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Publication Detail
An Aspect Oriented Design and Modelling Framework for Synthetic Biology.
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Publication Type:Conference
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Authors:Boeing P, Nesbeth DN, Finkelstein A, Barnes C
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Publication date:12/06/2014
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Name of conference:Sixth International Workshop on Bio-Design Automation (IWBDA) at Boston University.
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Conference place:Boston, MA, USA
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Conference start date:11/06/2014
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Conference finish date:12/06/2014
Abstract
Up until this point, work on synthetic biology has largely
used a component-based metaphor for system construction.
Here we present a design framework that steps away from
this paradigm by utilising aspect oriented software engineering
concepts. Though our approach does not rest upon this,
we think that the notion of concerns is a powerful and biologically
credible way of thinking about systems synthesis. By
casting the design question in terms of concerns, our framework
incorporates and builds upon many features of existing
tools. This framework is written in Python which facilitates
the adoption of standard software engineering tools and the
interaction with existing biological modelling systems. The
benefits of our approach are numerous and include improved
conceptualisation of synthetic biological systems and a design
workflow that iteratively adds complexity by adding
more aspects to the design. We demonstrate the effectiveness
of this framework by creating an oscillator system based
around the repressilator.
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