Collaborative Research: CNS Core: Small: Efficient Ways to Enlarge Practical DNA Storage Capacity by Integrating Bio-Computer Technologies

合作研究：中枢神经系统核心：小型：通过集成生物计算机技术扩大实用 DNA 存储容量的有效方法

• 批准号: 2343863
• 负责人: Bingzhe Li
• 金额: $ 30万
• 依托单位: University of Texas at Dallas
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-08-01 至 2025-06-30
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2343863&HistoricalAwards=false
• 关键词: Collaborative; Research; CNS; Core; Small

The world's digital data increases immensely each year. By 2025, it will reach 175 Zettabytes (ZB). Most human activities are recorded in digital format today. However, data recorded in digital media cannot last very long. Therefore, valuable data cannot be preserved today with our current storage technologies and devices for a long duration (beyond 15 years). The capacity of existing storage media cannot keep up with the growth of the amount of digital data. Also, all storage devices could become obsolete within several years, so the data stored are vulnerable as they perish as time goes by. Therefore, synthetic deoxyribonucleic acid (DNA) becomes an attractive alternative storage medium due to its high density and long durability. These characteristics of DNA storage make it a great candidate for archival storage. However, the preliminary study of the project indicates the practical DNA storage tube capacity based on current technologies is only around 250GB, which is much less than the expected capacity. The major reason is that primer-payload collisions in DNA storage can drastically reduce the number of usable primers in a tube as the data payload size increases. The use of primers is essential for random access to DNA data. In this project, an interdisciplinary team is formed to investigate both bio and storage approaches that can improve the scalability of DNA storage. Among the many factors that can scale up DNA storage, the project plans to investigate the following questions: 1) How to identify more primers for a primer library to be used in DNA storage? 2) Given a primer library, how to efficiently allocate payload data to avoid primer-payload collisions to increase DNA storage capacity? and 3) How to effectively use a popular technique called data deduplication in data backup applications to further increase the storage capability of DNA storage? With a deep understanding of molecular biology and computer storage technologies and systems, this interdisciplinary team fosters several innovative ways of understanding the fundamental issues of DNA storage and will develop necessary genome engineering, sequencing techniques, software, and new algorithms to optimize the process of converting the world's digital data to DNA storage for archiving and preserving today's valuable digital data for hundreds of years in the future. The goal of storing the world's digital data in DNA storage to preserve all human activities can move one step closer with this project. The potential research outcomes of the project include fostering the advancement of bioscience and storage technologies, preserving human activities in DNA storage for hundreds of years, and facilitating fundamental understanding, identifying tradeoffs, and creating efficient ways of scaling up DNA storage. The project will provide an ideal inter-disciplinary thinking, hands-on learning, and development environment to teach computer science and electrical and computer engineering graduate and undergraduate students important system building and experimental skills that are critical for today's and the future IT workforce. The research outcomes of the project will be incorporated into the classroom teaching of the team members, for both class projects and the core courses in computer science and electrical and computer engineering. The team plans to include the obtained research results in a new course on Storage Technologies /Systems for Big Data for students in a Data Science Program, as well as in undergraduate senior design and directed research studies. The team plans to disseminate the research advances to industrial collaborators, and through publications, presentations, and public release of research data, software tools, and prototype systems to the research community. The team is committed to recruiting underrepresented undergraduate and graduate students to the project. Research results will be made quickly available to the general public and disseminated via websites and open source repositories like GitHub.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

世界上的数字数据每年都大大增加。到2025年，它将达到175个Zettabytes（ZB）。如今，大多数人类活动都以数字格式记录。但是，在数字媒体中记录的数据不能持续很长时间。因此，今天我们目前的存储技术和设备很长一段时间（超过15年），今天无法保留有价值的数据。现有存储媒体的能力无法跟上数字数据量的增长。同样，所有存储设备都可能在几年内变得过时，因此随着时间的流逝，存储的数据随着它们的灭亡而脆弱。因此，由于其高密度和持久性，合成的脱氧核糖核酸（DNA）成为一种有吸引力的替代储存培养基。 DNA存储的这些特征使其成为档案存储的绝佳候选者。但是，该项目的初步研究表明，基于当前技术的实用DNA存储管的容量仅为250GB，远小于预期容量。主要原因是，随着数据有效载荷的增加，DNA存储中的引物付费碰撞可以大大减少管中的可用引物数量。引物的使用对于随机访问DNA数据至关重要。在这个项目中，组建了一个跨学科团队，以研究可以提高DNA存储可扩展性的生物和存储方法。在可以扩展DNA存储的众多因素中，该项目计划研究以下问题：1）如何识别用于DNA存储中的底漆库的更多引物？ 2）给定底漆库，如何有效地分配有效载荷数据以避免引物付费碰撞以增加DNA存储容量？ 3）如何在数据备份应用程序中有效使用称为数据删除的流行技术来进一步提高DNA存储的存储能力？ 有了深入了解分子生物学和计算机存储技术和系统，这个跨学科的团队促进了几种创新的方法来理解DNA存储的基本问题，并将开发必要的基因组工程，测序技术，软件和新的算法，以优化将世界数字存储的流程以归档数字和计算数字的数字数据，以使数字数据转换为数字数据，以实现数字数据的数字数据。将世界数字数据存储在DNA存储中以保存所有人类活动的目的可以使该项目更近一步。该项目的潜在研究结果包括促进生物科学和存储技术的发展，在DNA存储中保存人类活动数百年，并促进基本的理解，识别折衷方案并创造有效的扩展DNA存储方式。该项目将提供理想的跨学科思维，动手学习和开发环境，以教授计算机科学，电气和计算机工程研究生和本科生重要的系统建设和实验技能，这对于当今和未来的IT员工至关重要。该项目的研究成果将纳入团队成员的课堂教学中，用于课堂项目以及计算机科学以及电气和计算机工程的核心课程。该团队计划将获得的研究结果包括在数据科学计划中的大数据以及本科高级设计和指导研究的新课程中。该团队计划通过将研究数据，软件工具和原型系统发布给研究社区的出版物，演示和公开发布，将研究进展传播给工业合作者。该团队致力于将代表性不足的本科生和研究生招募到该项目。研究结果将迅速向公众提供，并通过网站和诸如GitHub之类的开源存储库进行传播。该奖项反映了NSF的法定使命，并使用基金会的知识分子优点和更广泛的影响审查标准，认为值得通过评估来获得支持。