Design methodology and modeling of synthetic biosystems

• Autorzy: Madec M. , Gendrault Y. , Lallement C. , Haiech J.
• Języki publikacji: EN

Abstrakty

EN

Synthetic biology is an emerging area of biotechnology for which main applications are in the field of Health and Environment However, it suffers from a lack of adapted CAD tools and methodology in order to fulfill efficiently and quickly the needs of these domains. In this paper, the strong relationship between circuits design in microelectronics and synthetic biology is highlighted. Most of synthesized biodevices behavior can be interpreted and modeled by BioLogic gate. As a consequence, bigger biosystems might be designed using methods and tools borrowed from microelectronics. These similarities lead to an efficient methodology, using microelectronics design flow, tools and methods, which should allow a top-down approach in synthetic biosystem design. The methodology is illustrated on the design of a biosystem (a T-flipflop), using top-down approach and HDL modeling languages. The proposed methods and their evolution prospects are discussed at the end of the paper,

Słowa kluczowe

EN

synthetic biology; design flow; top-down approach; HDL; biological gates; biological flip-flop

PL

syntetyczna biologia; projektowany przypływ; biologiczny przerzutnik

• Wydawca: Lodz University of Technology. Department of Microelectronics and Computer Science
• Czasopismo: International Journal of Microelectronics and Computer Science
• Rocznik: 2010
• Tom: Vol. 1, nr 2
• Strony: 147--155
• Opis fizyczny: Bibliogr. 40 poz.

Twórcy

autor

Madec M.

autor

Gendrault Y.

autor

Lallement C.

autor

Haiech J.

• Institut d`Electronique du Solide el des Systemes (InESS), UMR 7163 (Centre National de Recherches Scientifiques / Universite de Strasbourg), 23 rue du Loess, 67037 STRASBOURG CEDEX 02, France

Bibliografia

• [1] R. Endy, "Foundations for engineering biology," Nature, vol. 438, no. 24, pp. 449-453, 2005.
• [2] F. Reza, K, Chandran, M. Feltz, A. Heinz, E. Josephs, P, O'Brien, B. V. Dyke, H. Chung, S. Indurkhya, N. Lakhani, J. Lee. S. Lin, N. Tang, T. LaBean, L. You, F. Yuan, and J. Tian, "Engineering novel synthetic biological system," IET Synthetic Biology, vol. 1, pp. 48-52, 2007.
• [3] Z. Ying. C. Zhou, and O. Oglesby, "Large-scale drag function prediction by integrating qid d2 in biospice," in Computational Systems Bioinformatics Conference, pp. 118-122, 2002.
• [4] J. Aleksic, F. Bizzari. Y. Cai, B. Davidson, K. de Mora, S. Ivakhno, S. Seshasayee, J. Nicholson. J. Wilson, A. Elfick, C. French, L. Kozma-Bognar, H. Ma, and A. Millar, "Development of a novel biosensor for the detection of arsenic in drinking water," IET Synthetic biology, vol. 1, pp. 87-90, 2007.
• [5] G. van den Bogaart, V. Krasnikov, and D. Poolman, "Dual-color fluorescence-burst analysis to probe protein efflux through the mechanosensitive channel mscl," Biophysics Journal, vol. 94, no. 4, pp. 1233-1240, 2007.
• [6] T. F. Knight, "Idempotent vector design for standard assembly of biobricks," MIT Synthetic Biology Working Group.
• [7] The BioBrick Fundation website. http://bbf.openwetware.org.
• [8] B. Kramer, C. Fischer, and M. Fussenegger, "Biologic gates enable logical transcription control in mammalian cells," Biotechnology and Bioengineering, vol. 87, no. 4, pp. 478-484, 2004.
• [9] J. R. Gibson, Electronic Logic Circuits, ed. Butterworth-Heinemann Ltd, 1992.
• [10] EDA Industry Working Groups, http://www.vhdl.org.
• [11] P. Ashenden, The Designer Guide to VHDL. ed. Morgan Jaufmann Publisher Inc. 2008.
• [12] Verilog dot com website. http://www.verilog.com.
• [13] P. Ashenden, Digital Design Verilog: An Embedded Systems Approach Using Verilog. ed. Morgan Jaufmann Publisher Inc., 2007.
• [14] System C website http://www.systemC.org.
• [15] T. Grotker, S. Liao, G. Martin, and S. Swan, System Design With SystemC. ed. Kluwer Academic Publishers, 2002.
• [16] Register of standard biological parts, http://www.partsregistry.org.
• [17] COPASI homepage. http://www.copasi.org.
• [18] S. Hoops, S. Sahle, R. Gauges, C. Lee, J Pahle. N. Simus, M. Singhal, L. Xu, P. Mendes, and U. Kummer, "Copasi: a complex pathway simulator," Bioinformatics, vol. 22, no. 24, pp. 3067-3074, 2006.
• [19] L. Loew and J. Schaff, "The virtual cell; a software environment for computational cell biology," TRENDS in Biotechnology, vol. 19, no. 10. pp. 401-407. 2001.
• [20] The Virtual Cell homepage. http://www.ibiblio.org/virtualcell.
• [21] D. Gerber and M. Fussenegger, "Mammalian synthetic biology; Engineering of sophisticated gene network," Journal of Biotechnology, vol. 130, pp. 329-345, 2007.
• [22] R. Weiss, G. Homsy, and T. K. Jr., 'Toward in vivo digital circuits," in DIMACS Workshop on evolution as computation towards in vivo digital circuits, 2005.
• [23] M. Simpson, C. Cox, G. Peterson, and G. Sayler, "Engineering in the biological substrate: information processing in genetics circuits,"Proceedings oj the IEEE, vol. 92, no. 5, pp. 848-863, 2004.
• [24] F. Pecheux, C. Lallement, and A. Vachous. "Vhdl-ams and verilog-ams as alternative hardware description languages for efficient modeling of multidiscipline systems," IEEE Transactions on Integrated Circuits and Systems, vol. 24, no, 2, pp. 204-225, 2005.
• [25] M, Madec, C. Lallement, K. Karstens, S. Dittman. M. Gersbacher, R. Sorg, M. Wild, M. Muller. P. Bourguine, M, Donzeau, and J. Haiech, "Synthetic biology and microelectronics; a similar design flow," in Proc. of Joint 7th International IEEE NEWCAS-TAISA 2009 Conference, Toulouse (France), June 28 July 1, 2009.
• [26] R. Krishnan and C. Purdy, "Circuit development using biological components: Principles, models and experimental feasibility source," Analog Integrated Circuits and Signal Processing, vol. 56, no. 1-2, pp. 153-161, 2008.
• [27] M. Madec, Y. Gendrault, C. Lallement, and J. Haiech, "Design methodology for synthetic biosystems," in 18th IEEE International Conference on Mixed Design of Integrated Circuits and Systems (MIXDES), Wrocław (Poland), 2010.
• [28] CADENCE website. http://www.cadence.com.
• [29] Intel website. http://www.intel.com.
• [30] Y. Hervé, "Virtual prototyping in vhdl-ams," in IEEE International Conference on Industrial Technology, 2003.
• [31] Y. Hervé and P. Desgreys, "Functional virtual prototyping design flow and vhdl-ams," in Forum on Specification and Design Languages, 2006.
• [32] P. Poure and S. Weber, "Vhdl-ams modeling for virtual prototyping of very large scale integration architecture for direct torque control of an ac machine," in 32nd IEEE Annual Conference on Industrial Electronics, 2006.
• [33] A. Vachoux, C. Grimm, and K. Einwich, "Towards analog and mixed-signal soc design with systemc-ams," in IEEE International Workshop on Electronic Design. Test and Applications (DELTA), 2004.
• [34] A. Vachoux, C. Grimm, and K. Einwieh, "Analog and mixed signal modelling with systemc-ams," in IEEE International Symposium on Circuits and Systems (ISCAS), 2003.
• [35] M. Vasilevski, F. Pecheux, N. Beilleau, H. Aboushady, and K. Einwich, "Modeling and refining heterogeneous systems with systemc-ams: Application to wsn," in Proceedings IEEE Date 2008 Conference, Munich, 2008.
• [36] F, Pecheux, M. Madec, and C. Lallement, "Is systemc-ams an appropriate promoter for the modeling and simulation of bio-compatible systems?," in IEEE International Symposium on Circuits and Systems (ISCAS), Paris (France), 2010.
• [37] T. Sera, "Zinc-finger-based articifial transcription factors and their application," Advanced Drug Delivery Reviews, vol. 61, pp. 513-526, 2009.
• [38] M, Terzer. M. Jovanovic, A. Choutko, O, Nikolayeva, A. Korn, D. Brockhoff, F. Zurcher, M. Friedmann, R. Schutz, E. Zitzler, J. Stelling, and S, Panke, "Design of a biological half adder," IET Synthetic Biology, vol. 1, pp. 53-58, 2007.
• [39] International Genetically Engineered Machine (iGEM) competition homepage. http://igem.org.
• [40] ESBS team homepage for iGEM 2008. http://2008.igem.org/Team:ESBS-Strasbourg.