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<!DOCTYPE html>
<html lang="" xml:lang="">
<head>
<title>.large[The disruptive nature of portable sequencing for community empowerment… and GPUs]</title>
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class: center, middle, inverse, title-slide
# .large[The disruptive nature of portable sequencing for community empowerment… and GPUs]
### <div class="line-block">Genomics Aotearoa Friday Seminar Series, 9<small><sup>th</sup></small> April 2021<br />
.large[<b>Dr Miles Benton</b>]<br />
<br />
<b>Human Genomics</b><br />
<b>Institute of Environmental Science and Research <a href="www.esr.cri.nz">(ESR)</a></b><br />
<b>Aotearoa</b> (New Zealand)</div>
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# .center[Advocates for reproducible research...]
## .center[Where possible all presentations and code are available online]
<br />
<p>
.center[
<img src="images/github_logo.png" style="width: 520px; margin-right: 1%; margin-top: 1.5em;"/>
<img src="images/sirselim_qrcode.png" style="width: 202px; margin-right: 1%; margin-top: 1.5em;"/>
]
</p>
<br />
.center[[sirselim.github.io/presentations](http://sirselim.github.io/presentations)]
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---
layout: false
class: middle hide_logo
<center>
<img src="images/ga_logo.jpg" style="width: 80%; margin-right: 1%; margin-top: 0em;"/>
</center>
---
class: middle
# Who are we?
.pull.right[
.large[<span style="color:#3498DB">**You may have seen recently**...</span>]
]
---
class: top
# Genomics in NZ's pandemic response
### A sequencing success story made possible by the awesome [**Una Ren**](https://twitter.com/sciolato), [**Matt Storey**](https://twitter.com/mathstorey) & [**Joep de Ligt**](https://twitter.com/joepdl)
<article class="cf">
<div class="fl w-50 bg-white tc">
<img src="images/JN_FirstGenome.PNG" style="width: 80%; margin-right: 1%; margin-top: 0em;"/>
</div>
<div class="fl w-40 bg-white tc">
<p style="text-align:center"> Give us some time and money and we'll demonstrate what this technology can do. <br /> <br /> <br /> </p>
</div>
<div class="fl w-40 bg-white tc">
<img src="images/NZChiefSCIAdvisor.PNG" style="width: 100%; margin-right: 1%; margin-top: 0em;"/>
</div>
</article>
---
layout: false
class: middle inverse
background-image: url("https://cdn.vox-cdn.com/thumbor/llQlREwACaitewdPcLm5HzWT_g0=/0x1:1100x734/920x613/filters:focal(0x1:1100x734):format(webp)/cdn.vox-cdn.com/imported_assets/1507663/DNA-sequence.jpg")
background-size: cover
.massive[**Genomic sequencing**]
???
DNA - A, T, C, G
Part of all 'living' things
---
# A snapshot of the Human Genomics group
* **Independent research**
* type-2 diabetes & obesity (genomics, epigenetics, protein 'omics)
* Guinea pigs! (<span style="color:#3498DB"><b>Max Berry, University of Otago</b></span>)
* empowering people to explore and interpret their data
<br>
* **Clinical diagnostics through genetics**
* Contract(s) with CCDHB <span style="color:#3498DB"><b>Wellington Regional Genetics Lab</b></span>
* Providing support to CCDHB for Clinical Genomics GA project (<span style="color:#3498DB"><b>Stephen Robertson</b></span>)
<br>
* **Clinical research**, in collaboration with local clinician (<span style="color:#3498DB"><b>Richard Carroll</b></span>) - hyperparathyroidism
* sequencing 100 exomes
* engaging clinicians from other DHBs
* exploring the replacement of gene panels with exome/genome
---
class: middle center
# A big part of what we do is sequencing
.center[<img src="images/dna_hackers.jpg" style="width: 30%; margin-right: 1%; margin-top: 0em;"/>]
---
layout: false
class: middle
<p>
.center[
<img src="https://www.illumina.com/content/dam/illumina-marketing/images/decade-in-sequencing/decade-in-sequencing-320-web-graphic.jpg" style="width: 820px; margin-right: 1%; margin-top: 1.5em;"/>
]
</p>
.small[.center[
(image source: [illumina.com](https://www.illumina.com/techniques/sequencing/dna-sequencing.html))
]]
???
I used the word portable in my previous slide, this is not a phrase one would attribute to machines from Illumina / PacBio.
These things are huge! ... and expensive.
---
class: middle
> *"Soon, It Will Cost Less To Sequence A Genome Than To Flush A Toilet -- And That Will Change Medicine Forever"*
<p>
.center[
<img src="images/seqCost.png" style="width: 620px; margin-right: 1%; margin-top: 1.5em;"/>
]
</p>
.small[.center[
(image source: [https://www.businessinsider.com.au/super-cheap-genome-sequencing](https://www.businessinsider.com.au/super-cheap-genome-sequencing-by-2020-2014-10))
]]
---
class: top
# Can we speed things up?
<b>Thanks to eResearch 2020<b> ...enter [Nvidia Clara Parabricks](https://www.nvidia.com/en-us/docs/parabricks/)
<article class="cf">
<div class="fl w-50 bg-white tc">
<img src="images/parabricks.png" style="width: 40%; margin-right: 1%; margin-top: 0em;"/>
</div>
<div class="fl w-50 bg-white tc">
<img src="images/nvidia.png" style="width: 50%; margin-right: 1%; margin-top: 1.5em;"/>
</div>
</article>
.center[<span style="color:#3498DB"><b> powered by GPU </b></span>]
.center[<img src="images/tesla_v100.jpg" style="width: 30%; margin-right: 1%; margin-top: 0em;"/>]
---
class: middle
.center[
<img src="images/parabricks_pipelines.png" style="width: 70%; margin-right: 1%; margin-top: 0em;"/>
]
<br>
.center[[www.nvidia.com/en-us/healthcare/clara-parabricks/](https://www.nvidia.com/en-us/healthcare/clara-parabricks/)]
---
# How much does that matter?
### Identical pipelines with a slight difference...
<article class="cf">
<div class="fl w-100 w-50-ns bg-white">
<ul>
<li><b>Pipeline [CPU]</b></li>
<ul>
<li>Exomes: >100X exome takes between 8-12 hours</li>
<li>Genomes: ~30X genome takes between 30-48 hours</li>
</ul>
</ul>
<br>
<ul>
<li><b>Pipeline [GPU - Parabricks]</b></li>
<ul>
<li>Exomes: >100X exome takes between <span style="color:#3498DB"><b>6-12 mins</b></span></b></li>
<li>Genomes: 100X genome takes <span style="color:#3498DB"><b>~4 hours</b></span></li>
<br>
<li>was on 2x V100 GPUs, now also have 2x A100s</li>
</ul>
</ul>
</div>
<div class="fl w-100 w-50-ns bg-white tc">
<img src="images/fast-turtle.png" style="width: 70%; margin-right: 1%;"/>
</div>
</article>
---
class: middle
<center>
<img src="images/clara_parabricks_toolkit.png" style="width: 65%; margin-right: 1%; margin-top: 0em;"/>
</center>
<br>
.center[[www.nvidia.com/en-us/healthcare/clara-parabricks/](https://www.nvidia.com/en-us/healthcare/clara-parabricks/)]
---
class: middle
<center>
<img src="images/A100s.jpg" style="width: 65%; margin-right: 1%; margin-top: 0em;"/>
<br>
<img src="images/NESI_logo.jpg" style="width: 35%; margin-right: 1%; margin-top: 0em;"/>
</center>
---
class: middle
<center>
<img src="https://i.imgur.com/2bZPSLj.png" style="width: 45%; margin-right: 1%; margin-top: 0em;"/>
</center>
<center>
<a href="https://twitter.com/LeahKem63535098/status/1380108139119267840" target="blank">Fun with Nvidia A100s!!</a>
</center>
---
class: top
# Complete Overhaul! [Leah Kemp]
<br>
<article class="cf">
<div class="fl w-100 w-50-ns bg-white">
<br>
<br>
<br>
<ul>
<li>Alignment and Variant Calling Workflow</li>
<ul>
<li><a href="https://github.com/ESR-NZ/human_genomics_pipeline" target="blank">[human_genomics_pipeline]</a></li>
</ul>
<br>
<br>
<li>Variant Annotation Workflow</li>
<ul>
<li><a href="https://github.com/ESR-NZ/vcf_annotation_pipeline" target="blank">[annotation_pipeline]</a></li>
</ul>
</ul>
</div>
<div class="fl w-100 w-50-ns bg-white tc">
<article class="mw5 center bg-white br3 pa3 pa4-ns mv3 ba b--black-10">
<div class="tc">
<img src="images/Leah.jpeg" class="br-100 h4 w4 dib ba b--black-05 pa2" title="Photo of team member">
<h4 class="f3 mb2">Leah Kemp</h4>
<h4 class="f5 fw4 gray mt0">(ESR)</h4>
</div>
</article>
</div>
</article>
.center[.huge[ESR GitHub: [https://github.com/ESR-NZ](https://github.com/ESR-NZ)]]
---
class: middle
# Another type of sequencing technology
.pull-right[...sorry PacBio I'm ignoring you today...]
---
layout: false
class: middle
<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
---
layout: false
class: hide_logo
background-image: url("images/david_slide.png")
background-size: contain
<a href="https://f1000research.com/slides/8-1947" style="position:absolute; top:625px; left:190px">slide kindly supplied by David Eccles (f1000 presentation)</a>
<a href="https://www.youtube.com/watch?v=CHCAb-PAqUI" style="position:absolute; top:652px; left:190px">"Sequencing DNA with Linux Cores and Nanopores"</a>
???
David's talk and a live demo are linked.
---
layout: false
class: middle hide_logo
<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>
---
layout: false
class: middle
# Example squiggle plot
.small[.center[
(image source: [tombo manual](https://nanoporetech.github.io/tombo/plotting.html))
]]
???
What we 'see' when DNA passes through the pores.
---
class: middle
# GPUs accelerate basecalling of Nanopore long-read data (a lot)
.center[
<img src="images/gpu_magic.jpg" style="width: 110%; margin-right: 1%; margin-top: 1em;"/>
]
<br>
.center[
Nanopore basecalling benchmarking: [link (ESR GitHub)](https://esr-nz.github.io/gpu_basecalling_testing/gpu_benchmarking.html)
]
---
class: middle
# Why GPUs?
.pull-left[
New type of sequencing data requires new type of 'analysis'
* squiggle data lends itself nicely to neural nets
* GPUs are very capable in this space
- CUDA cores
ESR GPU basecalling benchmarks [(link)](https://esr-nz.github.io/gpu_basecalling_testing/gpu_benchmarking.html)
* Titan RTX & 2x Tesla V100
]
.pull-right[
]
<br>
.small[.center[
[UPDATE:] guppy is now able to scale across multiple GPUs!
]]
---
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
# a personal story
.large[
<br>
* had a lumbar puncture ('9 days' old)
* (after being born 8 weeks early)
<br>
* suspected meningitis (bacteria/viral)?
* told after the fact
<br>
* \>**48 hours** for results return
]
---
class: top
# a personal story
.large[
... imagine a more ‘real-time’ procedure:
]
<br>
--
.large[
* a sample (i.e. blood) taken,
* DNA/RNA extracted/enriched,
* sequencing library prepared,
* nanopore sequencing initiated,
* sequence starts coming in almost instantly,
* **<span style="color:#3498DB">time to first read-match detection <1 hr</span>**
]
--
<br>
.center[.huge[
**This isn't a stretch of the imagination anymore, soon to be reality**
]]
???
Stress how fast and low cost this has the potential to be.
---
class: top
# what are we doing?
.large[
Portable ‘real-time’ sequencing for the masses?
]
--
* <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
--
.center[
Community Science | "United in Data"
]
---
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;"/>
]]
.center[
<img src="images/jetson_xavier_jtop_screenshot.png" style="width: 650px;"/>
]
???
Talk about the Xavier specs:
* 8 core arm
* 16 GB of RAM
* 512 CUDA core and 64 tensor cores
* 512 GB SSD NVMe
---
class: top
# Benchmarking [(link)<sup>*</sup>](https://gist.github.com/sirselim/2ebe2807112fae93809aa18f096dbb94)
.small[
\* spoilers for those following along live
]
--
<br>
Most Jetson devices have the ability to be put into different power modes
<br>
<div id="htmlwidget-9e9ea86ed6ddeaef53d8" style="width:100%;height:auto;" class="datatables html-widget"></div>
<script type="application/json" data-for="htmlwidget-9e9ea86ed6ddeaef53d8">{"x":{"filter":"none","fillContainer":false,"data":[["10W","15W","30W 2 cores","30W 4 cores","30W MAX (8 cores)"],["33.4 mins","14.3 mins","10.8 mins","10.8 mins","7.5 mins"]],"container":"<table class=\"display\">\n <thead>\n <tr>\n <th>Power.mode<\/th>\n <th>Time<\/th>\n <\/tr>\n <\/thead>\n<\/table>","options":{"dom":"t","order":[],"autoWidth":false,"orderClasses":false}},"evals":[],"jsHooks":[]}</script>
.small[
***Note:*** this table represents basecalling performed when running on a portable powerbank.
]
???
Why is 10W mode exciting?
We're running in 30W MAX mode for this live demo - running on a portable powerpack.
---
class: top
## Very rough comparison of Nvidia ecosystem<sup>#</sup>
<div id="htmlwidget-7573f7bbe3372dc41045" style="width:100%;height:auto;" class="datatables html-widget"></div>
<script type="application/json" data-for="htmlwidget-7573f7bbe3372dc41045">{"x":{"filter":"none","fillContainer":false,"data":[["Jetson Nano","Jetson Xavier NX*","Jetson Xavier","Geforce 1080 Ti","Geforce 2080 Ti","Titan RTX","Tesla V100"],["~0.5","6","11","11.3","~13-14","16.3","16.4"],["$99","$399","$699","~$650","~$800-$1000","~$3000","~$8500"],["5-10W","10-15W","10-30W","215W","250W","280W","250W"]],"container":"<table class=\"display\">\n <thead>\n <tr>\n <th>Card<\/th>\n <th>TFLOPS<\/th>\n <th>Price<\/th>\n <th>Power<\/th>\n <\/tr>\n <\/thead>\n<\/table>","options":{"dom":"t","order":[],"autoWidth":false,"orderClasses":false}},"evals":[],"jsHooks":[]}</script>
.small[Price in USD]
.small[<sup>#</sup> a very small selection of what Nvidia offers obviously!]
.small[\* this can fit in an existing Jetson Nano carrier boards]
???
V100 could rip through this data in a couple of mins, but consider the cost, power, etc.
Xavier NX is exciting, module that can slot into the Nano body [**hold up Nano device**]
---
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
<article class="cf">
<div class="fl w-50 bg-white tc">
<img src="images/geforce2070_JB.png" style="width: 65%; margin-right: 1%; margin-top: 0em;"/>
</div>
<div class="fl w-50 bg-white tc">
<img src="images/six_pin_plugs.png" style="width: 64%; margin-right: 63%; margin-top: 0em;"/>
</div>
</article>
---
# Success
<article class="cf">
<div class="fl w-50 bg-white tc">
<img src="images/duct_tape.png" style="width: 65%; margin-right: 1%; margin-top: 0em;"/>
</div>
<div class="fl w-40 bg-white tc">
<img src="images/nvidia_smi.png" style="width: 70%; margin-right: 1%; margin-top: 0em;"/>
</div>
<div class="fl w-40 bg-white tc">
<img src="images/guppy_2070.png" style="width: 70%; margin-right: 1%; margin-top: 0em;"/>
</div>
</article>
---
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...~~
<article class="cf">
<div class="fl w-50 bg-white tc">
<img src="images/xaviernx_seqkit.jpg" style="width: 97%; margin-right: 1%; margin-top: 0.5em;"/>
</div>
<div class="fl w-50 bg-white tc">
<img src="images/xaviernx_compact_seqkit.jpg" style="width: 97%; margin-right: 1%; margin-top: 0.5em;"/>
</div>
</article>
.center[
<img src="images/nvidia_tegra.jpg" style="width: 40%; margin-right: 1%; margin-top: 1.65em;"/>
]
---
class: hide_logo
# The present!
<article class="cf">
<div class="fl w-100 w-33-m w-50-l pa1">
<a class="db aspect-ratio aspect-ratio--1x1">
<span role="img" style="background-image:url(images/xavier-ont.gif);" class="bg-center cover aspect-ratio--object"></span>
</a>
</div>
<div class="fl w-50 w-33-m w-25-l pa1">
<a class="db aspect-ratio aspect-ratio--1x1">
<span role="img" style="background-image:url(images/xavnx_board.jpg);" class="bg-center cover aspect-ratio--object"></span>
</a>
</div>
<div class="fl w-50 w-33-m w-25-l pa1">
<a class="db aspect-ratio aspect-ratio--1x1">
<span role="img" style="background-image:url(images/xavnx_screen.jpg);" class="bg-center cover aspect-ratio--object"></span>
</a>
</div>
<div class="fl w-50 w-33-m w-25-l pa1">
<a class="db aspect-ratio aspect-ratio--1x1">
<span role="img" style="background-image:url(images/Matt_hand.jpg);" class="bg-center cover aspect-ratio--object"></span>
</a>
</div>
<div class="fl w-50 w-33-m w-25-l pa1">
<a class="db aspect-ratio aspect-ratio--1x1">
<span role="img" style="background-image:url(images/full_kit.jpg);" class="bg-center cover aspect-ratio--object"></span>
</a>
</div>
</article>
---
class: hide_logo
# The present!
<article class="cf">
<div class="fl w-100 w-33-m w-50-l pa1">
<a class="db aspect-ratio aspect-ratio--1x1">
<span role="img" style="background-image:url(images/IMG_20210203_102006.jpg);" class="bg-center cover aspect-ratio--object"></span>
</a>
</div>
<div class="fl w-50 w-33-m w-25-l pa1">
<a class="db aspect-ratio aspect-ratio--1x1">
<span role="img" style="background-image:url(images/IMG_20210209_212836.jpg);" class="bg-center cover aspect-ratio--object"></span>
</a>
</div>
<div class="fl w-50 w-33-m w-25-l pa1">
<a class="db aspect-ratio aspect-ratio--1x1">
<span role="img" style="background-image:url(images/IMG_20210211_125758.jpg);" class="bg-center cover aspect-ratio--object"></span>
</a>
</div>
<div class="fl w-50 w-33-m w-25-l pa1">
<a class="db aspect-ratio aspect-ratio--1x1">
<span role="img" style="background-image:url(images/IMG_20210205_155440.jpg);" class="bg-center cover aspect-ratio--object"></span>
</a>
</div>
<div class="fl w-50 w-33-m w-25-l pa1">
<a class="db aspect-ratio aspect-ratio--1x1">
<span role="img" style="background-image:url(images/IMG_20210204_112338.jpg);" class="bg-center cover aspect-ratio--object"></span>
</a>
</div>
</article>
---
class: hide_logo
# The present!
Can you sequence SARS-Cov2 on ~$100 USD compute? ... **YES!**
.center[
<img src="images/nano_seq.jpg" style="width: 55%; margin-right: 1%; margin-top: 0em;"/>
]
---
layout: false
class: hide_logo
background-image: url("images/HeTangata.jpg")
background-size: contain
---
# 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!
.center[
<img src="https://i.imgur.com/lhVYBf0.png" style="width: 65%; margin-right: 1%; margin-top: 1.65em;"/>
<br>
[Data generated a few hours ago... (excuse the mess!)](https://hackmd.io/_fMMOiDvRRiZ1f0cS0uchg?view)
]
---
# 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>
---
## 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
<br>
#### 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)
]
---
## Our experiences with the Jeston Xaviers
.small[
#### Documentation
* [GPU musings (with an eye on genomics)](https://hackmd.io/@Miles/B1U-cOMyu)
* [Setting up live GPU basecalling on Linux](https://github.com/sirselim/jetson_nanopore_sequencing/blob/main/live_basecalling.md)
<br>
#### Presentations
##### **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
##### **eResearch 2021 presentation**
* [Harnessing the disruptive nature of portable sequencing for community empowerment](https://sirselim.github.io/eResearch-Presentation-2021/index.html)
* live sequencing and presentation run from the Xavier NX (SARS-COV2 sequencing)
##### **Nvidia Spring GPU Technology Conference 2021**
* [The disruptive nature of portable sequencing](https://sirselim.github.io/NvidiaGTC_2021/)
]
---
# If you're interested in GPUs and genomics...
.center[
<img src="images/gpu_musing_tweet.png" style="width: 45%; margin-right: 1%; margin-top: 1.65em;"/>
<br />
[GPU musings (with an eye on genomics)](https://hackmd.io/@Miles/B1U-cOMyu)
]
---
class: middle hide_logo
.center[
<img src="images/gtc21_mbenton.jpg" style="width: 90%; margin-right: 1%; margin-top: 1.65em;"/>
]
---
class: middle hide_logo
# Some parting thoughts
---
class: top
# acknowledgements (people to 'nerd' out with!)
<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>
.pull-left[.medium[
**Georgia Bell** (ESR)
Una Ren (ESR)
Leah Kemp (ESR)
]]
.pull-right[.medium[
Matthew Walton (ESR)
Richard Dean (ESR)
Russell Smithies (ESR)
]]