CNS Core: Small: Rethinking the Software Architecture for Mobile DNA Analysis

CNS 核心：小型：重新思考移动 DNA 分析的软件架构

• 批准号: 1910193
• 负责人: Jaroslaw Zola
• 金额: $ 49.68万
• 依托单位: SUNY at Buffalo
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-10-01 至 2024-09-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1910193&HistoricalAwards=false
• 关键词: CNS; Core; Small; Rethinking; Software

Portable DNA (Deoxyribonucleic Acid) sequencers are new technology enabling analysis of DNA in the field, outside of high-end biological laboratories. When attached to mobile devices such as laptops or tablets, they provide in real-time signals describing detected DNA. However, the current software tools required to process and analyze these signals are not well suited for portable DNA sequencing, limiting its possible applications. This project aims to develop, and test in real-world use scenarios, new software system and algorithms to enable DNA processing directly on mobile devices, without the need to access advanced computational infrastructure.The project's goal is to make DNA analytics feasible directly on mobile supercomputers and smartphones. The project breaks the rigid structure of the current tools in three steps. First, it introduces new software abstractions, complete with application programming interface, to express metagenomics DNA classification workflows. Second, it provides supporting operating system components, including domain specific memory manager for DNA databases, and heterogeneous tasks scheduler. Third, it offers new algorithms for performing DNA reads mapping directly in signal space, instead of the common string space. The validation of the resulting solutions involves metagenomics survey of Great Lakes fisheries, conducted in collaboration with the United States Geological Survey (USGS) team.The software platform developed in this project makes DNA analytics accessible to the end-users who have no access to advanced computational infrastructure. By enhancing the USGS fish assessment procedures with metagenomics, it contributes to the improved sustainability of both fisheries and the communities that depend on them. Furthermore, the project creates cross-disciplinary training opportunities, including new educational modules and research internships, for graduate and undergraduate students in Computer Science, Biomedical Informatics, and Environmental Engineering, contributing to competitive workforce development. It also engages students from inner-city Buffalo (New York) high schools to encourage their participation in computing.The central project repository, including project source codes and data, is open and publicly available, and maintained at: http://www.score-group.org/doku.php?id=SMARTEn.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.

便携式DNA(脱氧核糖核酸)测序仪是一种新技术，能够在高端生物实验室以外的领域进行DNA分析。当连接到笔记本电脑或平板电脑等移动设备时，它们可以实时提供描述检测到的DNA的信号。然而，目前处理和分析这些信号所需的软件工具不太适合便携式DNA测序，限制了其可能的应用。该项目旨在开发新的软件系统和算法，并在现实世界的使用场景中进行测试，使其能够直接在移动设备上进行DNA处理，而不需要访问先进的计算基础设施。该项目的目标是使DNA分析直接在移动超级计算机和智能手机上实现。该项目分三步打破了目前工具的僵化结构。首先，它引入了新的软件抽象，并完成了应用程序编程接口，以表达元基因组DNA分类工作流。其次，它提供了支持操作系统的组件，包括DNA数据库的特定于域的内存管理器和异类任务调度器。第三，它提供了直接在信号空间执行DNA读取映射的新算法，而不是普通的字符串空间。所产生的解决方案的验证涉及与美国地质调查局(USGS)团队合作进行的五大湖渔业元基因组学调查。在该项目中开发的软件平台使无法使用先进计算基础设施的最终用户能够获得DNA分析。通过用元基因组学加强美国地质调查局鱼类评估程序，它有助于改善渔业和依赖渔业的社区的可持续性。此外，该项目还为计算机科学、生物医学信息学和环境工程专业的研究生和本科生创造了跨学科的培训机会，包括新的教育模块和研究实习机会，有助于具有竞争力的劳动力发展。它还邀请来自市中心布法罗(纽约)高中的学生鼓励他们参与计算。中央项目库，包括项目源代码和数据，是开放的和公开的，并维护在：http://www.score-group.org/doku.php?id=SMARTEn.This奖反映了国家科学基金会的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

项目成果

Identifying Taxonomic Units in Metagenomic DNA Streams on Mobile Devices

识别移动设备上宏基因组 DNA 流中的分类单元

• DOI: 10.1109/tcbb.2022.3172661
• 发表时间: 2021
• 期刊: IEEE/ACM Transactions on Computational Biology and Bioinformatics
• 作者: Zheng, Vicky;Sariyuce, A. Erdem;Zola, Jaroslaw
• 通讯作者: Zola, Jaroslaw

Identifying Taxonomic Units in Metagenomic DNA Streams

识别宏基因组 DNA 流中的分类单元

• DOI: 10.1101/2020.08.21.261313
• 发表时间: 2020
• 期刊: BIOKDD - 19th International Workshop on Data Mining in Bioinformatics
• 作者: Zheng, V;Sariyuce, AE;Zola, J
• 通讯作者: Zola, J