title: STOCKS: STOChastic Kinetic Simulations of biochemical systems with Gillespie algorithm.
abstract: BACKGROUND
  The availability of a huge amount of molecular data concerning various biochemical reactions provoked numerous attempts to study the dynamics of cellular processes by means of kinetic models and computer simulations. Biochemical processes frequently involve small numbers of molecules (e.g. a few molecules of a transcriptional regulator binding to one 'molecule' of a DNA regulatory region). Such reactions are subject to significant stochastic fluctuations. Monte Carlo methods must be employed to study the functional consequences of the fluctuations and simulate processes that cannot be modelled by continuous fluxes of matter. This provides the motivation to develop software dedicated to Monte Carlo simulations of cellular processes with the rigorously proven Gillespie algorithm.
  
  
  RESULTS
  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.
  
  
  BACKGROUND
  The software is available at ftp://ibbrain.ibb.waw.pl/stocksand http://www.ibb.waw.pl/stocks.
  
  
  BACKGROUND
  Parameters of the model of prokaryotic gene expression are available in example files of software distribution.
authors.affiliation: Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warszawa, Poland. andrezejk@ibb.waw.pl
authors.forename: Andrzej M
authors.initials: AM
authors.lastname: Kierzek
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D016208:Databases, Factual; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D005786:Gene Expression Regulation / Q000235:genetics; D007700:Kinetics; D008956:Models, Chemical; D015233:Models, Statistical; D009010:Monte Carlo Method; D014176:Protein Biosynthesis / Q000235:genetics; D011506:Proteins / Q000235:genetics / Q000493:pharmacokinetics*; D012984:Software; D013269:Stochastic Processes; D014158:Transcription, Genetic / Q000235:genetics
chemical_list: D011506:Proteins