttler, Heinz-Bernd; Arnold, Jonathan; Taha, Thiab R.: KINSOLVER: A simulator for computing large ensembles of biochemical and gene regulatory networks (2009)
  9. Ilie, Silvana; Enright, Wayne H.; Jackson, Kenneth R.: Numerical solution of stochastic models of biochemical kinetics (2009)
  10. Andrecut, M.; Cloud, D.; Kauffman, S. A.: Monte Carlo simulation of a simple gene network yields new evolutionary insights (2008)
  11. Bracciali, Andrea; Brunelli, Marcello; Cataldo, Enrico; Degano, Pierpaolo: Synapses as stochastic concurrent systems (2008)
  12. Sahu, Sudheer; Wang, Bei; Reif, John H.: A framework for modeling DNA based molecular systems (2008)
  13. Soloveichik, David; Cook, Matthew; Winfree, Erik; Bruck, Jehoshua: Computation with finite stochastic chemical reaction networks (2008)