.large[Harnessing the disruptive nature of portable sequencing for community empowerment]

# .large[Harnessing the disruptive nature of portable sequencing for community empowerment]
### <div class="line-block">Institute of Environmental Science and Research (ESR)<br />
<br />
.large[<b>CMDHB Visit</b>, 28<small><sup>th</sup></small> January 2021]<br />
<br />
<br />
<a href="https://twitter.com/miles_benton">Miles Benton</a><br />
<br />
.center[<img src="images/ESR_SFC_logo.png" style="width: 25%; border: 3px solid white;"/>]</div>

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# .center[Advocates for reproducible research...]

## .center[Where possible all presentations and code are available online]

<br />

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<p>
.center[
<img src="https://cdn-a.william-reed.com/var/wrbm_gb_food_pharma/storage/images/publications/food-beverage-nutrition/foodnavigator.com/article/2018/03/21/oxford-nanopore-raises-funds-to-support-commercial-expansion/7992741-1-eng-GB/Oxford-Nanopore-raises-funds-to-support-commercial-expansion_wrbm_large.jpg" style="width: 620px; margin-right: 1%; margin-top: 1.5em;"/>
]
</p>

.small[.center[
(image source: [nanoporetech](https://nanoporetech.com/about-us/news/oxford-nanopore-announces-ps100-million-140m-fundraising-global-investors))
]]

???

flongle: ~$500 USD for 5
1 might be enough for a metagenome

minION: $1000

smidgION: still just a concept

gridION: ~$50K

promethION: ~$230K

---
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<center>
<iframe width="1000" height="562" src="https://www.youtube.com/embed/RcP85JHLmnI" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
<br />
&copy; Oxford Nanopore Technologies
</center>

---
class: middle

# Let's step back a couple of years

.pull.right[
.large[<span style="color:#3498DB">... **a personal story** ...</span>]
]

---
class: middle

<p>
.center[
<img src="images/jamie_sm.jpg" style="width: 330px; margin-right: 1%; margin-top: 1.5em; border: 3px solid white;"/>
<img src="images/jamie_big.jpg" style="width: 334px; margin-right: 1%; margin-top: 1.5em; border: 3px solid white;"/>
]
</p>

---
class: top

# what are we doing?

* <span style="color:#3498DB">**the idea**</span>

* low cost (< many mobile phones)
  * accessible
  * portable
  * robust (...may have "performed" a drop test...)
  * fun!

--
  
* <span style="color:#3498DB">**example use cases**</span>

* field sequencing (real-time monitoring, forensics, agriculture, waterways, ...)
  * clinical settings
  * community outreach / teaching

---
class: middle

# Our experiences with the Xavier [(link)](https://hackmd.io/@Miles/HkumH7sBH)

.pull-left[.right[
<img src="images/IMG_20191021_165639.jpg" style="width: 200px;"/>
<img src="images/IMG_20191025_094614.jpg" style="width: 200px;"/>
]]

.pull-right[.left[
<img src="images/battery_charge.jpg" style="width: 200px;"/>
<img src="images/xavier_in_use.jpg" style="width: 200px;"/>
]]

???

Talk about the Xavier specs:

* 8 core arm 
 * 16 GB of RAM
 * 512 CUDA core and 64 tensor cores
 * 512 GB SSD NVMe

---
class: middle

# Community engagement leading to empowerment

.pull.right[
<span style="color:#3498DB">... **a few stories of the journey** ...</span>
]

---

# So how about unlocking it for everyone?

.center[
<img src="images/JB_twitterprofile.png" style="width: 60%; margin-right: 1%; margin-top: 1em;"/>
]

---

# The unboxing and a slight snag

---

# Success

---
class: middle

# A global cast of many

* [***Kenya***] Jean-Bakka Domelevo Entfellner ([@JeanBakaDE](https://twitter.com/JeanBakaDE))

* [***USA***] John Erb-Downward ([@Bombanat](https://twitter.com/bombanat))

* [***Italy***] Luigi Faino ([@lfaino](https://twitter.com/lfaino))

* [***Switzerland***] Jürgen Hench

* [***USA***] Nvidia Clara Team ([Clara AGX site](https://developer.nvidia.com/clara-agx-devkit))

<br >

.center[You can follow the story here: [GitHub Gist - Xavier basecalling notes](https://gist.github.com/sirselim/2ebe2807112fae93809aa18f096dbb94)]

---

# ~~The future...~~

.center[
<img src="images/jetson_family.jpg" style="width: 45%; margin-right: 1%; margin-top: 0em;"/>
]

.center[
<img src="images/nvidia_tegra.jpg" style="width: 40%; margin-right: 1%; margin-top: 0em;"/>
]

---

# ~~The (not so distant) future...~~

.center[
<img src="images/nvidia_tegra.jpg" style="width: 40%; margin-right: 1%; margin-top: 1.65em;"/>
]

---
class: hide_logo

# The present!

---

# Hot off the press!

.center[
<img src="images/adaptive_sampling.jpeg" style="width: 85%; margin-right: 1%; margin-top: 1.65em;"/>
<br />
&copy; Oxford Nanopore Technologies
]
.center[
<br />
Jürgen Hench, Basel, Switzerland ([cancer methylation sequencing](https://gist.github.com/sirselim/2ebe2807112fae93809aa18f096dbb94#gistcomment-3547889))
]

---

# Hot off the press!

<article class="cf">
  <div class="fl w-50 bg-white tc">
    <img src="images/xavnx_phone.png" style="width: 45%; margin-right: 1%; margin-top: 0.5em;"/>
  </div>
  <div class="fl w-50 bg-white tc">
    <img src="images/minknowui.jpg" style="width: 97%; margin-right: 1%; margin-top: 0.5em;"/>
    <br>
    <br>
    <br>
    <br>
    <br>
    <b>Can now control all of this from our pockets!</b>  
    <br>
    <br>
    Available now on <a href="https://play.google.com/store/apps/details?id=com.nanoporetech.minknowui&hl=en_CA&gl=US" target="blank">Android</a> and <a href="https://apps.apple.com/us/app/minknow/id1504645283" target="blank">iOS</a>
  </div>
</article>

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---

## Our experiences with the Jeston Xaviers

.small[
#### Article in the NZ Herald
  * The Genius of Genomics ([link](https://www.nzherald.co.nz/nz/the-genius-of-genomics-the-revolution-that-helped-nz-quash-covid-19/EFJWSHSL3TTYNNKYA5WEROIKHY/))
  * Story also on ESR website ([link](https://www.esr.cri.nz/home/about-esr/media-releases/esr-scientists-showcase-benefits-of-collaboration-for-rapid-dna-sequencing/))

#### Jetson Nanopore Sequencing 
  * [A place to collate notes and resources of our journey into porting nanopore sequencing over to accessible, portable technology](https://github.com/sirselim/jetson_nanopore_sequencing)
    * up to date information, including parts list and set up guide

#### eResearch 2020 presentation 
  * [Assessing the potential of ~~autonomous AI devices~~ cool tech for portable real-time sequencing](https://sirselim.github.io/presentations/eResearch_2020/eResearch_presentation_livedemo_2020#1)
    * live base-calling and presentation run from the Xavier

#### Xavier AGX setup and notes
  * [Xavier AGX unboxing and setup](https://hackmd.io/@Miles/HkumH7sBH)

#### Xavier base-calling benchmarking and notes
  * [Xavier benchmarking](https://gist.github.com/sirselim/2ebe2807112fae93809aa18f096dbb94#file-basecalling_notes-md)
]

---

# acknowledgements

<div class="dt dt--fixed">
  <div class="dtc tc pv4 bg-white">
    <article class="mw5 center bg-white br3 pa3 pa4-ns mv3 ba b--black-10">
      <div class="tc">
        <img src="images/Matt_sm.png" class="br-100 h4 w4 dib ba b--black-05 pa2" title="Photo of team member">
        <h4 class="f3 mb2">Matt Storey</h4>
        <h4 class="f5 fw4 gray mt0">(ESR)</h4>
      </div>
    </article>
  </div>
  <div class="dtc tc pv4 bg-white">
    <article class="mw5 center bg-white br3 pa3 pa4-ns mv3 ba b--black-10">
      <div class="tc">
        <img src="images/Joep.jpg" class="br-100 h4 w4 dib ba b--black-05 pa2" title="Photo of team member">
        <h4 class="f3 mb2">Joep de Ligt</h4>
        <h4 class="f5 fw4 gray mt0">(ESR)</h4>
      </div>
    </article>
  </div>
  <div class="dtc tc pv4 bg-white">
    <article class="mw5 center bg-white br3 pa3 pa4-ns mv3 ba b--black-10">
      <div class="tc">
        <img src="images/Donia.png" class="br-100 h4 w4 dib ba b--black-05 pa2" title="Photo of team member">
        <h4 class="f3 mb2">Donia Macartney-Coxson</h4>
        <h4 class="f5 fw4 gray mt0">(ESR)</h4>
      </div>
    </article>
  </div>
</div>

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