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

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.