class: center, middle, inverse, title-slide # .large[The disruptive nature of portable sequencing & edge compute for community empowerment] ###
Nvidia GTC, 12
th
- 16
th
April 2021
.large[
Dr Miles Benton
]
Human Genomics
Institute of Environmental Science and Research
(ESR)
Aotearoa
(New Zealand)
--- class: middle hide_logo
# .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)] <!-- SVG Icons are from https://simpleicons.org --> <footer class="pv3 ph3 ph5-ns tc"> <a class="link near-black hover-blue dib h2 w2 mr3" href="https://github.com/sirselim" title="GitHub"> <svg fill="currentColor" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 16 16" fill-rule="evenodd" clip-rule="evenodd" stroke-linejoin="round" stroke-miterlimit="1.414"><path d="M8 0C3.58 0 0 3.582 0 8c0 3.535 2.292 6.533 5.47 7.59.4.075.547-.172.547-.385 0-.19-.007-.693-.01-1.36-2.226.483-2.695-1.073-2.695-1.073-.364-.924-.89-1.17-.89-1.17-.725-.496.056-.486.056-.486.803.056 1.225.824 1.225.824.714 1.223 1.873.87 2.33.665.072-.517.278-.87.507-1.07-1.777-.2-3.644-.888-3.644-3.953 0-.873.31-1.587.823-2.147-.083-.202-.358-1.015.077-2.117 0 0 .672-.215 2.2.82.638-.178 1.323-.266 2.003-.27.68.004 1.364.092 2.003.27 1.527-1.035 2.198-.82 2.198-.82.437 1.102.163 1.915.08 2.117.513.56.823 1.274.823 2.147 0 3.073-1.87 3.75-3.653 3.947.287.246.543.735.543 1.48 0 1.07-.01 1.933-.01 2.195 0 .215.144.463.55.385C13.71 14.53 16 11.534 16 8c0-4.418-3.582-8-8-8"/></svg> </a> <a class="link hover-blue near-black dib h2 w2 mr3" href="https://twitter.com/miles_benton" title="Twitter"> <svg fill="currentColor" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 16 16" fill-rule="evenodd" clip-rule="evenodd" stroke-linejoin="round" stroke-miterlimit="1.414"><path d="M16 3.038c-.59.26-1.22.437-1.885.517.677-.407 1.198-1.05 1.443-1.816-.634.375-1.337.648-2.085.795-.598-.638-1.45-1.036-2.396-1.036-1.812 0-3.282 1.468-3.282 3.28 0 .258.03.51.085.75C5.152 5.39 2.733 4.084 1.114 2.1.83 2.583.67 3.147.67 3.75c0 1.14.58 2.143 1.46 2.732-.538-.017-1.045-.165-1.487-.41v.04c0 1.59 1.13 2.918 2.633 3.22-.276.074-.566.114-.865.114-.21 0-.416-.02-.617-.058.418 1.304 1.63 2.253 3.067 2.28-1.124.88-2.54 1.404-4.077 1.404-.265 0-.526-.015-.783-.045 1.453.93 3.178 1.474 5.032 1.474 6.038 0 9.34-5 9.34-9.338 0-.143-.004-.284-.01-.425.64-.463 1.198-1.04 1.638-1.7z" fill-rule="nonzero"/></svg> </a> <a class="link hover-blue near-black dib h2 w2 mr3" href="https://scholar.google.co.nz/citations?user=iEhBavEAAAAJ&hl=en" title="Google Scholar"> <svg fill="currentColor" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24" fill-rule="evenodd" clip-rule="evenodd" stroke-linejoin="round" stroke-miterlimit="1.414"><path d="M12 24a7 7 0 1 1 0-14 7 7 0 0 1 0 14zm0-24L0 9.5l4.838 3.94A8 8 0 0 1 12 9a8 8 0 0 1 7.162 4.44L24 9.5z" fill-rule="nonzero"/></svg> </a> <a class="link hover-blue near-black dib h2 w2 mr3" href="http://orcid.org/0000-0003-3442-965X" title="ORCID"> <svg fill="currentColor" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24" fill-rule="evenodd" clip-rule="evenodd" stroke-linejoin="round" stroke-miterlimit="1.414"><path d="M12 0C5.372 0 0 5.372 0 12s5.372 12 12 12 12-5.372 12-12S18.628 0 12 0zM7.369 4.378c.525 0 .947.431.947.947s-.422.947-.947.947a.95.95 0 0 1-.947-.947c0-.525.422-.947.947-.947zm-.722 3.038h1.444v10.041H6.647V7.416zm3.562 0h3.9c3.712 0 5.344 2.653 5.344 5.025 0 2.578-2.016 5.025-5.325 5.025h-3.919V7.416zm1.444 1.303v7.444h2.297c3.272 0 4.022-2.484 4.022-3.722 0-2.016-1.284-3.722-4.097-3.722h-2.222z" fill-rule="nonzero"/></svg> </a> </footer> --- 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> </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 # 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 /> © Oxford Nanopore Technologies </center> --- layout: false class: middle # Example squiggle plot ![](https://nanoporetech.github.io/tombo/_images/single_samp.png) .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[ ![Titan RTX](images/titan.jpg) ] <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>
.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>
.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 /> © 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> --- ## 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) ] --- # 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 # 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) Richard Dean (ESR) ]] .pull-right[.medium[ Matthew Walton (ESR) Shane Sturrock (ESR) Russell Smithies (ESR) ]] --- layout: false class: hide_logo background-image: url("images/TaiHuaRoa.jpg") background-size: contain