CAREER: Integrative Synthetic Biology: A Scalable Framework for Modular Multilevel Design

在用于系统级的合成电路设计的计算机辅助工具领域中，最近取得了显著的进展。虽然大多数方法侧重于提供可视化和仿真功能供用户探索，但缺乏一个非常需要的端到端集成框架，能够基于用户定义的约束条件自动优化合成电路。拟议项目的目标是开发一个综合合成生物学框架和工具，用于混合信号合成电路的自动化系统级设计。该框架将作为合成生物学家的计算工具，并将为系统级合成电路设计奠定理论基础。该项目将探索一个具有近似和精确技术的全球优化平台，以找到任何给定配置的最佳部件集，这将为解决方案的最佳性、重复性或范围提供保证。这项工作将通过使用图查询和图划分算法来探索将过去经过验证的设计与手头电路进行匹配，这些算法将把原始设计转换为可有效求解的等价图。这将促进模块化和可重复使用的设计，并导致可实现的复杂性水平的提高和建造成本的降低。

There have been recent and notable advances in the field of computer-aided tools for synthetic circuit design at the system level. While most approaches focus on providing visualization and simulation capabilities for the users to explore, there is a lack of a much needed end-to-end integrated framework capable of automated optimization of synthetic circuits based on user-defined constraints. The goal of the proposed project is to develop an integrated synthetic biology framework and tools for the automated systems-level design of mixed-signal synthetic circuits. This framework will serve as a computational tool for synthetic biologists and will lay the theoretical foundations for system level synthetic circuit design. The project will explore a global optimization platform with both approximate and exact techniques for finding the optimal set of parts for any given configuration, which will provide guarantees on the optimality, reproducibility or bounds of the solution. This work will explore matching past validated designs to the circuit at hand, by employing graph-querying and graph partitioning algorithms that will transform the original design to equivalent graphs which can be solved efficiently. This will promote modular and reusable designs, and result in an increase in the level of achievable complexity and a decrease in the cost of construction.