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Protocols for Implementing an Escherichia coli Based TX-TL Cell-Free Expression System for Synthetic Biology

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

Philipp Boeing¹, Miriam Leon², Darren N Nesbeth³

¹Department of Computer Science, UCL, London WC1E 6BT, UK.

Processes (Basel, Switzerland)

|December 21, 2018

Summary

This study introduces a new synthetic biology design framework using aspect-oriented programming concepts. It separates core design aims from system-wide attributes for more complex biological system construction.

Keywords:

CAD SynBioWeaver aspect-oriented software engineering host context mathematical modelling modularity synthetic biology

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Area of Science:

Synthetic Biology
Computational Biology
Software Engineering

Background:

Traditional synthetic biology relies on a component-based approach.
Incorporating contextual design issues (compositional, host, environmental) is crucial for complex applications.

Purpose of the Study:

To present a novel design framework for synthetic biology using aspect-oriented software engineering concepts.
To move beyond a purely parts-based paradigm by introducing the concept of 'concerns' for system synthesis.

Main Methods:

Utilized aspect-oriented software engineering concepts to separate core design concerns from cross-cutting concerns.
Developed the Python tool SynBioWeaver to implement this framework, enabling the 'weaving' of concerns.
Demonstrated the framework's application through examples including part context and context-dependent circuit design.

Main Results:

The framework successfully separates modular design aims (core concerns) from system-wide attributes (cross-cutting concerns).
Explicit handling of cross-cutting concerns allows for modular integration of contextual information.
SynBioWeaver generated rule, logic, and reaction models from synthetic circuit designs.

Conclusions:

The aspect-oriented approach offers a powerful and biologically credible method for synthetic biology system synthesis.
This framework enhances the modularity and flexibility of designing complex biological systems by managing contextual information.
The SynBioWeaver tool provides a practical implementation for combining core and cross-cutting concerns in synthetic biology design.