Experimentally driven verification of synthetic biological circuits

Proceedings -Design, Automation and Test in Europe, DATE

Volumn , Issue , 2012, Pages 236-241

  Yordanov, Boyan ^c   Appleton, Evan ^a   Ganguly, Rishi ^a   Gol, Ebru Aydin ^a   Carr, Swati Banerjee ^a   Bhatia, Swapnil ^b   Haddock, Traci ^b   Belta, Calin ^a   Densmore, Douglas ^a,b  

^a BOSTON UNIVERSITY   (United States)

^b Boston University   (United States)

^c MICROSOFT RESEARCH   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

HIGH LEVEL LANGUAGES; MODEL CHECKING; SPECIFICATIONS; SYNTHETIC BIOLOGY; TEMPORAL LOGIC; TIMING CIRCUITS;

ANALYSIS TECHNIQUES; BEHAVIORAL SPECIFICATION; EXPERIMENTAL PROCEDURE; FINITE ABSTRACTION; GENETIC REGULATORY NETWORKS; LINEAR TEMPORAL LOGIC; SYNTHESIS TOOL; SYNTHETIC GENE CIRCUITS;

ELECTRIC NETWORK ANALYSIS;

EID: 84862075811     PISSN: 15301591     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/date.2012.6176468     Document Type: Conference Paper

References (24)

1. E. Andrianantoandro, S. Basu, D. K. Karig, and R. Weiss, "Synthetic biology: new engineering rules for an emerging discipline," Mol. Sys. Biol., vol. 2, 2006.
2. D.-K. Ro, E. M. Paradise, M. Ouellet, K. J. Fisher, K. L. Newman, J. M. Ndungu, K. A. Ho, R. A. Eachus, T. S. Ham, J. Kirby, and et al., "Production of the antimalarial drug precursor artemisinic acid in engineered yeast." Nature, vol. 440, no. 7086, pp. 940-943, 2006.
3. J. D. Keasling and H. Chou, "Metabolic engineering delivers next-generation biofuels," Nature Biotech., vol. 26, no. 3, pp. 298-299, 2008.
4. Z. Xie, L. Wroblewska, L. Prochazka, R. Weiss, and Y. Benenson, "Multi-input rnai-based logic circuit for identification of specific cancer cells," Science, vol. 333, no. 6047, pp. 1307-1311, 2011.
5. M. J. Dunlop, J. D. Keasling, and A. Mukhopadhyay, "A model for improving microbial biofuel production using a synthetic feedback loop," Systems and synthetic biology, vol. 4, no. 2, pp. 95-104, 2010.
6. J. Monod and F. Jacob, "Teleonomic mechanisms in cellular metabolism, growth, and differentiation," in Cold Spring Harbor Symposia on Quantitative Biology, vol. 26, 1961, pp. 389-401.
7. T. S. Gardner, C. R. Cantor, and J. J. Collins, "Construction of a genetic toggle switch in escherichia coli." Nature, vol. 403, no. 6767, 2000.
8. E. M. Judd, M. T. Laub, and H. H. McAdams, "Toggles and oscillators: new genetic circuit designs," BioEssays, vol. 22, no. 6, 2000.
9. J. Hasty, M. Dolnik, V. Rottschäfer, and J. J. Collins, "Synthetic gene network for entraining and amplifying cellular oscillations," Phys. Rev. Lett., vol. 88, p. 148101, Mar 2002.
10. A. E. Friedland, T. K. Lu, X. Wang, D. Shi, G. Church, and J. J. Collins, "Synthetic gene networks that count," Science, vol. 324, no. 5931, 2009.
11. A. Tamsir, J. J. Tabor, and C. A. Voigt, "Robust multicellular computing using genetically encoded NOR gates and chemical 'wires'," Nature, vol. 469, pp. 212-215, Jan. 2011.
12. C. J. Myers, Engineering Genetic Circuits. Chapman and Hall, 2009.
13. J. C. Anderson, C. A. Voigt, and A. P. Arkin, "Environmental signal integration by a modular and gate," Molecular Systems Biology, vol. 3, no. 133, p. 133, 2007.
14. P. E. M. Purnick and R. Weiss, "The second wave of synthetic biology: from modules to systems," Nat Rev Mol Cell Biol, 2009.
15. B. Alberts, A. Johnson, J. Lewis, M. Raff, K. Roberts, and P. Walter, Molecular biology of the cell, 4th ed. Garland Science, 2002.
16. R. M. Hill, "Evaluation of susceptibility functions," physica status solidi (b), vol. 103, no. 1, pp. 319-328, 1981.
17. R. Ghamari, B. Stanton, T. Haddock, S. Bhatia, K. Clancy, T. Peterson, C. Voigt, and D. Densmore, "Applying hardware description languages to genetic circuit design," in Proc. of IWBDA, 2011.
18. K. Keutzer, "Dagon: technology binding and local optimization by dag matching," in Proc. of the 24th ACM/IEEE Design Automation Conference, ser. DAC '87. New York, NY, USA: ACM, 1987.
19. E. M. Clarke, Model Checking. MIT Press, 1999.
20. B. Yordanov and C. Belta, "A Formal Verification Approch to the Design of Synthetic Gene Networks," in Proceedings of the 50th IEEE Conference on Decision and Control (CDC), Orlando,FL, Dec. 2011.
21. -, "Formal Analysis of Discrete-Time Piecewise Affine Systems,"IEEE Transactions on Automatic Control, vol. 55, no. 12, Dec. 2010.
22. S. Drulhe, G. Ferrari-Trecate, and H. de Jong, "The Switching Threshold Reconstruction Problem for Piecewise-Affine Models of Genetic Regulatory Networks," IEEE Transactions on Automatic Control, vol. 53, no. Special Issue, pp. 153-165, 2008.
23. 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 escherichia coli," Bioinformatics, vol. 21, no. suppl 1, 2005.
24. R. Milner, Communication and concurrency. Prentice-Hall, 1989.