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class: center, middle, inverse, title-slide # What can RSEs do for U? ###
Anna Krystalli
<i class="fab fa-twitter faa-float animated "></i>@annakrystalli
###
9th July 2019 | #BESQuantMove2019
--- # 👋 Hello ### me: **Dr Anna Krystalli** - **Research Software Engineer**, _University of Sheffield_ + twitter **@annakrystalli** + github **@annakrystalli** + email **a.krystalli[at]sheffield.ac.uk** - **Editor [rOpenSci](http://onboarding.ropensci.org/)** - **Software Sustainability Institute Fellow 2019** <br> ### slides: **bit.ly/bes_rse** --- class: bg-main2 split-70 hide-slide-number .column.slide-in-left[ .sliderbox.vmiddle.shade_main.center[ # .font_large[Motivation]]] .column[ ] --- class: middle, center # The paper is the advertisement > “an article about computational result is advertising, not scholarship. The **actual scholarship is the full software environment, code and data, that produced the result.**” *John Claerbout paraphrased in [Buckheit and Donoho (1995)](https://statweb.stanford.edu/~wavelab/Wavelab_850/wavelab.pdf)* -- <br> <br> ### Yet, our main focus is on the advertisement. --- class: bg-main3 # Research increasingly computational -- .font_large[ - 92% of academics use research software - 69% say their research won't be practical without it - 56% develop their own software (21% with no formal training) ] <br> _S.J. Hettrick et al, UK Research Software Survey 2014, [DOI:10.5281/zenodo.1183562](https://zenodo.org/record/1183562)._ --- class: bg-main1, middle, center # Consequences --- class: center # Reproducibility crisis .img-fill[![](assets/woes.png)] --- class: center background-image: url("https://media0.giphy.com/media/TS0HT0Km06WmQ/giphy.gif?cid=790b76115d1e0a44616f45567759dc42&rid=giphy.gif") background-size: cover # .bg-white[ Reinventing the wheel] .bg-white[In often complex and inefficient ways!] --- background-image: url("https://media2.giphy.com/media/7QOd9u8qQ4Hio/giphy.gif?cid=790b76115d2075bd565342382eb865f4&rid=giphy.gif") background-size: contain # Missed opportunities --- # The birth of RSE .img-cover[![](assets/RSE_history.png)] --- class: bg-main2 split-70 hide-slide-number background-image: url("https://cdn-images-1.medium.com/max/1600/1*v-AmdN95tAiNrpO9EMc86g.jpeg") background-size: cover .column.slide-in-left[ .sliderbox.vmiddle.shade_main.center[ # .font_large[Who are RSEs?]]] .column[ ] .bottom_abs.font_small[CC-BY Antonia Cozacu, Jan Philipp Dietrich, de-RSE e.V.] --- background-image: url("assets/detail-illustration.png") background-position: right background-size: contain # .bg-white-transp[Software Engineering Practices] - **Version Control** - **Testing** - **Continuous Integration** - **Documentation** -- <br> <br> <br> ### User focused --- background-image: url("assets/domains.png") background-position: center # Background in Research --- background-image: url("https://yoast.com/app/uploads/2017/06/Open_Source_FI.jpg") background-size: cover class: bg-main4 # Open Source Ethos * .font_large[ - .bg-brown[**Transparent materials**] - .bg-brown[**Ability to clone, adapt and collaborate**] - .bg-brown[**Sustainability through community**] - .bg-brown[**Clear record of contributions**] ] _\* personal opinion_ .bottom_abs.font_small[image source: https://yoast.com/interview-with-joost-on-open-source/] --- class: middle, center # Where we live (@ Sheffield) .figb90[![](assets/rse_home.png)] --- class: bg-main1, middle, center # In summary --- class: bg-main3 .image_speech[![](assets/mike_speech.png)] .slide-in-bottom[ ![](assets/mike.png) ] --- class: bg-main2 split-70 hide-slide-number .column.slide-in-left[ .sliderbox.vmiddle.shade_main.center[ # .font_large[What can they do for U?]]] .column[ ] --- class: bg-main4, middle, center # Areas of expertise .font_large[ High Performance computing Code optimisation Code & Data packaging Software development Training Community building ] --- class: split-33 with-thick-border .column.bg-main1[.content[.pad10px[ .center[ # .font_small[**Bessemer Cluster**] .image_profile[![](assets/Will_Furnass_profile.jpg)] ### **Will Furnass** Working with the central IT department’s infrastructure and research computing teams to help set up a new HPC cluster <br> .font_small[ **Funding:** University of Sheffield Central IT ] ]]]] .column[ .content.nopadding[ .img-fill[![](assets/HPC.png)] .img-fill[ <a title="Chemical Engineer [Public domain], via Wikimedia Commons" href="https://commons.wikimedia.org/wiki/File:Bessemer_5180.JPG"><img width="512" alt="Bessemer 5180" src="https://upload.wikimedia.org/wikipedia/commons/thumb/3/3a/Bessemer_5180.JPG/512px-Bessemer_5180.JPG"></a> ] ]] --- class: split-33 with-thick-border .column.bg-main1[.content[.pad10px[ .center[ # .font_small[**Rumour Analysis Service**] .image_profile[![](assets/TwinCropped_small.jpg)] ### **Twin Karmakharm** Open-source web-based rumour analysis tool that can continuously learn from journalists. <br> .font_small[ **Funding:** Digital News Initiative Fund (Google) ] ]]]] .column[ .content.nopadding[ .img-fill[![](assets/rumour-analysis-service-screenshot-nasa.jpg)]]] --- class: split-33 with-thick-border .column.bg-main1[.content[.pad10px[ .center[ # .font_small[**Immune system simulations**] .image_profile[![](assets/heywood-profile.jpg)] ### **Peter Heywood** Graphics Processing Unit (GPU) accelerated immune system simulations for the evaluation of alternate TB vaccine administration policies <br> .font_small[ **Funding:** European Research Council (ERC) under EU's Horizon 2020. ] ]]]] .column[ .content.nopadding[ .img-fill[![](assets/flamegpu-keratinocyte-not-actually-strituvad.gif)]]] --- class: split-33 with-thick-border .column.bg-main1[.content[.pad10px[ .center[ # .font_small[**Flame GPU 2.0**] .image_profile[![](assets/mozhgan.jpg)] ### **Mozhgan Kabiri Chimeh** Developing v2.0 of Flame GPU a framework for writing agent-based models deployed on GPUs <br> .font_small[ **Funding:** EPSRC fellowship “Accelerating Scientific Discovery with Accelerated Computing”. ] ]]]] .column[ .content.nopadding[ .img-fill[![](assets/flamegpu-logo.jpg)] <iframe width="560" height="315" src="https://www.youtube.com/embed/u1LBLSlMUFo?start=97" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe> ] _First developed by Sheffield RSE Co-Founder Paul Richmond_ ] --- class: split-33 with-thick-border .column.bg-main1[.content[.pad10px[ .center[ # .font_small[**Sedmaps web app**] .image_profile[![](assets/anna_profile.jpg)] ### **Anna Krystalli** Access, visualise, summarise and extract raster maps of the north-west European Shelf sedimentary environment. <br> .font_small[ **Funding:** NERC through the Marine Ecosystems Research Programme ] ]]]] .column[ .content.nopadding[ .img-fill[ <video src="assets/sedmaps_demo.mp4" width=100% controls autoplay></video> ]] **https://sheffield-university.shinyapps.io/sedmap_shiny/** .font_small[Wilson, R. J., Speirs, D. C., Sabatino, A., and Heath, M. R.: ***A synthetic map of the north-west European Shelf sedimentary environment for applications in marine science***, Earth Syst. Sci. Data, 10, 109-130, <https://doi.org/10.5194/essd-10-109-2018>, 2018 ] ] --- class: split-33 with-thick-border .column.bg-main1[.content[.pad10px[ .center[ # .font_small[**SeabirddietDB**] .image_profile[![](assets/anna_profile.jpg)] ### **Anna Krystalli** Seabird diet data product prepared for depositing in KNB + as R package <br> .font_small[ **Funding:** NERC through the Marine Ecosystems Research Programme ] ]]]] .column[ .content.nopadding[ ```r seabirddietDB::seabirddiet ``` ``` ## # A tibble: 2,911 x 34 ## id year startyear endyear multiyear location latitude longitude ## <int> <dbl> <dbl> <dbl> <lgl> <chr> <dbl> <dbl> ## 1 1 1973 1973 1973 FALSE Co. Ker… 52.2 -9.75 ## 2 2 1973 1973 1973 FALSE Co. Ker… 52.2 -9.75 ## 3 3 1973 1973 1973 FALSE Co. Ker… 52.2 -9.75 ## 4 4 1973 1973 1973 FALSE Co. Ker… 52.2 -9.75 ## 5 5 1973 1973 1973 FALSE Co. Ker… 52.2 -9.75 ## 6 6 1973 1973 1973 FALSE Co. Ker… 52.2 -9.75 ## 7 7 1973 1973 1973 FALSE Co. Ker… 52.2 -9.75 ## 8 8 1983 1983 1983 FALSE East An… 52.5 1 ## 9 9 1983 1983 1983 FALSE East An… 52.5 1 ## 10 10 1983 1983 1983 FALSE East An… 52.5 1 ## # … with 2,901 more rows, and 26 more variables: pred_common_name <chr>, ## # pred_species <chr>, pred_rank <chr>, pred_aphia_id <int>, ## # pred_valid_name <chr>, pred_valid_aphia_id <int>, ## # pred_breeding_status <chr>, pred_age_group <chr>, ## # prey_orig_descr <chr>, prey_taxon <chr>, prey_rank <chr>, ## # prey_aphia_id <int>, prey_valid_name <chr>, prey_valid_aphia_id <int>, ## # prey_size <chr>, prey_sd <chr>, prey_age_group <chr>, freq_occ <dbl>, ## # freq_num <dbl>, freq_biomass <dbl>, sample_size <dbl>, ## # sample_type <chr>, ref_n <dbl>, ref_ids <chr>, source <chr>, ## # notes <chr> ``` .font_small[_Dataset prepared by R. Nager, J. Grecian and A. Olin_] ]] --- class: split-33 with-thick-border .column.bg-main1[.content[.pad10px[ .center[ # .font_small[**SeabirddietDB**] .image_profile[![](assets/anna_profile.jpg)] ### **Anna Krystalli** Seabird diet data product prepared for depositing in KNB + as R package <br> .font_small[ **Funding:** NERC through the Marine Ecosystems Research Programme ] ]]]] .column[ .content.nopadding[ ```r seabirddietDB::sbd_plot_predators(year = 1973) ```
.font_small[_Dataset prepared by R. Nager, J. Grecian and A. Olin_] ]] --- class: bg-main2 split-70 hide-slide-number .column.slide-in-left[ .sliderbox.vmiddle.shade_main.center[ # .font_large[Capacity Building]]] .column[ ] --- class: middle center <blockquote class="twitter-tweet" data-lang="en"><p lang="en" dir="ltr">Here we go with <a href="https://twitter.com/gvwilson?ref_src=twsrc%5Etfw">@gvwilson</a> : the gulf between the computing scientific "elite" and those emailing spreadsheets is growing, and that's bad.</p>— Ian Hawke (@IanHawke) <a href="https://twitter.com/IanHawke/status/664081682480373760?ref_src=twsrc%5Etfw">November 10, 2015</a></blockquote> <script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script> -- # RSE skills are a benefit to all! --- class: split-two bg-main4 middle center .column[.content[ [.figb90[![](assets/bes_reproducible_code.png)]](https://www.britishecologicalsociety.org/wp-content/uploads/2019/06/BES-Guide-Reproducible-Code-2019.pdf) ]] .column[.content[ [.figb90[![](assets/bes_data-mgmt.png)]](https://www.britishecologicalsociety.org/wp-content/uploads/2019/06/BES-Guide-Data-Management-2019.pdf) ]] --- class: bg-main1, middle, center # Training --- class: split-two .column[.content[ ![](https://carpentries.org/assets/img/TheCarpentries.svg) <br> #### Training community teaching foundational coding and data science skills to researchers worldwide <br> University of Sheffield is Member Organisation ]] .column.bg-black[.content[ .figb90[![](assets/carpentries.png)] ]] --- # Bespoke training ### [ACCE DTP Data & Project management](https://annakrystalli.me/rrresearch/) _2 day course for 1st year ACCE DTP postgraduates since 2015_ <br> -- ###[Reproducible research with `rrtools`](https://annakrystalli.me/rrtools-repro-research/) _North Western Universities R Day 2018_ <br> ### [Practical Data management](https://github.com/annakrystalli/dataspice-tutorial) _Summer School on Reproducibility in Computational Sciences 2018_ --- class: bg-main1, middle, center # Support --- background-image: url("https://media2.giphy.com/media/5YiRHZtcSeiEyOpSV7/giphy.gif?cid=790b76115d2070523958673849c75d9e&rid=giphy.gif") background-size: cover class: bg-main1 # Get your lab in order <br> -- ## Get help with: -- - .font_large[**Organising your research group's digital assets**] -- - .font_large[**Developing protocols**] -- - .font_large[**Developing templates & checklists**] --- background-image: url("assets/code-c.png") background-size: contain background-position: right # Code Clinics <br> .font_small.bg-white-transp.strong[ ### Are you... - Thinking of ways to improve your code? - Want to automate a task (e.g: series of scripts)? - Unsure of which software tools to use for your project? - You have a lot of data and need help organising, storing, accessing or visualising it? - Need some advice on optimising your code? - Want to know whether your code could run faster on multiple cores or GPUs? - Want to re-write your code written in one language (e.g: Excel) in another language such as Python? - Need help with version control? - Want to know more about making your code open and/or citable? **We can help!** ] --- class: bg-main1, middle, center # Community --- class: split-three with-border .row.bg-main1[.content.vmiddle[ # Hackathons <br> _Fun and informal spaces for practice and Peer-to-Peer Learning_ ]] .row.bg-main4[.content.vmiddle[ # ReproHack Series <br> .font_large[**Hands on reproducibility hackathons**] ]] .row.bg-black[.content.nopadding[ .figb[![](assets/gpu_hackathon.png)] ]] --- class: split-two center with-thick-border .column.bg-main1[.content[ ### Sheffield R Users Group <blockquote class="twitter-tweet" data-lang="en"><p lang="en" dir="ltr">Great evening at <a href="https://twitter.com/Sheffield_R_?ref_src=twsrc%5Etfw">@Sheffield_R_</a> meet up hearing about phylogenetic methods with <a href="https://twitter.com/ChrisCooney101?ref_src=twsrc%5Etfw">@ChrisCooney101</a> and computer learning with Yichen He, both from our lab group (<a href="https://twitter.com/MacrobirdEvol?ref_src=twsrc%5Etfw">@MacrobirdEvol</a>).<br><br>Great bird-y science, and great coding 😊 <a href="https://twitter.com/hashtag/rstats?src=hash&ref_src=twsrc%5Etfw">#rstats</a> 🐦 <a href="https://t.co/4d9H7zHb9Q">pic.twitter.com/4d9H7zHb9Q</a></p>— Emma Hughes (@EHughes27) <a href="https://twitter.com/EHughes27/status/1059888635745656832?ref_src=twsrc%5Etfw">November 6, 2018</a></blockquote> <script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script> ]] .column[.content[ ### Women in HPC ![](https://womeninhpc.org/wp-content/uploads/2015/11/WHPC_long_logo_rgb_slogan-e1446833818584.png) .fig90[![](assets/WHPC_Workshop_Group.png)] ]] --- class: bg-main2 split-70 hide-slide-number .column.slide-in-left[ .sliderbox.vmiddle.shade_main.center[ # .font_large[What's possible]]] .column[ ] --- background-image: url("assets/hanslibdata.png") background-size: cover class: bg-main1 # gapminder.org: 2006 ### .bg-white-transp[[liberating stories from data](https://youtu.be/hVimVzgtD6w?t=15m3s)] --- class: bg-main1 # Gapminder today ```r library(ggplot2) p <- ggplot(gapminder::gapminder, aes(gdpPercap, lifeExp, size = pop, color = continent, frame = year)) + geom_point() + scale_x_log10() + theme_bw() ``` ```r plotly::ggplotly(p) ```
--- background-image: url("https://github.com/ropensci/roweb2/blob/master/themes/ropensci/static/img/community-scroll/c6.jpg?raw=true") background-size: cover class: split-two .column.bg-ro.center[.content[ # rOpenSci *** ![](https://d33wubrfki0l68.cloudfront.net/aa488a0570cdf44d956942df324bb26cba77c4a2/3919e/img/icon_short_white.svg) <br> > ### Transforming science through open data and software <br> ![](https://d33wubrfki0l68.cloudfront.net/dd77315d03290f3570cc09a3b68ea83c09192e72/286f1/img/numfocus.png) ]] .column.bg-ro-transp[.content.vmiddle[ - **Technical infrastructure: peer-reviewed, community-contributed R scientific software tools.** - Creating social infrastructure through a welcoming and diverse community - Making the right data, tools and best practices more discoverable - Building capacity of software users and developers. - Promoting advocacy for a culture of data sharing and reusable software. .fig90[![](assets/meeropensci-logo-1)] ]] --- class: bg-main1, middle, center # tl;dr --- class: bg-main3 center # .font_large[We can have nice things!] -- ### More robust, innovative, efficient & impactful research that's accessible to more people <img src="assets/SSIHex.png" height=300px><img src="https://media0.giphy.com/media/GiXbMe92rt9NS/giphy.gif?cid=790b76115d1b7980625653776b9da236&rid=giphy.gif" height=300px> --- class: bg-main1, middle, center # .font_large[Thanks for listening! 👋]