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smarten [2019/09/02 22:14]
Jaroslaw Zola
smarten [2019/11/22 10:43] (current)
Jaroslaw Zola
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   * **[[https://​www.usfca.edu/​faculty/​lauren-sassoubre|Dr. ​ Lauren Sassoubre]]** (University of San Francisco and UB Department of Civil, Structural and Environmental Engineering),​   * **[[https://​www.usfca.edu/​faculty/​lauren-sassoubre|Dr. ​ Lauren Sassoubre]]** (University of San Francisco and UB Department of Civil, Structural and Environmental Engineering),​
   * **[[http://​engineering.buffalo.edu/​civil-structural-environmental/​people/​faculty_directory/​ian-bradley.html|Dr. Ian Bradley]]** (UB Department of Civil, Structural and Environmental Engineering).   * **[[http://​engineering.buffalo.edu/​civil-structural-environmental/​people/​faculty_directory/​ian-bradley.html|Dr. Ian Bradley]]** (UB Department of Civil, Structural and Environmental Engineering).
 +
 +===== Our Hardware =====
 +
 +To run the project we are using two key pieces of technology. The first one is [[https://​nanoporetech.com/​products/​minion|MinION sequencer]] from Oxford Nanopore Technology. The pictures below show one of the three devices we are using in our labs.
 +
 +{{::​minion.jpg?​200|}}{{:​coffee.jpg?​200|}}
 +
 +The second component is a Supercomputer On a Chip (SCoC). The specific platform we are using is based on NVIDIA'​s [[https://​www.nvidia.com/​en-us/​autonomous-machines/​embedded-systems/​jetson-nano/​|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).
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 +{{::​1.jpg?​200|}}{{::​2.jpg?​200|}}{{::​3.jpg?​200|}}
 +
 +\\
 +
 +==== SCoC Harware Specification ====
 +
 +  * [[https://​www.nvidia.com/​en-us/​autonomous-machines/​embedded-systems/​jetson-nano/​|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)''​. ​
 +  * [[https://​tinyurl.com/​y57twou6|Geekworm NVIDIA Jetson Nano Metal Case]] – nice and small form factor package.
 +  * [[https://​amzn.com/​B071FNHVXN|NOCTUA NF-A4x20 PWM 5V fan]] – fan is critical to sustain Nano's operation under heavy load, it has to be 5V.
 +  * [[https://​tinyurl.com/​y5k5gpcz|Intel Dual Band Wireless-AC 8265]] with [[https://​tinyurl.com/​y35tfvpp|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.
 +  * [[https://​tinyurl.com/​y285psp8|Samsung 256GB U3 MicroSDXC EVO internal memory card]] – this is internal storage used by OS and software tools.
 +  * [[https://​tinyurl.com/​y42xrka6|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 smaller SSDs.
 +  * [[https://​tinyurl.com/​y64k4elx|TOGUARD 7in 1024x600 TFT LCD display]] – we are not entirely happy with this option, you may consider a better solution.
 +  * [[https://​tinyurl.com/​y4hw4uew|Pwr+ 5V Micro-USB charger]] – we use this particular type of charger a lot, no complaints.
 +
 +**We will be sharing our experiences and updating this web page as the project progresses!**
 +
 +===== References =====
 +
 +  - [[https://​dl.acm.org/​citation.cfm?​doid=3177102.3177114|S. Ko, L. Sassoubre, J. Zola, Applications and Challenges of Real-time Mobile DNA Analysis, HotMobile 2018.]]
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