CAREER: Design Automation Infrastructure for DNA Assembly in Synthetic Biology

合成生物学试图设计新的生物系统来解决生物能源、生物治疗和生物修复方面的许多挑战。合成生物学计算工具必须与实验需求紧密结合，才能改变这一领域。这种耦合的一个关键机会是DNA组装过程。该项目解决了在自动化，优化和高效的软件和液体处理工作流程中物理组装DNA的挑战，适用于许多应用和组装化学。该项目将：(1)开发DNA组装协议的软件库；(2)开发应用软件，创建和操作DNA协议和组装图；(3)开发抽象低层液体处理的通用指令集；(4)通过实验建立大型、复杂的遗传调控网络（grn）；(5)将合成生物学扩展到K-12、本科生、研究生和博士后，包括自动化DNA组装。更广泛的影响使广泛使用的开源、免费的DNA组装软件将改变合成生物学提出的整个“设计-构建-测试”周期。工业支持的液体处理机器人操作将统一这一领域，并使创造新的生命系统更便宜、更可靠、更容易获得。该项目的软件将是同类软件中第一个公开可用的。教育外展将继续向代表性不足的群体、本科生和高中生介绍合成生物学，从而培养下一代工程专业的学生。DNA组装教育将提供给国际基因工程机器（iGEM）软件部门。“合成生物学软件工具注册”将扩展为生物设计自动化软件的社区资源。最后，国际生物设计自动化研讨会（IWBDA）将扩大其教育使命，提供额外的DNA组装教程，博士论坛和正式的指导计划，以匹配学生与学术和工业导师。

Intellectual MeritSynthetic biology attempts to design novel biological systems to address a number of challenges in bioenergy, biotherapeutics, and bioremediation. Synthetic biology computational tools must be closely coupled to experimental needs to transform the field. A critical opportunity for this coupling is the DNA assembly process. This project addresses the challenge of physically assembling DNA in an automated, optimized and efficient software and liquid handling workflow for a number of applications and assembly chemistries. This project will: (1) Develop a software library for DNA assembly protocols; (2) develop application software to create and manipulate DNA protocol and assembly graphs; (3) develop a common instruction set to abstract low level liquid handling; (4) experimentally create large, complex genetic regulatory networks (GRNs); and (5) expand synthetic biology outreach to K-12, undergraduate, graduate, and postdoctoral students to include automated DNA assembly. Broader ImpactsMaking open source, freely available DNA assembly software widely employed will change the entire "design-build-test" cycle proposed by synthetic biology. Industrially supported liquid handling robotic operations will unify the domain and make the creation of novel living systems cheaper, more reliable, and more accessible. The project's software will be the first of its kind publicly available. Educational outreach will be continued to introduce synthetic biology to underrepresented groups, undergraduates, and high school students thus training a future generation of engineering students. DNA assembly education will be made available to the International Genetically Engineered Machine (iGEM) software division. A "Registry of Synthetic Biology Software Tools" will be expanded to provide a community resource for bio-design automation software. Finally, the International Workshop on Bio-Design Automation (IWBDA) will expand its educational mission to provide additional DNA assembly tutorials, a PhD forum, and a formal mentorship program to match students with academic and industrial mentors.