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smarten [2019/09/02 22:14] Jaroslaw Zola |
smarten [2019/11/22 10:41] Jaroslaw Zola |
* **[[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). |
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| ===== Our Hardware ===== |
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| 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. |
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| {{::minion.jpg?200|}}{{:coffee.jpg?200|}} |
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| 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|}} |
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| \\ |
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| ==== SCoC Harware Specification ==== |
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| * [[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 charge a lot, no complaints. |
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| **We will be sharing our experiences and updating this web page as the project progresses!** |
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| ===== References ===== |
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| - [[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.]] |