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

便携式 DNA（脱氧核糖核酸）测序仪是一种新技术，可在高端生物实验室之外的现场进行 DNA 分析。当连接到笔记本电脑或平板电脑等移动设备时，它们会提供描述检测到的 DNA 的实时信号。然而，当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。该项目旨在开发并在现实使用场景中测试新的软件系统和算法，以便直接在移动设备上进行 DNA 处理，而无需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可行。该项目分三步打破了当前工具的僵化结构。首先，它引入了新的软件抽象，并配有应用程序编程接口，以表达宏基因组 DNA 分类工作流程。其次，它提供支持操作系统组件，包括用于 DNA 数据库的域特定内存管理器和异构任务调度程序。第三，它提供了直接在信号空间而不是公共字符串空间中执行 DNA 读取映射的新算法。最终解决方案的验证涉及五大湖渔业的宏基因组学调查，该调查是与美国地质调查局 (USGS) 团队合作进行的。该项目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可以进行 DNA 分析。通过利用宏基因组学增强美国地质调查局鱼类评估程序，有助于提高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领域的研究生和本科生创造了跨学科培训机会，包括新的教育模块和研究实习机会，有助于培养有竞争力的劳动力。它还吸引来自布法罗（纽约）市中心高中的学生，鼓励他们参与计算。中央项目存储库，包括项目源代码和数据，是开放和公开的，并维护在：http://www.score-group.org/doku.php?id=SMARTEn。该奖项反映了 NSF 的法定使命，并通过使用基金会的智力价值和更广泛的影响审查标准进行评估，被认为值得支持。

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.