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smarten [2019/09/20 14:32]
Jaroslaw Zola
smarten [2020/03/25 12:59] (current)
Jaroslaw Zola
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 ===== Our Hardware ===== ===== Our Hardware =====
  
-To run the project we are using two key pieces of technology. The firstis [[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.+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|}} {{::​minion.jpg?​200|}}{{:​coffee.jpg?​200|}}
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 ==== SCoC Harware Specification ==== ==== 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://​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]] +  * [[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 +  * [[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 +  * [[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/​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/​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/​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]]+  * [[https://​tinyurl.com/​y4hw4uew|Pwr+ 5V Micro-USB charger]] ​– we use this particular type of charger a lot, no complaints. 
 + 
 +==== 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. 
 + 
 +{{ ::​2020-03-06_09.52.53-1.jpg?​300 |}} 
 + 
 +\\
  
 **We will be sharing our experiences and updating this web page as the project progresses!** **We will be sharing our experiences and updating this web page as the project progresses!**
 +
 +\\
  
 ===== References ===== ===== 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.]]   - [[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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