Published in Volume XXIII, Issue 1, 2013, pages 1-38, doi: 10.7561/SACS.2013.1.1

Authors: A. Basso-Blandin, F. Delaplace


In this article, we propose a domain specific language, GUBS (Genomic Unified Behaviour Specification), dedicated to the behavioural specification of synthetic biological devices, viewed as discrete open dynamical systems. GUBS is a rule-based declarative language. In contrast to a closed system, a program is always a partial description of the behaviour of the system. The semantics of the language accounts the existence of some hidden non-specified actions that possibly alter the behaviour of the programmed devices.
The compilation framework follows a scheme similar to automated theorem proving, aiming at improving synthetic biological design safety.

Full Text (PDF)


[1] P.J. Ashenden. The Designer’s Guide to VHDL. Morgan Kaufmann Publishers, 2008.

[2] F. Baader and W. Snyder. Unification Theory. In Andrei Robinson, Alan and Voronkov, editor, Handbook of automated reasoning, chapter 8, pages 441–533. The MIT Press, 2001. .

[3] S. Basu, Y. Gerchman, C. H. Collins, F. H. Arnold, and R. Weiss. A Synthetic Multicellular System for Programmed Pattern Formation. Nature, 434(7037):1130–1134, April 2005. .

[4] J. Beal, T. Lu, and R. Weiss. Automatic Compilation from High-Level Biologically-Oriented Programming Language to Genetic Regulatory Networks. PLoS ONE, 6(8):e22490, August 2011. .

[5] 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, 6(4):e18882, January 2011. .

[6] P. Blackburn, J. F. A. K. van Benthem, and F. Wolter. Handbook of Modal Logic, Volume 3 (Studies in Logic and Practical Reasoning). Elsevier Science Inc., December 2006. .

[7] T. Bra¨uner. Hybrid Logic and Its Proof-Theory. Springer, 2011. .

[8] Y. Cai, M. W Lux, L. Adam, and J. Peccoud. Modeling Structurefunction Relationships in Synthetic DNA Sequences Using Attribute Grammars. PLoS Computational Biology, 5(10):e1000529, 2009. .

[9] L. Calzone, F. Fages, and S. Soliman. BIOCHAM: An Environment for Modeling Biological Systems and Formalizing Experimental Knowledge. Bioinformatics, 22(14):1805–1807, July 2006. .

[10] S. Cerrito and M. C. Mayer. A tableaux based decision procedure for a broad class of hybrid formulae with binders. In Proceedings of the 20th International Conference on Automated Reasoning with Analytic Tableaux and Related Methods, TABLEAUX’11, pages 104–118. Springer-Verlag, 2011. .

[11] F. Ciocchetta and J. Hillston. Bio-PEPA: A Framework for the Modelling and Analysis of Biological Systems. Theoretical Computer Science, 410(33-34):3065–3084, August 2009. .

[12] K. Clancy and C. A Voigt. Programming Cells: Towards an Automated Genetic Compiler. Current Opinion in Biotechnology, 21(4):572–581, August 2010. .

[13] C. A. Coello. A comprehensive survey of evolutionary-based multiobjective optimization techniques. Knowledge and Information systems, 1(3):269–308, 1999. .

[14] M. J Czar, Y. Cai, and J. Peccoud. Writing DNA with GenoCAD. Nucleic Acids Research, 37(Web Server issue):W40–W47, July 2009. .

[15] M. D’Agostino, D. M. Gabbay, R. H¨ahnle, and J. Posegga, editors. Handbook of Tableau Methods. Springer Netherlands, Dordrecht, 1999. .

[16] V. Danos, J. Feret, W. Fontana, R. Harmer, and J. Krivine. Rule-based modelling of cellular signalling. In Proceedings of CONCUR’07, pages 17–41, 2007. 36 A. Basso-Blandin, F. Delaplace

[17] F. Delaplace, H. Klaudel, and A. Cartier-Michaud. Discrete Causal ModelView of Biological Networks. In Proceedings of the 8th International Conference on Computational Methods in Systems Biology – CMSB ’10, pages 4–13, New York, New York, USA, September 2010. ACM Press. .

[18] F. Fages. Associative-commutative unification. J. Symb. Comput., 3(3):257–275, June 1987. .

[19] P. Francois and V. Hakim. Design of genetic networks with specified functions by evolution in silico. PNAS, 101(2):580–585, 2004. .

[20] M. R. Garey and D. S. Johnson. Computers and Intractability: A Guide to the Theory of NP-Completeness. W. H. Freeman & Co., 1979 .

[21] A. Ghosh and S. Dehuri. Evolutionary algorithms for multi-criterion optimization: A survey. International Journal of Computing & Information Sciences, 2(1):38–57, 2004 .

[22] J.L. Giavitto, O. Michel, J. Cohen, and A. Spicher. Computations in space and space in computations. In Unconventional Programming Paradigms, volume 3566 of Lecture Notes in Computer Science, pages 137–152. Springer Berlin / Heidelberg, 2005. .

[23] D.G. Gibson, J.I. Glass, C. Lartigue, V.N. Noskov, R.Y. Chuang, M.A. Algire, G.A. Benders, M.G. Montague, L. Ma, M.M. Moodie, and al. Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome. Science, 329(5987):52–56, May 2010. .

[24] D. Hume. A Treatise of Human Nature, Being an Attempt to Introduce the Experimental Method of Reasoning into Moral Subjects. Clarendon Press, 1739. .

[25] D. Kapur and P. Narendran. NP-completeness of the set unification and matching problems. In 8th International Conference On Automated Deduction, volume 230 of Lecture Notes in Computer Science, pages 489–495, 1986. GUBS, a Behaviour-Based Language for Design in Synthetic Biology 37

[26] D. Lewis. Causation as Influence. The Journal of Philosophy, 97(4):182– 197, 2000. .

[27] T. K Lu, A. S Khalil, and J. J Collins. Next-generation Synthetic Gene Networks. Nature Biotechnology, 27(12):1139–1150, 2009. .

[28] M. P. Pedersen. Towards Programming Languages for Genetic Engineering of Living Cells. Journal of the Royal Society, Interface, 6 Suppl 4:S437–S450, 2009. .

[29] C. Priami, A. Regev, E. Shapiro, and W. Silverman. Application of a Stochastic Name-passing Calculus to Representation and Simulation of Molecular Processes. Information Processing Letters, 80(1):25–31, October 2001. .

[30] P. E M Purnick and R. Weiss. The Second Wave of Synthetic Biology: From Modules to Systems. Nature Reviews. Molecular Cell Biology, 10(6):410–422, 2009. .

[31] S. Regot, J. Macia, N. Conde, K. Furukawa, J. Kjell´en, T. Peeters, S. Hohmann, E. de Nadal, F. Posas, and R. Sol´e. Distributed Biological Computation with Multicellular Engineered Networks. Nature, 469(7329):207–211, 2011. .

[32] G. Rodrigo, J. Carrera, T. E. Landrain, and A. Jaramillo. Perspectives on the automatic design of regulatory systems for synthetic biology. FEBS letters, 586(15):2037–2042, July 2012. .

[33] G. Rodrigo and A. Jaramillo. AutoBioCAD: full biodesign automation of genetic circuits. ACS synthetic biology, 2(5):230–236, May 2013. .

[34] H. M. Salis, E. Mirsky, and C. Voigt. Automated design of synthetic ribosome binding sites to control protein expression. Nature biotechnology, 27(10):946–950, 2009. .

[35] M.E. Stickel. A unification algorithm for associativecommutative functions. Journal of the ACM, 28(3):423–434, 1981. 38 A. Basso-Blandin, F. Delaplace

[36] F. Stolzenburg. An algorithm for general set unification and its complexity. Journal of Automated Reasoning, 22(1):45–63, 1999. .

[37] D. E. Thomas and P. Moorby. The Verilog Hardware Description Language. Kluwer Academic Publishers, 1998. .

[38] P. Umesh, F. Naveen, C.U.M. Rao, and S.A. Nair. Programming languages for synthetic biology. Systems and Synthetic Biology, 4(4):265– 269, 2010. .

[39] H. Ye, M. Daoud-El Baba, R-W. Peng, and M. Fussenegger. A Synthetic Optogenetic Transcription Device Enhances Bloodglucose Homeostasis in Mice. Science, 332(6037):1565–1568, 2011. .

[40] A. Zhou, B.Y. Qu, H. Li, S.Z. Zhao, P. N. Suganthan, and Q. Zhang. Multiobjective evolutionary algorithms: A survey of the state of the art. Swarm and Evolutionary Computation, 1(1):32–49, 2011. .


  title={GUBS, a Behaviour-Based Language for Design in Synthetic Biology},
  author={A. Basso-Blandin and F. Delaplace},
  journal={Scientific Annals of Computer Science},
  organization={``A.I. Cuza'' University, Iasi, Romania},
  publisher={``A.I. Cuza'' University Press}