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smarten [2019/05/06 10:45]
Jaroslaw Zola
smarten [2019/09/20 14:32] (current)
Jaroslaw Zola
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 ====== SMARTEn ====== ====== SMARTEn ======
 +===== System for Mobile Analysis in Real-Time of ENvironment =====
  
-**System for Mobile Analysis in Real-Time of ENvironment**+This project is supported by the [[https://​www.nsf.org/​|National Science Foundation]] under the award [[https://​www.nsf.gov/​awardsearch/​showAward?​AWD_ID=1910193|CNS-1910193]].
  
-Stay tuned!+Portable DNA sequencers, such as [[https://​nanoporetech.com/​products/​minion|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 ([[https://​dl.acm.org/​citation.cfm?​doid=3177102.3177114|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: 
 +  * [[https://​nsr.cse.buffalo.edu/​|Networked Systems Research (NSR) Group]] of **[[https://​nsr.cse.buffalo.edu/?​page_id=272|Dr. Steve Ko]]**, 
 +  * **[[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). 
 + 
 +===== Our Hardware ===== 
 + 
 +To run the project we are using two key pieces of technology. The first, 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). 
 + 
 +{{::​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 
 +  * [[https://​tinyurl.com/​y57twou6|Geekworm NVIDIA Jetson Nano Metal Case]] 
 +  * [[https://​amzn.com/​B071FNHVXN|NOCTUA NF-A4x20 PWM 5V fan]] – fan is critical to sustain Nano's operation under heavy load 
 +  * [[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 
 +  * [[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) 
 +  * [[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 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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