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

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 com...

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Autores principales: Boeing, Philipp, Leon, Miriam, Nesbeth, Darren N., Finkelstein, Anthony, Barnes, Chris P.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6296438/
https://www.ncbi.nlm.nih.gov/pubmed/30568914
http://dx.doi.org/10.3390/pr6090167
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author Boeing, Philipp
Leon, Miriam
Nesbeth, Darren N.
Finkelstein, Anthony
Barnes, Chris P.
author_facet Boeing, Philipp
Leon, Miriam
Nesbeth, Darren N.
Finkelstein, Anthony
Barnes, Chris P.
author_sort Boeing, Philipp
collection PubMed
description 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.
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spelling pubmed-62964382018-12-17 Towards an Aspect-Oriented Design and Modelling Framework for Synthetic Biology Boeing, Philipp Leon, Miriam Nesbeth, Darren N. Finkelstein, Anthony Barnes, Chris P. Processes (Basel) Article 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. 2018-09-15 /pmc/articles/PMC6296438/ /pubmed/30568914 http://dx.doi.org/10.3390/pr6090167 Text en http://creativecommons.org/licenses/by/4.0/ This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Boeing, Philipp
Leon, Miriam
Nesbeth, Darren N.
Finkelstein, Anthony
Barnes, Chris P.
Towards an Aspect-Oriented Design and Modelling Framework for Synthetic Biology
title Towards an Aspect-Oriented Design and Modelling Framework for Synthetic Biology
title_full Towards an Aspect-Oriented Design and Modelling Framework for Synthetic Biology
title_fullStr Towards an Aspect-Oriented Design and Modelling Framework for Synthetic Biology
title_full_unstemmed Towards an Aspect-Oriented Design and Modelling Framework for Synthetic Biology
title_short Towards an Aspect-Oriented Design and Modelling Framework for Synthetic Biology
title_sort towards an aspect-oriented design and modelling framework for synthetic biology
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6296438/
https://www.ncbi.nlm.nih.gov/pubmed/30568914
http://dx.doi.org/10.3390/pr6090167
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