AF: SHF: BCSP: Small: Genetic Design Automation

生物学家和工程师正在共同努力发展合成生物学领域。这些研究人员正试图设计合成遗传电路，使细菌能够消耗有毒废物，破坏肿瘤，并产生药物和生物燃料。虽然基因工程的实验方法已经存在了很长时间，但合成生物学增加了一种有原则的设计方法，该方法由标准部件存储库、高级模型抽象和自动化构建过程支持。由于这些是电子设计自动化（EDA）的基石，每年都能设计出更复杂的计算机芯片，因此在遗传设计自动化（GDA）的发展过程中，EDA的经验将被利用是合乎逻辑的。智力优势：该项目将开发一套全面和集成的GDA工具，以支持合成遗传电路的有效分析和设计。这些工具将利用和扩展标准，例如系统生物学标记语言（SBML）和合成生物学开放语言（SBOL），以允许与其他研究人员交换模型和设计。我们的研究将开发新的建模、分析和可视化方法，使研究细菌群体的动态行为成为可能。使用自动模型抽象和并行计算机算法，这些工具的效率将得到提高。PI的设计工具将利用异步（无时钟）集成电路开发的技术。PI将与实验合作者一起验证研究结果。更广泛的影响：由于合成生物学的广泛应用，从药物生产和基因治疗到生物燃料，这项研究的潜在影响是重大的。这项研究将把从事理论和建模的人与从事实验工作的人聚集在一起。该项目还将支持标准扩展的开发，使开发更加复杂的系统成为可能。这些标准以及在这个项目中开发的所有软件将被发布到公共领域。PI致力于通过开发课程材料和与本科生合作，将研究与教育相结合。

Biologists and engineers are working together to develop the field of synthetic biology. These researchers are attempting to design synthetic genetic circuits that enable bacteria to consume toxic waste, destroy tumors, and produce drugs and bio-fuels. While experimental methods for genetic engineering have existed for a long time, synthetic biology adds a principled design methodology that is supported by repositories of standard parts, high-level model abstractions, and an automated construction process. Since these are the cornerstones of electronic design automation (EDA) which has enabled the design of more complex computer chips each year, it is logical that experiences with EDA will be leveraged during the development of genetic design automation (GDA). Intellectual merit: This project will develop a comprehensive and integrated suite of GDA tools to support efficient analysis and design of synthetic genetic circuits. These tools will leverage and extend standards, such as the Systems Biology Markup Language (SBML) and Synthetic Biology Open Language (SBOL), to allow for the exchange of models and designs with other researchers. Our research will develop new modeling, analysis, and visualization methods that enable the study of the dynamic behavior of bacterial populations. The efficiency of these tools will be enhanced using automated model abstraction and parallel computer algorithms. PI's design tools will exploit techniques developed for asynchronous (clock-less) integrated circuits. PI will work with experimental collaborators to validate the research results.Broader Impacts: Due to the wide applications being proposed for synthetic biology ranging from drug production and gene therapies to biofuels, the potential impact of this research is significant. This research will bring together people in theory and modeling with those doing experimental work. This project will also support the development of extensions to standards enabling the development of ever more complex systems. These standards as well as all software developed in this project will be released into the public domain. The PI is committed to the integration of research with education through the development of course materials and working with undergraduates.