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Processes 2018, 6(9), 167; https://doi.org/10.3390/pr6090167

Towards an Aspect-Oriented Design and Modelling Framework for Synthetic Biology

1
Department of Computer Science, UCL, London WC1E 6BT, UK
2
Department of Cell and Developmental Biology, UCL, London WC1E 6BT, UK
3
Department of Biochemical Engineering, UCL, London WC1E 6BT, UK
*
Author to whom correspondence should be addressed.
Received: 29 June 2018 / Revised: 3 September 2018 / Accepted: 12 September 2018 / Published: 15 September 2018
(This article belongs to the Special Issue Computational Synthetic Biology)
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Abstract

Work on synthetic biology has largely used a component-based metaphor for system construction. While this paradigm has been successful for the construction of numerous systems, the incorporation of contextual design issues—either compositional, host or environmental—will be key to realising more complex applications. Here, we present a design framework that radically steps away from a purely parts-based paradigm by using aspect-oriented software engineering concepts. We believe that the notion of concerns is a powerful and biologically credible way of thinking about system synthesis. By adopting this approach, we can separate core concerns, which represent modular aims of the design, from cross-cutting concerns, which represent system-wide attributes. The explicit handling of cross-cutting concerns allows for contextual information to enter the design process in a modular way. As a proof-of-principle, we implemented the aspect-oriented approach in the Python tool, SynBioWeaver, which enables the combination, or weaving, of core and cross-cutting concerns. The power and flexibility of this framework is demonstrated through a number of examples covering the inclusion of part context, combining circuit designs in a context dependent manner, and the generation of rule, logic and reaction models from synthetic circuit designs. View Full-Text
Keywords: synthetic biology; CAD; mathematical modelling; host context; modularity; SynBioWeaver; aspect-oriented software engineering synthetic biology; CAD; mathematical modelling; host context; modularity; SynBioWeaver; aspect-oriented software engineering
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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Boeing, P.; Leon, M.; Nesbeth, D.N.; Finkelstein, A.; Barnes, C.P. Towards an Aspect-Oriented Design and Modelling Framework for Synthetic Biology. Processes 2018, 6, 167.

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