Utilizing stochastic model checking to analyze genetic circuits

2012 IEEE Symposium on Computational Intelligence and Computational Biology, CIBCB 2012

Volumn , Issue , 2012, Pages 379-386

  Madsen, Curtis ^a   Myers, Chris J ^a   Roehner, Nicholas ^a   Winstead, Chris ^b   Zhang, Zhen ^a  

^a UNIVERSITY OF UTAH   (United States)

^b UTAH STATE UNIVERSITY   (United States)

Author keywords

continuous stochastic logic; genetic circuits; markov chain analysis; stochastic model checking; synthetic biology

Indexed keywords

CONTINUOUS STOCHASTIC LOGIC; CONTINUOUS TIME MARKOV CHAIN; GENETIC CIRCUITS; GENETIC TOGGLE SWITCHES; LIKELIHOOD OF FAILURES; MARKOV CHAIN ANALYSIS; SIMULATION-BASED ANALYSIS; STATE PROBABILITY; SYNTHETIC BIOLOGY; TIME-SERIES DATA; TIME-SERIES SIMULATION; TRANSIENT MARKOV CHAINS;

ARTIFICIAL INTELLIGENCE; BIOINFORMATICS; MARKOV PROCESSES; MODEL CHECKING; STOCHASTIC MODELS; STOCHASTIC SYSTEMS; TIME SERIES;

LOGIC CIRCUITS;

EID: 84864056388     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/CIBCB.2012.6217255     Document Type: Conference Paper

References (38)

1. D. Endy, "Foundations for engineering biology," Nature, vol. 438, pp. 449-453, 2005.
2. A. Arkin, "Setting the standard in synthetic biology," Nature Biotech., vol. 26, pp. 771-774, 2008.
3. J. Beal and J. Bachrach, "Cells are plausible targets for high-level spatial languages," Proceedings of the 2008 Second IEEE International, pp. 284-291, 2008.
4. L. Bilitchenko, A. Liu, S. Cheung, E. Weeding, B. Xia, M. Leguia, J. C. Anderson, and D. Densmore, "Eugene - a domain specific language for specifying and constraining synthetic biological parts, devices, and systems," PLoS ONE, vol. 6, no. 4, 2011.
5. Y. Cai, M. L. Wilson, and J. Peccoud, "GenoCAD for iGEM: a grammatical approach to the design of standard-compliant constructs," Nucleic Acids Res., vol. 38, no. 8, pp. 2637-44, 2010.
6. D. Chandran, F. T. Bergmann, and H. M. Sauro, "TinkerCell: modular CAD tool for synthetic biology," J. Biol. Eng., vol. 3, no. 19, 2009.
7. M. A. Marchisio and J. Stelling, "Computational design of synthetic gene circuits with composable parts," Bioinform., vol. 24, no. 17, pp. 1903-10, 2008.
8. C. J. Myers, N. Barker, K. Jones, H. Kuwahara, C. Madsen, and N.- P. D. Nguyen, "iBioSim: a tool for the analysis and design of genetic circuits," Bioinform., vol. 25, no. 21, pp. 2848-2849, 2009.
9. M. A. Marchisio and J. Stelling, "Automatic design of digital synthetic gene circuits," PLoS Comput Biol, vol. 7, no. 2, Feb. 2011.
10. M. Pedersen and A. Phillips, "Towards programming languages for genetic engineering of living cells," J. R. Soc. Interface, vol. 6, no. (Suppl. 4), pp. S437-S450, 2009.
11. B. Yordanov, J. Tumova, C. Belta, I. Cerna, and J. Barnat, "Formal analysis of piecewise affine systems through formula-guided refinement," in 49th IEEE Conference on Decision and Control (CDC), 2010, pp. 5899-5904.
12. P. Waage and C. M. Guldberg, "Studies concerning affinity," Forhandlinger: Videnskabs - Selskabet i Christinia, vol. 35, 1864.
13. W. H. Press, B. P. Flannery, S. A. Teukolsky, and W. T. Vetterling, Numerical Recipes in C: The art of Scientic Computing, 2nd ed. Cambridge University Press, 1992.
14. S. H. Strogatz, Nonlinear Dynamics And Chaos: With Applications To Physics, Biology, Chemistry And Engineering. Westview Press, 1994.
15. D. T. Gillespie, "Exact stochastic simulation of coupled chemical reactions," J. Phys. Chem., vol. 81, no. 25, pp. 2340-2361, 1977.
16. M. Gibson and J. Bruck, "Efficient exact stochastic simulation of chemical systems with many species and many channels," J. Phys. Chem., vol. A 104, pp. 1876-1889, 2000.
17. Y. Cao, D. T. Gillespie, and L. R. Petzold, "Efficient step size selection for the tau-leaping simulation method," J. Chem. Phys., vol. 124, 2006.
18. D. T. Gillespie and L. R. Petzold, "Tau leaping," J. Chem. Phys., vol. 119, pp. 8229-8234, 2003.
19. H. Kuwahara, C. Myers, N. Barker, M. Samoilov, and A. Arkin, "Automated abstraction methodology for genetic regulatory networks," Trans. Comp. Syst. Biol., vol. VI, pp. 150-175, 2006.
20. H. Kuwahara, "Model abstraction and temporal behavior analysis of genetic regulatory networks," Ph.D. dissertation, U. of Utah, 2007.
21. D. Thieffry and R. Thomas, "Dynamical behaviour of biological networks: II. Immunity control in bacteriophage lamabda," Bull. Math. Biol., vol. 57, no. 2, pp. 277-297, 1995.
22. R. Thomas, "Regulatory networks seen as asynchronous automata: A logical description," Journal of Theoretical Biology, vol. 153, pp. 1-23, 1991.
23. T. Henzinger, M. Mateescu, and V. Wolf, "Sliding window abstraction for infinite markov chains," in Computer Aided Verification, ser. Lecture Notes in Computer Science, A. Bouajjani and O. Maler, Eds. Springer Berlin / Heidelberg, 2009, vol. 5643, pp. 337-352.
24. F. Ciocchetta, A. Degasperi, J. Hillston, and M. Calder, "Some investigations concerning the CTMC and the ODE model derived from Bio-PEPA," Electronic Notes in Theoretical Computer Science, vol. 229, no. 1, pp. 145 - 163, 2009, proceedings of the Second Workshop From Biology to Concurrency and Back (FBTC 2008).
25. M. Kwiatkowska, G. Norman, and D. Parker, "Stochastic model checking," in Formal Methods for the Design of Computer, Communication and Software Systems: Performance Evaluation (SFM'07), ser. LNCS (Tutorial Volume), M. Bernardo and J. Hillston, Eds., vol. 4486. Springer, 2007, pp. 220-270.
26. T. S. Gardner, C. R. Cantor, and J. J. Collins, "Construction of a genetic toggle switch in escherichia coli," Nature, vol. 403, pp. 339-342, 2000.
27. M. Hucka et al., "The Systems Biology Markup Language (SBML): A medium for representation and exchange of biochemical network models," Bioinform., vol. 19, no. 4, pp. 524-531, 2003.
28. N. Nguyen, "Design and analysis of genetic circuits," Master's thesis, U. of Utah, 2008.
29. N. Nguyen, C. Myers, H. Kuwahara, C. Winstead, and J. Keener, "Design and analysis of a robust genetic Muller C-element," Journal of Theoretical Biology, vol. 264, no. 2, pp. 174 - 187, 2010.
30. H. Younes, M. Kwiatkowska, G. Norman, and D. Parker, "Numerical vs. statistical probabilistic model checking," International Journal on Software Tools for Technology Transfer (STTT), vol. 8, pp. 216-228, 2006, 10.1007/s10009-005-0187-8.
31. A. Hinton, M. Kwiatkowska, G. Norman, and D. Parker, "PRISM: A tool for automatic verification of probabilistic systems," in Proc. 12th International Conference on Tools and Algorithms for the Construction and Analysis of Systems (TACAS'06), ser. LNCS, H. Hermanns and J. Palsberg, Eds., vol. 3920. Springer, 2006, pp. 441-444.
32. A. Aziz, K. Sanwal, V. Singhal, and R. Brayton, "Model-checking continuous-time markov chains," ACM Trans. Comput. Logic, vol. 1, pp. 162-170, July 2000.
33. W. J. Stewart, Introduction to the Numerical Solution of Markov Chains. 41 William Street, Princeton, NJ, 08540: Priceton University Press, 1994.
34. C. J. Myers, Engineering Genetic Circuits. Chapman and Hall/CRC, 2009.
35. H. Kuwahara and I. Mura, "An efficient and exact stochastic simulation method to analyze rare events in biochemical systems," The Journal of Chemical Physics, vol. 129, no. 16, 2008.
36. D. T. Gillespie, M. Roh, and L. R. Petzold, "Refining the weighted stochastic simulation algorithm," J Chem Phys, vol. 130, no. 17, 2009.
37. C. Winstead, C. Madsen, and C. J. Myers, "iSSA: An incremental stochastic simulation algorithm for genetic circuits," in International Symposium on Circuits and Systems (ISCAS). IEEE, 2010, pp. 553-556.
38. H. Kuwahara, C. Madsen, I. Mura, C. Myers, A. Tejada, and C. Winstead, "Efficient stochastic simulation to analyze targeted properties of biological systems," in Stochastic Control, C. Myers, Ed. Sciyo, 2010, pp. 505-532.