Welcome
SMARTEn (System for Mobile Analysis in Real-Time of ENvironment)
SMARTEn aims to provide new ways to analyze metagenomic DNA using fully mobile setup. The project is run by an interdisciplinary team of experts in computer science and environmental engineering.
Our codebase is open source and free and available from our official GitLab repository. Here you can find out more about software tools we are developing.
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
- Jetson Nano – quad-core ARM Cortex-A57 processor, NVIDIA Maxwell with 128 GPU cores, 4 GB 64-bit LPDDR4 1600MHz RAM. Very powerful SCoC, running Ubuntu Linux:
18.04.3 LTS (GNU/Linux 4.9.140-tegra aarch64). - Geekworm NVIDIA Jetson Nano Metal Case – nice and small form factor package.
- NOCTUA NF-A4x20 PWM 5V fan – fan is critical to sustain Nano’s operation under heavy load, it has to be 5V.
- Intel Dual Band Wireless-AC 8265 with 6dBi RP-SMA Dual Band 2.4GHz 5GHz Antennas – Nano board comes with standard GbEth port only. If you need WiFi connectivity, this solution requires almost no effort.
- Samsung 256GB U3 MicroSDXC EVO internal memory card – this is internal storage used by OS and software tools.
- WD 4TB Elements USB External Hard Drive – this is external storage to keep data (we recommend that you pick tested hard drive). Overall, a standard spinning hard drive is not optimal (it draws too much energy). When we do not need that much extra storage we use a smaller SSD.
- TOGUARD 7in 1024x600 TFT LCD display – we are not entirely happy with this option, you may consider a better solution.
- Pwr+ 5V Micro-USB charger – we use this particular type of charger a lot, no complaints.
SCoC 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. Note that in order to get access to the sourcecode you have to joint ONT developers program. Below is a glimpse at MinKNOW running on NVIDIA Nano.
Emulating MinION
The mGRUE team of undergraduate students under supervision of Dr. Kris Schindler built a hardware/software combo that allows us to emulate MinION sequencer. You can learn more about the project from their repository. This project was done as part of the fantastic CSE 453 “Hardware/Software Integrated Systems Design 2” course.
The mGRUE team are:
- Jonathan Baffo
- Warren Green
- Christian Palladino
- Brian Scorcia
- Aaron Siegel
- Lucas Simpson
References
- V. Zheng, A.E. Sariyuce, J. Zola, Identifying Taxonomic Units in Metagenomic DNA Streams on Mobile Devices, TCBB 2022.
- V. Zheng, A.E. Sariyuce, J. Zola, Identifying Taxonomic Units in Metagenomic DNA Streams, BioKDD 2020.
- S. Ko, L. Sassoubre, J. Zola, Applications and Challenges of Real-time Mobile DNA Analysis, HotMobile 2018.