A formal verification approach to the design of synthetic gene networks

Proceedings of the IEEE Conference on Decision and Control

Volumn , Issue , 2011, Pages 4873-4878

  Yordanov, Boyan ^a   Belta, Calin ^b  

^a MICROSOFT RESEARCH   (United Kingdom)

^b Boston University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

FORMAL VERIFICATION; GENES;

FULLY AUTOMATED; FUNCTIONAL SPECIFICATION; GENETIC NETWORKS; IN-SILICO; SYNTHETIC GENE NETWORK;

SYNTHETIC BIOLOGY;

EID: 84860673255     PISSN: 07431546     EISSN: 25762370     Source Type: Conference Proceeding    
DOI: 10.1109/CDC.2011.6160969     Document Type: Conference Paper

References (25)

1. Registry of Standard Biological Parts. http://partsregistry.org/.
2. M. Antoniotti, F. Park, A. Policriti, N. Ugel, and B. Mishra. Foundations of a query and simulation system for the modeling of biochemical and biological processes. In PSB'03, volume 58, pages 116-127, 2003.
3. G. Batt, C. Belta, and R. Weiss. Temporal Logic Analysis of Gene Networks Under Parameter Uncertainty. IEEE Trans. Autom. Control, 53(Special Issue):215-229, 2008.
4. G. Batt, D. Ropers, H. de Jong, J. Geiselmann, R. Mateescu, M. Page, and D. Schneider. Validation of qualitative models of genetic regulatory networks by model checking: analysis of the nutritional stress response in E. coli. Bioinformatics, 21 Suppl 1:i19-28, June 2005.
5. G. Batt, B. Yordanov, R. Weiss, and C. Belta. Robustness analysis and tuning of synthetic gene networks. Bioinformatics, 23(18):2415-22, Sept. 2007.
6. Y. Cai, M. W. Lux, L. Adam, and J. Peccoud. Modeling structure-function relationships in synthetic DNA sequences using attribute grammars. PLoS computational biology, 5(10):e1000529, Oct. 2009.
7. B. Canton, A. Labno, and D. Endy. Refinement and standardization of synthetic biological parts and devices. Nature biotechnology, 26(7):787-93, July 2008.
8. E. M. Clarke. Model Checking. MIT Press, 1999.
9. H. de Jong. Modeling and Simulation of Genetic Regulatory Systems: A Literature Review. J. Comput. Biol., 9(1):67-103, 2002.
10. H. de Jong. Genetic Network Analyzer: qualitative simulation of genetic regulatory networks. Bioinformatics, 19(3):336-344, 2003.
11. D. Densmore, A. Van Devender, M. Johnson, and N. Sritanyaratana. A platform-based design environment for synthetic biological systems. In TAPIA '09, page 24, New York, New York, USA, 2009. ACM Press.
12. S. Drulhe, G. Ferrari-Trecate, and H. de Jong. The Switching Threshold Reconstruction Problem for Piecewise-Affine Models of Genetic Regulatory Networks. IEEE Trans. Autom. Control, 53(Spe-cial Issue):153-165, 2008.
13. T. Gardner, C. Cantor, and J. Collins. Construction of a genetic toggle switch in Escherichia coli. Nature, 403:339-342, 2000.
14. E. Gasteiger, C. Hoogland, A. Gattiker, S. Duvaud, M. R. Wilkins, R. D. Appel, and A. Bairoch. Protein Identification and Analysis Tools on the ExPASy Server. In J. M. Walker, editor, The Proteomics Protocols Handbook, pages 571-607. Humana Press, 2005.
15. A. L. Juloski, W. Heemels, G. Ferrari-Trecate, R. Vidal, S. Paoletti, and J. H. G. Niessen. Comparison of Four Procedures for the Identification of Hybrid Systems. In Hybrid Systems: Computation and Control, volume 3414 of LNCS, pages 354-369. 2005.
16. T. Knight. Idempotent Vector Design for Standard Assembly of Biobricks Standard Biobrick Sequence Interface, 2003.
17. J. N. Lin and R. Unbehauen. Canonical piecewise-linear approximations. IEEE Trans. Circuits Syst. I, Fundam. Theory Appl., 39(8):697-699, 1992.
18. S. Little, D. Walter, K. Jones, C. Myers, and A. Sen. Analog/Mixed-Signal Circuit Verification Using Models Generated from Simulation Traces. IJFCS, 21(02):191, 2010.
19. R. Milner. Communication and concurrency. Prentice-Hall, 1989.
20. M. Pedersen and A. Phillips. Towards programming languages for genetic engineering of living cells. Journal of The Royal Society Interface, 6(Suppl 4):S437-S450, 2009.
21. P. E. M. Purnick and R. Weiss. The second wave of synthetic biology: from modules to systems. Nature reviews. Molecular cell biology, 10(6):410-22, June 2009.
22. N. Rosenfeld, J. W. Young, U. Alon, P. S. Swain, and M. B. Elowitz. Gene regulation at the single-cell level. Science (New York, N.Y.), 307(5717):1962-5, Mar. 2005.
23. E. Sontag. Nonlinear regulation: The piecewise linear approach. IEEE Trans. Autom. Control, 26(2):346-358, Apr. 1981.
24. B. Yordanov and C. Belta. Formal Analysis of Discrete-Time Piece-wise Affine Systems. IEEE Trans. Autom. Control, 55(12):2834-2840, Dec. 2010.
25. B. Yordanov and C. Belta. A formal verification approach to the design of synthetic gene networks. Technical Report arXiv:1109.1275v1 [cs.SY], Sept. 2011.