Abstract
The field of synthetic biology is looking forward principles and tools to make the biological devices inter-operable and programmable with, as long-term goal, the design of de-novo synthetic genome [14].
In this endeavour, computer-aided-design (CAD) environments play a central role by providing the required features to engineer systems: specification, analysis, and tuning [9,17,20,12]. Scaling up the complexity of devices necessitates to harness the development of CAD environments based on an automatic conversion of the design specification into DNA sequences, like compilers for programming languages.
Currently, domain specific languages for synthetic biology mainly address the design of structure, namely the biological component assembly, where programming relates to DNA sequence description. Although the structural description is an indispensable step in the design-to-manufacture chain and provide an accurate description of devices, the required size of program for sequence description likely makes the task error-prone and infeasible.
In this context, high level programming language for synthetic biology is announced as a key milestone for the second wave of synthetic biology to overcome the complexity of such large synthetic system design.
We have proposed a domain specific language, Gubs [5] (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 (trigged by the environment for example) that possibly alter the behaviour of the programmed devices.
Here we describe in detail the compilation framework,Ggc(Gubs Genetic Compiler), an automated compiler translating a program into biological components usable in living cells. The compilation process assemble biological components from a database to behaviourally cover the behaviour described by a program.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Aho, A., Lam, M., Ullman, J., Sethi, R.: Compilers: Principles, Techniques, and Tools. Pearson Education (1986)
Aho, A., Ullman, J.: Principles of Compiler Design. Addison-Wesley Series in Computer Science and Information Processing. Addison-Wesley Publ. (1977)
Baader, F., Snyder, W.: Unification Theory. In: Robinson, A., Voronkov, A. (eds.) Handbook of Automated Reasoning, ch. 8, pp. 441–523. The MIT Press (2001)
Baader, F., Büttner, W.: Unification in commutative idempotent monoids. Theoretical Computer Science 56, 345–352 (1988)
Basso-Blandin, A., Delaplace, F.: Gubs, a behavior-based language for open system dedicated to synthetic biology. CoRR abs/1206.6098 (2012)
Basso-Blandin, A., Delaplace, F.: Gubs, a behaviour-based language for design in synthetic biology. Sci. Ann. Comp. Sci. 23(1), 1–38 (2013)
Beal, J., Bachrach, J.: Cells Are Plausible Targets for High-Level Spatial Languages. In: 2008 Second IEEE International Conference on Self-Adaptive and Self-Organizing Systems Workshops, pp. 284–291 (October 2008)
Beal, J., Lu, T., Weiss, R.: Automatic Compilation from High-Level Biologically-Oriented Programming Language to Genetic Regulatory Networks. PLoS ONE 6(8), e22490 (2011)
Bilitchenko, L., Liu, A., Cheung, S., Weeding, E., Xia, B., Leguia, M., Anderson, J.C., Densmore, D.: Eugene–A Domain Specific Language for Specifying and Constraining Synthetic Biological Parts, Devices, and Systems. PloS One 6(4), e18882 (2011)
Cerrito, S., Cialdea Mayer, M.: A tableaux based decision procedure for a broad class of hybrid formulae with binders. In: Brünnler, K., Metcalfe, G. (eds.) TABLEAUX 2011. LNCS, vol. 6793, pp. 104–118. Springer, Heidelberg (2011)
Clancy, K., Voigt, C.A.: Programming Cells: Towards an Automated Genetic Compiler. Current Opinion in Biotechnology 21(4), 581–572 (2010)
Czar, M.J., Cai, Y., Peccoud, J.: Writing DNA with GenoCAD. Nucleic Acids Research 37(Web Server issue), W40–W47 (2009)
Elowitz, M.B., Leibler, S.: A synthetic oscillatory network of transcriptional regulators. Nature 403(6767), 335–338 (2000)
Gibson, D., Glass, J., Lartigue, C., Noskov, V., Chuang, R., Algire, M., Benders, G., Montague, M., Ma, L., Moodie, M., et al.: Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome. Science 329(5987), 52 (2010)
Knight, K.: Unification: a multidisciplinary survey. ACM Computing Surveys 21(1), 93–124 (1989)
Lewis, D.: Causation as Influence. The Journal of Philosophy 97(4), 182–197 (2000)
Pedersen, M.P.: Towards Programming Languages for Genetic Engineering of Living Cells. Journal of the Royal Society, Interface 6(suppl. 4), S437–S450 (2009)
Regot, S., Macia, J., Conde, N., Furukawa, K., Kjellén, J., Peeters, T., Hohmann, S., de Nadal, E., Posas, F., Solé, R.: Distributed Biological Computation with Multicellular Engineered Networks. Nature 469(7329), 207–211 (2011)
Shetty, R., Endy, D., Knight, T.: Engineering BioBrick vectors from BioBrick parts. Journal of Biological Engineering 2, 5+ (2008)
Umesh, P., Naveen, F., Rao, C., Nair, S.: Programming languages for synthetic biology. Systems and Synthetic Biology 4(4), 265–269 (2010)
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2014 Springer International Publishing Switzerland
About this paper
Cite this paper
Basso-Blandin, A., Delaplace, F. (2014). GUBS a Language for Synthetic Biology: Specification and Compilation. In: Ibarra, O., Kari, L., Kopecki, S. (eds) Unconventional Computation and Natural Computation. UCNC 2014. Lecture Notes in Computer Science(), vol 8553. Springer, Cham. https://doi.org/10.1007/978-3-319-08123-6_4
Download citation
DOI: https://doi.org/10.1007/978-3-319-08123-6_4
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-08122-9
Online ISBN: 978-3-319-08123-6
eBook Packages: Computer ScienceComputer Science (R0)