Exploring motif-based design patterns for biological computation

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In software engineering, design patterns provide reusable solutions to frequently encountered problems that are independent of the programming language used for implementation. In this project, we explore whether biology also exploits design patterns in the regulatory programs controlling life. Focusing on the role of small regulatory motifs that are known to be enriched in living systems, and which cluster in specific ways, we will employ formal methods to study the cellular functions that motifs support and their robustness to being used in different ways. This information will form the foundation of a computational tool where motifs and their clustering are used as design patterns to synthesise new regulatory programs. To test their generality, several programs implementing broad functionalities (e.g. logic, oscillations and pulse generation) will be verified in living cells with synthetic regulatory components not used by nature. Insight from this work will fuel new approaches for the design of our own biological programs, while also providing a deeper understanding of the way biology harnesses the computational substrate of life itself. This project is a collaboration with the Biological Computation Group at Microsoft Research, Cambridge, UK and falls directly within the EPSRC's strategically important area of Synthetic Biology with potential applications spanning Engineering, Manufacturing the Future, and Heathcare Technologies themes.