LAPSE:2019.0477
Published Article
LAPSE:2019.0477
Towards an Aspect-Oriented Design and Modelling Framework for Synthetic Biology
Philipp Boeing, Miriam Leon, Darren N. Nesbeth, Anthony Finkelstein, Chris P. Barnes
April 8, 2019
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.
Keywords
aspect-oriented software engineering, CAD, host context, mathematical modelling, modularity, SynBioWeaver, synthetic biology
Subject
Suggested Citation
Boeing P, Leon M, Nesbeth DN, Finkelstein A, Barnes CP. Towards an Aspect-Oriented Design and Modelling Framework for Synthetic Biology. (2019). LAPSE:2019.0477
Author Affiliations
Boeing P: Department of Computer Science, UCL, London WC1E 6BT, UK
Leon M: Department of Cell and Developmental Biology, UCL, London WC1E 6BT, UK
Nesbeth DN: Department of Biochemical Engineering, UCL, London WC1E 6BT, UK [ORCID]
Finkelstein A: Department of Computer Science, UCL, London WC1E 6BT, UK
Barnes CP: Department of Cell and Developmental Biology, UCL, London WC1E 6BT, UK [ORCID]
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Journal Name
Processes
Volume
6
Issue
9
Article Number
E167
Year
2018
Publication Date
2018-09-15
Published Version
ISSN
2227-9717
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Original Submission
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PII: pr6090167, Publication Type: Journal Article
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LAPSE:2019.0477
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doi:10.3390/pr6090167
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Apr 8, 2019
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CC BY 4.0
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Apr 8, 2019
 
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Original Submitter
Calvin Tsay
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