SMARTEn

System for Mobile Analysis in Real-Time of ENvironment

This project is supported by the National Science Foundation under the award CNS-1910193.

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.

Team

This project is a collaboration between the SCoRe Group and:

Our Hardware

To run the project we are using two key pieces of technology. The first one is MinION sequencer from Oxford Nanopore Technology. The pictures below show one of the three devices we are using in our labs.

The second component is a Supercomputer On a Chip (SCoC). The specific platform we are using is based on NVIDIA's Jetson Nano. Below we provide pictures of the entire setup. We include also specification if you are interested in building a similar box for your project (please note that we are not endorsing any particular provider).


SCoC Harware Specification

Software Specification

Jetson Nano comes with its own variant of Ubuntu Linux for Tegra – the specific version is Ubuntu 18.04.4 LTS (GNU/Linux 4.9.140-tegra aarch64). Since this is fully functional Linux, we have access to all common tools, including compilers, like gcc and clang, and the entire NVIDIA CUDA development environment (currently we are using CUDA 10.0).

Of course, the key requirement is to be able to run Oxford Nanopore tools. ONT provides MinKNOW framework in its repository. Just running fairly standard chain of Debian/Ubuntu apt commands brings in all tools (notice that we are using xenial repository):

echo “deb http://mirror.oxfordnanoportal.com/apt xenial-stable-minit non-free” > /etc/apt/sources.list.d/nanoporetech.list

apt update && apt upgrade

apt install minknow-core-minit-offline ont-bream4-minit ont-configuration-customer-minit ont-minknow-frontend-minit ont-minknow-static-frontend

The only caveat is that currently, it is not possible to install guppy basecaller directly from packages (there are several reasons: first, dependencies that cannot be satisfied without downgrading Ubuntu, second, lack of support for NVIDIA SM53 in the default package). However, we were able to easily bypass these problems by compiling (with a bit of editing) guppy from sources (we will share the process soon). Below is a glimpse at MinKNOW running on NVIDIA Nano.


We will be sharing our experiences and updating this web page as the project progresses!


References

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