STOCKS: STOChastic Kinetic Simulation of biochemical processes with Gillespie algorithm.

Andrzej M. Kierzek

Institute of Biochemistry and Biophysics, PAS, Pawinskiego 5a, 02-106 Warszawa, POLAND

andrzejk@ibb.waw.pl

STOCKS is a public domain (GNU GPL) software for stochastic simulations of biochemical processes. The features of the software are briefly listed below. For more details see manual and example files in software distribution.

Algorithm: STOCKS uses Gillespie's direct method [1] to simulate time evolution of the system composed of large number of first and second order chemical reactions. The program can perform simulations in the time scale of several cellular generations using linearly growing volume of reaction environment and simple model of cell division. Substances which are in equilibrium resulting from the competition of large number of processes can be modeled as random pools with Gaussian distribution.

Tests: The program has been already applied to study the dependence between transcription and translation initiation rates and the magnitude of stochastic fluctuations in prokaryotic gene expression [2,3]. Reference [3] shows also the performence of the software in the simulation involving reactions with rates varying by several orders of magnitude - gene expression and enzymatic activities of expressed proteins.

Platform: STOCKS is best suited to be run as a background process under UNIX operating system. Current distribution is tested under Linux and IRIX. The program can be compiled also for the other platforms as the source codes in standard C++ are available.

Utility programs: Distribution of STOCKS includes utility programs for averaging trajectories collected during simulations. The 2 dimensional phase plot presented here have been computed automatically with the use of PERL script running STOCKS and utility programs. The script is also available in the software distribution.

Availability: STOCKS is available under GNU GPL license from : http://www.ibb.waw.pl/stocks/stocks1.02.tar.gz Distribution contains C++ source codes, executables for Linux and IRIX, documentation and examples including the model of prokaryotic gene expression presented here.

REFERENCES

[2] Kierzek A.M., Zaim J. and Zielenkiewicz P, (2001) The effect of transcription and translation initiation frequencies on the stochastic fluctuations in prokaryotic gene expression. J. Biol. Chem. 276, 8165-8172. [Free full text at JBC]