A temporal logic approach to modular design of synthetic biological circuits

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 8130 LNBI, Issue , 2013, Pages 164-177

  Bartocci, Ezio ^a   Bortolussi, Luca ^b,c   Nenzi, Laura ^d  

^a VIENNA UNIVERSITY OF TECHNOLOGY   (Austria)

^b UNIVERSITY OF TRIESTE   (Italy)

^c ISTI CNR   (Italy)

^d IMT SCHOOL FOR ADVANCED STUDIES LUCCA   (Italy)

Author keywords

Parameter synthesis; Synthetic biology; Temporal logic

Indexed keywords

INPUT/OUTPUT; LOGICAL GATES; MODULAR DESIGNS; NEW APPROACHES; PARAMETER SPACES; PARAMETER SYNTHESIS; SYNTHETIC BIOLOGY; TARGET CIRCUITS;

BIOLOGY; COMPUTATIONAL METHODS; INTEGRATED CIRCUIT MANUFACTURE; SEMANTICS; SPECIFICATIONS;

TEMPORAL LOGIC;

EID: 84886003781     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-40708-6_13     Document Type: Conference Paper

References (33)

1. Alur, R., Feder, T., Henzinger, T.A.: The benefits of relaxing punctuality. J. ACM (1996)
2. Bartocci, E., Bortolussi, L., Nenzi, L.: Supplementary material for "A temporal logic approach to modular design of synthetic biological circuits". CoRR (2013), http://arxiv.org/abs/1306.4493v1
3. Batt, G., Yordanov, B., Weiss, R., Belta, C.: Robustness analysis and tuning of synthetic gene networks. Bioinformatics 23(18), 2415-2422 (2007)
4. Beal, J., Weiss, R., Densmore, D., Adler, A., Appleton, E., Babb, J., Bhatia, S., Davidsohn, N., Haddock, T., Loyall, J., Schantz, R., Vasilev, V., Yaman, F.: An End-to-End Workflow for Engineering of Biological Networks from High-Level Specifications. ACS Synth. Biol. 1(8), 317-331 (2012)
5. Belta, C., Habets, L.C.G.J.M.: Controlling a class of nonlinear systems on rectangles. IEEE Trans. of Automatic Control 51(11), 1749-1759 (2006)
6. Chen, B.S., Hsu, C.Y., Liou, J.J.: Robust design of biological circuits: evolutionary systems biology approach. J. Biomed. Biotechnol. 2011, 304236 (2011)
7. Dasika, M.S., Maranas, C.D.: OptCircuit: an optimization based method for computational design of genetic circuits. BMC Syst. Biol. 2, 24 (2008)
8. Densmore, D., Anderson, J.C.: Combinational logic design in synthetic biology. In: IEEE International Symposium on Circuits and Systems, ISCAS 2009., pp. 301-304 (2009)
9. Donzé, A.: Breach, A toolbox for verification and parameter synthesis of hybrid systems. In: Touili, T., Cook, B., Jackson, P. (eds.) CAV 2010. LNCS, vol. 6174, pp. 167-170. Springer, Heidelberg (2010)
10. Donzé, A., Clermont, G., Langmead, C.J.: Parameter synthesis in nonlinear dynamical systems: Application to systems biology. Journal of Computational Biology 17(3), 325-336 (2010)
11. Donzé, A., Fanchon, E., Gattepaille, L.M., Maler, O., Tracqui, P.: Robustness analysis and behavior discrimination in enzymatic reaction networks. PLoS One 6(9), e24246 (2011)
12. Donzé, A., Ferrère, T., Maler, O.: Efficient robust monitoring for STL. In: Sharygina, N., Veith, H. (eds.) CAV 2013. LNCS, vol. 8044, pp. 264-279. Springer, Heidelberg (2013)
13. Donzé, A., Maler, O.: Robust satisfaction of temporal logic over real-valued signals. In: Chatterjee, K., Henzinger, T.A. (eds.) FORMATS 2010. LNCS, vol. 6246, pp. 92-106. Springer, Heidelberg (2010)
14. Francois, P., Hakim, V.: Design of genetic networks with specified functions by evolution in silico. PNAS 101(2), 580-585 (2004)
15. Fu, P., Panke, S.: Systems Biology and Synthetic Biology. John Wiley & Sons (2009)
16. Jones, K.D., Konrad, V., Nickovic, D.: Analog property checkers: A ddr2 case study. Formal Methods in System Design 36(2), 114-130 (2010)
17. De Jong, H.: Modeling and simulation of genetic regulatory systems: A literature review. Journal of Computational Biology 9, 67-103 (2002)
18. Karnaugh, M.: The map method for synthesis of combinational logic circuits. Trans. American Institute of Electrical Engineers 72(2) (1953)
19. Knight, T.: Idempotent vector design for standard assembly of biobricks. Technical Report MIT Synthetic Biology Working Group, MIT (2003)
20. Madec, M., Lallement, C., Gendrault, Y., Haiech, J.: Design methodology for synthetic biosystems. In: Proc. of MIXDES, pp. 621-626 (2010)
21. Maler, O., Nickovic, D.: Monitoring temporal properties of continuous signals. In: Lakhnech, Y., Yovine, S. (eds.) FORMATS/FTRTFT 2004. LNCS, vol. 3253, pp. 152-166. Springer, Heidelberg (2004)
22. Marchisio, M.A., Stelling, J.: Automatic design of digital synthetic gene circuits. PLoS Comput. Biol. 7(2), e1001083 (2011)
23. Myers, C.J.: Engineering Genetic Circuits. Chapman & Hall/CRC (2009)
24. Pnueli, A.: The temporal logic of programs. In: IEEE Annual Symposium on Foundations of Computer Science, pp. 46-57 (1977)
25. Rodrigo, G., Jaramillo, A.: AutoBioCAD: Full Biodesign Automation of Genetic Circuits. ACS Synth. Biol. (November 2012)
26. Salah, R.B., Bozga, M., Maler, O.: On timing analysis of combinational circuits. In: Larsen, K.G., Niebert, P. (eds.) FORMATS 2003. LNCS, vol. 2791, pp. 204-219. Springer, Heidelberg (2004)
27. Smith, H.L.: Systems of odes which generate an order preserving flow. A survey of results. SIAM Review 30(1), 87-113 (1988)
28. Szallasi, Z., Stelling, J., Periwal, V.: System Modelling in Cellular Biology: from concepts to nuts and bolts. The Mit Press (2006)
29. Terzer, M., Jovanovic, M., Choutko, A., Nikolayeva, O., Korn, A., Brockhoff, D., Zurcher, F., Friedmann, M., Schutz, R., Zitzler, E., Stelling, J., Panke, S.: Design of a biological half adder. IET Synthetic Biology 1(1-2), 53-58 (2007)
30. Van Kampen, N.G.: Stochastic Processes in Physics and Chemistry. Elsevier (1992)
31. von Dassow, G., Meir, E., Munro, E.M., Odell, G.M.: The segment polarity network is a robust developmental module. Nature (2000)
32. Voy, B.H., Scharff, J.A., Perkins, A.D., Saxton, A.M., Borate, B., Chesler, E.J., Branstetter, L.K., Langston, M.A.: Extracting gene networks for low-dose radiation using graph theoretical algorithms. PLoS Comput. Biol. (2006)
33. Yaman, F., Bhatia, S., Adler, A., Densmore, D., Beal, J.: Automated selection of synthetic biology parts for genetic regulatory networks. ACS Synth. Biol. 1(8), 332-344 (2012)