SMARTEn (System for Mobile Analysis in Real-Time of ENvironment)
Portable DNA sequencers, such as Oxford Nanopore MinION, are fundamentally changing how DNA-based diagnostics is done. Instead of spending days in a lab, working with bulky bench-top machines, we can now take a pocket-size sequencer into the field, and do sequencing in-situ. In many cases, such capability is essential for, e.g., detecting and tracking spread of infectious diseases or metagenomic surveys in rapidly changing environments (see our HotMobile 2018 paper for more extensive discussion). When attached to mobile devices such as laptops or tablets, portable DNA sequencers provide in real-time signals describing detected DNA. However, the current software tools required to process and analyze these signals are not well suited to execute directly in the field, where energy, Internet connectivity, and compute power are extremely limited.
In this project, we aim 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.