Simulation of biochemical networks using COPASI: a complex pathway simulator

ABSTRACT

Simulation and modeling is becoming one of the standard approaches to understand complex biochemical processes. Therefore, there is a big need for software tools that allow access to diverse simulation and modeling methods as well as support for the use of these methods. Here, we present a new software tool that is platform independent, user friendly and offers several unique features. In addition, we discuss numerical considerations and support for the switching between simulation methods.

REFERENCES

• 1: Alfonsi, A., E. Cancès, G. Turinici, B. Di Ventura, and W. Huisinga. 2005. Adaptive simulation of hybrid stochastic and deterministic models for biochemical systems. ESAIM Proceedings 14: 1--13.
• 2: Yang Cao , Dan Gillespie , Linda Petzold, Multiscale stochastic simulation algorithm with stochastic partial equilibrium assumption for chemically reacting systems, Journal of Computational Physics, v.206 n.2, p.395-411, 1 July 2005 [doi>10.1016/j.jcp.2004.12.014]
• 3: ECell. The ECell Website. <http://www.e-cell.org/software/> {accessed June 4, 2006}
• 4: Fell, D. 1997. Understanding the control of metabolism. Portland Press.
• 5: Gibson, M. A., and J. Bruck. 2000. Efficient exact stochastic simulation of chemical systems with many species and many channels. Journal of Physical Chemistry A104 (9): 1876--1889.
• 6: Gillespie, D. T. 1976. A general method for numerically simulating the stochastic time evolution of coupled chemical reactions. Journal of Computational Physics 22: 402--434.
• 7: Heinrich, R., and S. Schuster. 1996. The regulation of cellular systems. Champman & Hall. International Thomson Publishing.
• 8: Haseltine, E. L., and J. B. Rawlings. 2002. Approximate simulation of coupled fast and slow reactions for stochastic chemical kinetics. Journal of Chemical Physics 117 (15): 6959--6969.
• 9: Stefan Hoops , Sven Sahle , Ralph Gauges , Christine Lee , Jürgen Pahle , Natalia Simus , Mudita Singhal , Liang Xu , Pedro Mendes , Ursula Kummer, COPASI---a COmplex PAthway SImulator, Bioinformatics, v.22 n.24, p.3067-3074, December 2006 [doi>10.1093/bioinformatics/btl485]
• 10: Thomas R. Kiehl , Robert M. Mattheyses , Melvin K. Simmons, Hybrid simulation of cellular behavior, Bioinformatics, v.20 n.3, p.316-322, February 2004 [doi>10.1093/bioinformatics/btg409]
• 11: Klamt, S., J. Stelling, M. Ginkel, and E. D. Gilles. 2003. FluxAnalyzer: exploring structure, pathways, and flux distributions in metabolic networks on interactive flux maps. Bioinformatics 19 (2): 261--269.
• 12: Le Novére, N., and T. S. Shimizu. 2001. StochSim: modelling of stochastic biomolecular processes. Bioinformatics 17: 575--576.
• 13: Meng, T., S. Somani, L. Ye, A. Sairam, Z. Hao, A. Krishnan, K. Sakharkar, and P. Dhar. 2004. Cellware: the grid-enabled tool for cell modeling and simulation. Bioinformatics 20: 1319--1321.
• 14: Petzold, L. 1983. Automatic selection of methods for solving stiff and nonstiff systems of ordinary differential equations. SIAM Journal on Scientific and Statistical Computing 4: 136--148.
• 15: Pfeiffer, T., I. Sanchez-Valdenebro, J. S. Nuño, F. Montero, and S. Schuster. 1999. METATOOL: for studying metabolic networks. Bioinformatics 15: 251--257.
• 16: Puchalka, J., and A. M. Kierzek. 2004. Bridging the gap between stochastic and deterministic regimes in the kinetic simulations of the biochemical reaction networks. Biophysical Journal 86: 1357--1372.
• 17: Rao, C. V., and A. P. Arkin. 2003. Stochastic chemical kinetics and the quasi-steady-state assumption: application to the Gillespie algorithm. Journal of Chemical Physics 118 (11): 4999--5010.
• 18: Sauro H. M., M. Hucka, A. Finney, C. Wellock, H. Bolouri, J. Doyle, and H. Kitano. 2003. Next generation simulation tools: the Systems Biology Workbench and BioSPICE integration. OMICS 7 (4): 355--372.
• 19: Salis, H., and Y. Kaznessis. 2005. Accurate hybrid stochastic simulation of a system of coupled chemical or biochemical reactions. Journal of Chemical Physics 122: 054--103.
• 20: SWB. The SWB Website, <http://sbw.kgi.edu/> {accessed June 4, 2006}
• 21: Ravishankar Rao Vallabhajosyula , Vijay Chickarmane , Herbert M. Sauro, Conservation analysis of large biochemical networks, Bioinformatics, v.22 n.3, p.346-353, February 2006 [doi>10.1093/bioinformatics/bti800]
• 22: Wolf, A., J. B. Swift, H. L. Swinney, and J. A. Vastano. 1985. Determining Lypunov exponents from a time series. Physica 16D (1985): 285--317.