Exploring motif-based design patterns for biological computation

在软件工程中，设计模式为经常遇到的问题提供可重用的解决方案，这些问题独立于用于实现的编程语言。在这个项目中，我们探索生物学是否也利用了控制生命的调节程序中的设计模式。关注已知在生命系统中丰富的小调控基序的作用，并以特定的方式聚集，我们将采用形式化方法来研究基序支持的细胞功能及其在不同方式下使用的稳健性。这些信息将构成一个计算工具的基础，其中基序及其聚类被用作设计模式来合成新的调节程序。为了测试它们的通用性，几个实现广泛功能的程序（例如逻辑，振荡和脉冲产生）将在活细胞中与自然界不使用的合成调节成分进行验证。这项工作的见解将为我们自己的生物程序的设计提供新的方法，同时也为生物学利用生命本身的计算基础的方式提供更深入的理解。该项目是与英国剑桥微软研究院的生物计算小组合作的，直接属于EPSRC合成生物学的战略重要领域，具有跨越工程、未来制造和医疗保健技术主题的潜在应用。

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.