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<title>From research software engineering to data science: how technology will impact the way we research</title>
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<div class="slides">
<section id="title-slide" data-background-image="img/first-slide.png" data-background-opacity="0.5" data-background-size="contain" class="quarto-title-block center">
<h1 class="title">From research software engineering to data science: how technology will impact the way we research</h1>
<div class="quarto-title-authors">
<div class="quarto-title-author">
<div class="quarto-title-author-name">
Florencia D’Andrea, Ph.D.
</div>
<p class="quarto-title-affiliation">
Postdoctoral fellow at the Master of Data Science program
</p>
<p class="quarto-title-affiliation">
University of British Columbia
</p>
</div>
</div>
</section>
<section class="slide level2">
<div class="cell">
</div>
<h4 id="slides">Slides</h4>
<p><a href="https://flor14.github.io/wsu-dandrea/slides.html#/title-slide">https://www.flor14.github.io/wsu-dandrea/slides.html</a></p>
<p><br><br>
<br></p>
<div class="small-text">
<p><a rel="license" href="http://creativecommons.org/licenses/by/4.0/"><img alt="Creative Commons License" style="border-width:0" src="https://i.creativecommons.org/l/by/4.0/88x31.png"></a><br>This work is licensed under a <a rel="license" href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution 4.0 International License</a>.</p>
<p><strong>Title slide illustration</strong>: The Turing Way Community, & Scriberia. (2020, March 3). Illustrations from the Turing Way book dashes. Zenodo. http://doi.org/10.5281/zenodo.3695300</p>
</div>
<div class="footer">
<p>Click here! I can be a link!</p>
</div>
</section>
<section id="hello" class="slide level2">
<h2>Hello</h2>
<h4 id="dr.-florencia-dandrea">Dr. Florencia D’Andrea</h4>
<div class="columns">
<div id="vcenter" class="column" style="width:40%;">
<div class="cell" data-layout-align="center">
<div class="cell-output-display">
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="https://res.cloudinary.com/flor/image/upload/w_1000,ar_1:1,c_fill,g_auto,e_art:hokusai/v1683580772/IMG_20220607_130734112_mu4fpd.jpg" width="250"></p>
</figure>
</div>
</div>
</div>
</div><div id="vcenter" class="column" style="width:60%;">
<p>🐦 <strong>Twitter</strong><br>
<a href="http://twitter.com/cantoflor_87"><span class="citation" data-cites="cantoflor_87">@cantoflor_87</span></a><br></p>
<p>📢 <strong>Mastodon</strong></p>
<p><a href="https://techhub.social/@florencia"><span class="citation" data-cites="florencia">@florencia</span><span class="citation" data-cites="techhub.social">@techhub.social</span></a></p>
<p>🌐 <strong>Web</strong></p>
<p><a href="https://florenciadandrea.com">https://florenciadandrea.com</a></p>
</div>
</div>
</section>
<section class="slide level2">
<div class="columns">
<div id="vcenter" class="column" style="width:50%;">
<p>lab <img data-src="img/researchers1.png"></p>
</div><div id="vcenter" class="column" style="width:50%;">
<p>field work <img data-src="img/researchers2.png"></p>
</div>
</div>
</section>
<section>
<section id="do-researchers-develop-software" class="title-slide slide level1 center" data-background-color="#E5E4E2">
<h1>Do researchers develop <span class="rn" data-rn-type="circle" data-rn-color="white">software</span>?</h1>
<div class="footer">
<p>Press R</p>
</div>
</section>
<section class="slide level2">
<div class="big-text">
<p><em>research software</em></p>
</div>
<p>Software that is used to generate, process or analyse results that you intend to appear in a publication</p>
<p>Research software can be anything <span class="rn" data-rn-type="highlight" data-rn-multiline="true">from a few lines of code written by yourself, to a professionally developed software package</span></p>
<div class="footer">
<p>Press R - <a href="https://doi.org/10.5281/zenodo.608046">Hettrick <em>et al.</em> (2014) UK Research Software Survey 2014. Zenodo</a></p>
</div>
</section></section>
<section>
<section id="do-researchers-develop-software-1" class="title-slide slide level1 center" data-background-color="#E5E4E2">
<h1>Do researchers develop <span class="rn" data-rn-type="circle" data-rn-color="white">software</span>?</h1>
<p><span class="rn" data-rn-type="highlight" data-rn-multiline="true">Yes, they do!</span></p>
<div class="footer">
<p>Press R</p>
</div>
</section>
<section id="section" class="slide level2" data-background-image="img/back-question.png" data-background-size="1000px">
<h2></h2>
<div class="fragment" data-fragment-index="1">
<p><strong>1.</strong> Are Researchers Software Developers?</p>
</div>
<div class="fragment" data-fragment-index="2">
<p><strong>2.</strong> Why is it important to write “good software” in research?</p>
</div>
<div class="fragment" data-fragment-index="3">
<p><strong>3.</strong> What kind of practices and/or tools we need to apply for creating better research software?</p>
<pre><code>- Examples</code></pre>
</div>
</section>
<section id="section-1" class="slide level2" data-background-image="img/back-question.png" data-background-size="1000px">
<h2></h2>
<div class="fragment" data-fragment-index="1">
<p><strong>4.</strong> We don’t have training !<br>
Where to find resources to learn?</p>
</div>
<div class="fragment" data-fragment-index="2">
<p><strong>5.</strong> Where can I find other researchers interested in software?</p>
</div>
<div class="fragment" data-fragment-index="3">
<p><strong>6.</strong> Career paths</p>
<pre><code>- Survey results</code></pre>
</div>
<div class="fragment" data-fragment-index="4">
<p><strong>Final comments</strong></p>
</div>
</section></section>
<section>
<section id="are-researchers-software-developers" class="title-slide slide level1 center" data-background-color="#67032F">
<h1>Are Researchers Software Developers?</h1>
<p>Scientists can create software as part of their research</p>
<div class="sectionhead">
<p>1 <span style="opacity:0.25">2 3 4 5 6</span></p>
</div>
</section>
<section class="slide level2">
<h3 id="software-quality-can-affect-research-results">Software quality can affect research results</h3>
<div class="columns">
<div id="vcenter" class="column" style="width:60%;">
<p><img data-src="img/bettersoftware.png"></p>
</div><div id="vcenter" class="column" style="width:40%;">
<p>What are the potential consequences of developing bad quality software?</p>
</div>
</div>
<div class="footer">
<p>Logo: <a href="https://www.software.ac.uk/about">https://www.software.ac.uk/about</a></p>
</div>
</section>
<section id="reproducibility-crisis" class="slide level2">
<h2>Reproducibility crisis</h2>
<div class="columns">
<div id="vcenter" class="column" style="width:50%;">
<p><img data-src="img/rep-crisis.png"></p>
</div><div id="vcenter" class="column" style="width:50%;">
<p>Code unavailable is <strong>one</strong> of the reasons why researchers can’t reproduce their articles</p>
</div>
</div>
<div class="footer">
<p><a href="https://www.nature.com/articles/533452a">Baker, M (2016) 1,500 scientists lift the lid on reproducibility - Nature</a></p>
</div>
</section>
<section id="reproducibility" class="slide level2">
<h2>Reproducibility</h2>
<img data-src="img/reproducible-matrix.jpg" style="width:50.0%" class="r-stretch"><div class="footer">
<p><a href="https://the-turing-way.netlify.app/reproducible-research/overview/overview-definitions.html">Definitions - The Turing Way Handbook</a></p>
</div>
</section>
<section class="slide level2">
<p>A result is reproducible when the <em>same</em> analysis steps performed on the <em>same</em> dataset consistently produces the <em>same</em> answer</p>
<img data-src="img/reproducible-definition-grid.png" class="r-stretch quarto-figure-center"><div class="footer">
<p><a href="DOI:%2010.5281/zenodo.3332807">The Turing Way project illustration by Scriberia. Used under a CC-BY 4.0 licence.</a></p>
</div>
</section>
<section class="slide level2">
<h3 id="reproducibility-1">Reproducibility</h3>
<div class="columns">
<div id="vcenter" class="column" style="width:60%;">
<p><img data-src="img/research-group.png"></p>
</div><div id="vcenter" class="column" style="width:40%;">
<ul>
<li class="fragment"><strong>Empirical</strong></li>
<li class="fragment"><strong>Statistical</strong></li>
<li class="fragment"><span class="rn"><strong>Computational</strong></span></li>
</ul>
</div>
</div>
<div class="footer">
<p>Press R - <a href="https://www.edge.org/response-detail/25340">Victoria Stodden (2014) What scientific idea is ready for retirement? - www.edge.org</a></p>
</div>
</section>
<section class="slide level2">
<div class="big-text-long">
<p><em>Computational reproducibility</em></p>
</div>
<p>When detailed information is provided about code, software, hardware and implementation details.</p>
<img data-src="img/computer.png" class="r-stretch quarto-figure-center"><div class="footer">
<p>Victoria Stodden (2014) <a href="https://www.edge.org/response-detail/25340">What scientific idea is ready for retirement? - www.edge.org</a></p>
</div>
</section></section>
<section>
<section id="why-is-it-important-to-write-good-software-in-research" class="title-slide slide level1 center" data-background-color="#67032F">
<h1>Why is it important to write “good software” in research?</h1>
<p>The more detailed information is provided about the software we create, the more likely it is to reproduce research results using it</p>
<div class="sectionhead">
<p><span style="opacity:0.25">1</span> 2 <span style="opacity:0.25">3 4 5 6</span></p>
</div>
</section>
<section id="example" class="slide level2">
<h2>Example</h2>
<div class="columns">
<div id="vcenter" class="column" style="width:40%;">
<p><strong>Situation 1</strong></p>
<p>Julia wants to share R code with her supervisor</p>
</div><div id="vcenter" class="column" style="width:60%;">
<p><img data-src="img/researcher3.png"></p>
</div>
</div>
</section>
<section class="slide level2">
<h4 id="plots-code">Plot’s code</h4>
<p>Julia is running this code on her computer ✅</p>
<div class="cell">
<details>
<summary>Show the code</summary>
<div class="sourceCode cell-code" id="cb3"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb3-1"><a href="#cb3-1"></a><span class="fu">library</span>(readr)</span>
<span id="cb3-2"><a href="#cb3-2"></a><span class="fu">library</span>(tidyr)</span>
<span id="cb3-3"><a href="#cb3-3"></a><span class="fu">library</span>(ggplot2)</span>
<span id="cb3-4"><a href="#cb3-4"></a></span>
<span id="cb3-5"><a href="#cb3-5"></a>coffee_data <span class="ot"><-</span> <span class="fu">read_csv</span>(<span class="st">"data/coffee_data.csv"</span>)</span>
<span id="cb3-6"><a href="#cb3-6"></a></span>
<span id="cb3-7"><a href="#cb3-7"></a>coffee_data <span class="sc">|></span> </span>
<span id="cb3-8"><a href="#cb3-8"></a> <span class="fu">pivot_longer</span>(<span class="at">cols=</span>aroma<span class="sc">:</span>moisture,</span>
<span id="cb3-9"><a href="#cb3-9"></a> <span class="at">names_to=</span><span class="st">"caracteristicas_cafe"</span>,</span>
<span id="cb3-10"><a href="#cb3-10"></a> <span class="at">values_to=</span><span class="st">"value"</span>) <span class="sc">|></span> </span>
<span id="cb3-11"><a href="#cb3-11"></a> <span class="fu">ggplot</span>(<span class="fu">aes</span>(value, total_cup_points)) <span class="sc">+</span></span>
<span id="cb3-12"><a href="#cb3-12"></a> <span class="fu">geom_smooth</span>(<span class="at">method=</span> <span class="st">"gam"</span>, <span class="at">span=</span><span class="fl">0.3</span>, <span class="at">color=</span><span class="st">'purple'</span>) <span class="sc">+</span></span>
<span id="cb3-13"><a href="#cb3-13"></a> <span class="fu">facet_wrap</span>(<span class="sc">~</span>caracteristicas_cafe, <span class="at">scale=</span><span class="st">"free_y"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</details>
</div>
<img data-src="slides_files/figure-revealjs/plot-1.png" width="960" class="r-stretch"></section>
<section id="but" class="slide level2">
<h2>But!</h2>
<h3 id="her-supervisor-gets-an-error">Her supervisor gets an error ❌</h3>
<div class="sourceCode" id="cb4"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb4-1"><a href="#cb4-1"></a>Error <span class="cf">in</span> <span class="fu">pivot_longer</span>(., </span>
<span id="cb4-2"><a href="#cb4-2"></a><span class="at">cols =</span> aroma<span class="sc">:</span>moisture,</span>
<span id="cb4-3"><a href="#cb4-3"></a><span class="at">names_to =</span> <span class="st">"types_coffe"</span>,</span>
<span id="cb4-4"><a href="#cb4-4"></a><span class="sc">:</span> could not find <span class="cf">function</span> <span class="st">"pivot_longer"</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<p>🤔 <strong>What could be going on?</strong></p>
</section>
<section id="new-package-version" class="slide level2">
<h2>New package version</h2>
<p>Code that is running in your computer now <span class="rn" data-rn-type="underline" data-rn-color="orange"><strong>may not work</strong> anymore if you upgrade the packages!</span></p>
<ul>
<li class="fragment"><code>tidyr</code> package version <code>0.8.3</code> does not include <code>pivot_longer()</code></li>
<li class="fragment">This functions was added in <code>tidyr</code> version <code>1.0.0</code></li>
</ul>
<div class="footer">
<p><a href="https://github.com/tidyverse/tidyr/releases?page=2"><code>tidyr</code> package - releases</a></p>
</div>
</section>
<section class="slide level2">
<div class="big-text">
<p><em>Computational environment</em></p>
</div>
<p>Characteristics of a 💻 that can affect the behavior of the work done on it, such as:</p>
<ul>
<li class="fragment"><p>your <strong>operating system</strong></p></li>
<li class="fragment"><p>what <strong>software</strong> do you have installed</p></li>
<li class="fragment"><p>software <strong>package versions</strong> are installed</p></li>
</ul>
<div class="footer">
<p><a href="https://the-turing-way.netlify.app/">The Turing Way: A Handbook for Reproducible Data Science (2019)</a></p>
</div>
</section>
<section id="computational-environments" class="slide level2">
<h2>Computational environments</h2>
<p>Important to capture them to avoid:</p>
<ul>
<li class="fragment"><p><span class="rn">Problems when sharing your code</span></p></li>
<li class="fragment"><p>That you code breaks with time</p></li>
</ul>
<img data-src="img/ErrorManagement.jpg" width="600" class="r-stretch quarto-figure-center"><div class="footer">
<p>Press R - <a href="http://doi.org/10.5281/zenodo.3695300">The Turing Way Community, & Scriberia. (2020)</a>]</p>
</div>
</section>
<section id="the-sleight-of-hand-trick-that-can-simplify-scientific-computing" class="slide level2">
<h2>The sleight-of-hand trick that can simplify scientific computing</h2>
<div class="columns">
<div id="vcenter" class="column" style="width:50%;">
<p>Computational environments and the tools to manage them can help researchers to deliver code that is reproducible, documented and shareable.</p>
</div><div class="column" style="width:50%;">
<p><img data-src="img/enviroment-nature.webp"></p>
</div>
</div>
<div class="footer">
<p><a href="https://www.nature.com/articles/d41586-023-01469-0">Perkel, J. (2023) The sleight-of-hand trick that can simplify scientific computing - Nature Article</a></p>
</div>
</section>
<section id="situation-1-bis" class="slide level2">
<h2>Situation 1-bis</h2>
<div class="columns">
<div id="vcenter" class="column" style="width:40%;">
<p>Julia wants to run the code 10 years later</p>
</div><div id="vcenter" class="column" style="width:60%;">
<p><img data-src="img/researcher3.png"></p>
</div>
</div>
</section>
<section id="challenge-to-scientists-does-your-ten-year-old-code-still-run" class="slide level2">
<h2>Challenge to scientists: does your ten-year-old code still run?</h2>
<div class="columns">
<div class="column" style="width:50%;">
<p><img data-src="img/failed-2.webp"></p>
</div><div class="column" style="width:50%;">
<p>‘Missing documentation and obsolete environments force participants in the Ten Years Reproducibility Challenge to get creative.’</p>
</div>
</div>
<div class="footer">
<p><a href="https://www.nature.com/articles/d41586-020-02462-7">Perkel, J. (2020) Challenge to scientists: does your ten-year-old code still run? - Nature Article</a></p>
</div>
</section>
<section id="computational-environments-1" class="slide level2">
<h2>Computational environments</h2>
<p>Important to capture them to avoid:</p>
<ul>
<li class="fragment"><p>Problems when sharing your code</p></li>
<li class="fragment"><p><span class="rn">That you code breaks with time</span></p></li>
</ul>
<img data-src="img/ErrorManagement.jpg" width="600" class="r-stretch quarto-figure-center"><div class="footer">
<p>Press R - <a href="http://doi.org/10.5281/zenodo.3695300">The Turing Way Community, & Scriberia. (2020)</a></p>
</div>
</section>
<section id="how-to-avoid-getting-this-error" class="slide level2">
<h2>How to avoid getting this error?</h2>
<p>Minimum: Documentation</p>
<div class="cell">
<div class="sourceCode cell-code" id="cb5"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb5-1"><a href="#cb5-1"></a><span class="fu">sessionInfo</span>()</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stdout">
<pre><code>R version 4.2.1 (2022-06-23)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Monterey 12.5
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] kableExtra_1.3.4 knitr_1.41 forcats_0.5.1 stringr_1.4.1
[5] dplyr_1.0.9 purrr_0.3.4 readr_2.1.2 tidyr_1.2.0
[9] tibble_3.1.8 ggplot2_3.4.0 tidyverse_1.3.2
loaded via a namespace (and not attached):
[1] lattice_0.20-45 svglite_2.1.0 lubridate_1.9.1
[4] assertthat_0.2.1 digest_0.6.29 utf8_1.2.2
[7] R6_2.5.1 cellranger_1.1.0 backports_1.4.1
[10] reprex_2.0.1 evaluate_0.16 httr_1.4.3
[13] pillar_1.8.0 rlang_1.0.6 googlesheets4_1.0.0
[16] readxl_1.4.0 rstudioapi_0.13 Matrix_1.4-1
[19] rmarkdown_2.16 labeling_0.4.2 splines_4.2.1
[22] webshot_0.5.3 googledrive_2.0.0 bit_4.0.4
[25] munsell_0.5.0 broom_1.0.0 compiler_4.2.1
[28] modelr_0.1.8 xfun_0.35 pkgconfig_2.0.3
[31] systemfonts_1.0.4 mgcv_1.8-40 htmltools_0.5.4
[34] tidyselect_1.2.0 fansi_1.0.3 viridisLite_0.4.0
[37] crayon_1.5.1 tzdb_0.3.0 dbplyr_2.2.1
[40] withr_2.5.0 grid_4.2.1 nlme_3.1-157
[43] jsonlite_1.8.0 gtable_0.3.0 lifecycle_1.0.3
[46] DBI_1.1.3 magrittr_2.0.3 scales_1.2.0
[49] cli_3.4.1 stringi_1.7.8 vroom_1.5.7
[52] farver_2.1.1 fs_1.5.2 xml2_1.3.3
[55] ellipsis_0.3.2 generics_0.1.3 vctrs_0.5.1
[58] tools_4.2.1 bit64_4.0.5 glue_1.6.2
[61] hms_1.1.1 parallel_4.2.1 fastmap_1.1.0
[64] yaml_2.3.5 timechange_0.2.0 colorspace_2.0-3
[67] gargle_1.2.0 rvest_1.0.2 haven_2.5.0 </code></pre>
</div>
</div>
</section>
<section id="tools-for-reproducibility" class="slide level2">
<h2>Tools for reproducibility</h2>
<p>We can use different tools to ensure the reproducibility of a project such as:</p>
<img data-src="img/rep-tools.png" class="r-stretch quarto-figure-center"></section></section>
<section>
<section id="capturing-the-computational-environment-is-needed-to-ensure-code-reproducibility" class="title-slide slide level1 center" data-background-color="#E5E4E2">
<h1>Capturing the computational environment is needed to ensure code reproducibility</h1>
</section>
<section id="situation-2" class="slide level2">
<h2>Situation 2</h2>
<div class="columns">
<div id="vcenter" class="column" style="width:60%;">
<p>Julia is writing code for an article. <strong>What is the best way to share the code with other colleagues?</strong></p>
</div><div id="vcenter" class="column" style="width:40%;">
<p><img data-src="img/researcher3.png"></p>
</div>
</div>
</section>
<section class="slide level2">
<div class="columns">
<div id="vcenter" class="column" style="width:50%;">
<p><strong>Git</strong></p>
<p>A version control system <img data-src="img/git-logo.png" width="250"></p>
</div><div id="vcenter" class="column" style="width:50%;">
<p><strong>GitHub</strong></p>
<p>Repository hosting service <img data-src="img/github-logo.png" width="300"></p>
</div>
</div>
<div class="footer">
<p><a href="https://git-scm.com/downloads/logos">Git logo</a></p>
</div>
</section>
<section class="slide level2">
<img data-src="img/vc-final-comic.png" width="500" class="r-stretch quarto-figure-center"><div class="footer">
<p><a href="http://www.phdcomics.com">“Piled Higher and Deeper” by Jorge Cham</a></p>
</div>
</section>
<section id="why-git-github-is-the-best-way-to-share-code" class="slide level2">
<h2>Why Git + GitHub is the best way to share code?</h2>
<div class="columns">
<div id="vcenter" class="column" style="width:40%;">
<p><img data-src="img/project-history.svg"></p>
</div><div id="vcenter" class="column" style="width:60%;">
<ul>
<li class="fragment"><p>It’s possible to assign names to each <strong>code version</strong> and revisit specific points in its history.</p></li>
<li class="fragment"><p>Your code is <strong>backed up online</strong> on GitHub.</p></li>
<li class="fragment"><p>It is easy to track the <strong>authorship</strong> of each change made</p></li>
</ul>
</div>
</div>
<div class="footer">
<p><a href="https://github.com/tidyverse/tidyr">Example repository</a></p>
</div>
</section>
<section id="why-git-github-is-the-best-way-to-share-code-1" class="slide level2">
<h2>Why Git + GitHub is the best way to share code?</h2>
<div class="columns">
<div id="vcenter" class="column" style="width:50%;">
<p><img data-src="img/pullrequest.jpg"></p>
</div><div id="vcenter" class="column" style="width:50%;">
<ul>
<li class="fragment"><p>You can share your code as an <strong>open source project</strong></p></li>
<li class="fragment"><p>Foster <strong>collaboration</strong></p>
<ul>
<li class="fragment">pull requests</li>
<li class="fragment">project boards</li>
<li class="fragment">github issues</li>
</ul></li>
</ul>
</div>
</div>
<div class="footer">
<p><a href="http://doi.org/10.5281/zenodo.3695300">The Turing Way Community, & Scriberia. (2020)</a> - <a href="https://github.com/flor14/wsu-dandrea/issues/1">Example 2</a></p>
</div>
</section>
<section class="slide level2">
<img data-src="img/openresearch.png" class="r-stretch quarto-figure-center"><div class="footer">
<p><a href="https://the-turing-way.netlify.app/reproducible-research/open/open-source.html#how-to-run-your-open-source-software-project">How to Run Your Open Source Software Project - The Turing Way Handbook</a> - <a href="http://doi.org/10.5281/zenodo.3695300">The Turing Way Community, & Scriberia. (2020)</a></p>
</div>
</section>
<section class="slide level2">
<h4 id="many-research-groups-have-their-github-organizations-online">Many research groups have their GitHub organizations online</h4>
<p><img data-src="img/github-lab.png"> :::footer https://github.com/dib-lab :::</p>
</section></section>
<section>
<section id="git-github-provide-much-more-than-just-version-control.-they-can-also-be-used-to-foster-collaboration-and-publish-code." class="title-slide slide level1 center" data-background-color="#E5E4E2">
<h1>Git + GitHub provide much more than just version control. They can also be used to foster collaboration and publish code.</h1>
</section>
<section id="situation-3" class="slide level2">
<h2>Situation 3</h2>
<div class="columns">
<div id="vcenter" class="column" style="width:60%;">
<p>Julia wants to publish her first article. <strong>How can she do it in a reproducible way?</strong></p>
</div><div id="vcenter" class="column" style="width:40%;">
<p><img data-src="img/researcher4.png"></p>
</div>
</div>
</section>
<section id="research-compendia" class="slide level2">
<h2>Research Compendia</h2>
<div class="columns">
<div id="vcenter" class="column" style="width:50%;">
<ol type="1">
<li class="fragment"><p><strong>Organize files</strong> according to a prevailing convention.</p></li>
<li class="fragment"><p>Provide <strong>separation between data, methods and results</strong> expressing the relationship between the three.</p></li>
<li class="fragment"><p>Specify the <strong>environment</strong></p></li>
</ol>
</div><div id="vcenter" class="column" style="width:40%;">
<div class="cell">
<div class="cell-output-display">
<p><img data-src="img/ResearchCompendium.jpg" width="400"></p>
</div>
</div>
</div>
</div>
<div class="footer">
<p><a href="https://github.com/benmarwick/rrtools"><code>rrtools</code> package</a> - <a href="https://the-turing-way.netlify.app/reproducible-research/compendia.html?highlight=research%20compendium">Research Compendia - The Turing Way: A Handbook for Reproducible Data Science (2019)</a></p>
</div>
</section>
<section id="documentation" class="slide level2">
<h2>Documentation</h2>
<p>Did you ever consider that your next scientific article <strong>can have not only readers but also users</strong>?</p>
<p><br></p>
<div class="text-c">
<p><span class="rn" data-rn-type="crossed-off" data-rn-color="purple">Readers</span></p>
<p><span class="rn" data-rn-type="circle" data-rn-color="green">Users</span></p>
</div>
<div class="footer">
<p>Press R</p>
</div>
</section></section>
<section>
<section id="project-organization-and-documentation-are-also-relevant-to-achieving-computational-reproducibility." class="title-slide slide level1 center" data-background-color="#E5E4E2">
<h1>Project organization and documentation are also relevant to achieving computational reproducibility.</h1>
</section>
<section id="other-practices" class="slide level2">
<h2>Other practices</h2>
<ul>
<li class="fragment">Testing</li>
<li class="fragment">Continuous integration / development (ci - cd)</li>
<li class="fragment">Package development</li>
<li class="fragment">Code review</li>
<li class="fragment">Basic computational practices</li>
<li class="fragment">Automation / use of pipelines</li>
</ul>
</section>
<section id="high-reproducibility-doesnt-mean-that-things-couldnt-fail" class="slide level2">
<h2>High reproducibility doesn’t mean that things couldn’t fail</h2>
<h4 id="what-happens-when-the-technology-fails">What happens when the technology fails?</h4>
<img data-src="img/links.png" width="600" class="r-stretch quarto-figure-center"></section>
<section id="some-factors-affecting-reproducibility" class="slide level2">
<h2>Some factors affecting <strong>Reproducibility</strong></h2>
<ul>
<li class="fragment">The tools that ensure the reproducibility (Docker, Conda) could change with time</li>
<li class="fragment">The software/hardware we use change with time</li>
</ul>
</section>
<section id="some-factors-affecting-reproducibility-1" class="slide level2">
<h2>Some factors affecting <strong>Reproducibility</strong></h2>
<h4 id="how-the-tools-that-ensure-the-reproducibility-docker-conda-change-with-time">How the tools that ensure the reproducibility (Docker, Conda) change with time</h4>
<p><strong>Example 1</strong> - <a href="https://github.com/docker/roadmap/issues/152">Inactive Image Retention Policy (Nov 1, 2020)</a>: DockerHub removing Docker images in free accounts after 6 months</p>
<img data-src="img/broken.png" class="r-stretch"></section>
<section id="some-factors-affecting-reproducibility-2" class="slide level2">
<h2>Some factors affecting <strong>Reproducibility</strong></h2>
<h4 id="the-softwarehardware-we-use-change-with-time">The software/hardware we use change with time</h4>
<p><strong>Example 2</strong> - Mac M1 - Apple silicon chip (hardware) (Oct 2021) Docker issues</p>
<p><img data-src="img/blog-docker.png">{fig.align:‘center’}</p>
<div class="footer">
<p><a href="https://kecci.medium.com/docker-comstrek-air-not-supported-linux-arm64-in-golang-with-macbook-m1-solved-f7997bd54ee">Image extracted from: Docker: comstrek/air doesn’t supported linux/arm64 in golang with Macbook M1</a></p>
</div>
</section>
<section id="software-mantainance" class="slide level2">
<h2>Software mantainance</h2>
<p>Should our code have <strong>maintainers</strong>?</p>
<img data-src="img/FixingLinks.jpg" width="600" class="r-stretch quarto-figure-center"><div class="footer">
<p><a href="https://the-turing-way.netlify.app/collaboration/maintain-review.html">Maintainers and Reviewers on GitHub</a> - <a href="http://doi.org/10.5281/zenodo.3695300">The Turing Way Community, & Scriberia. (2020)</a></p>
</div>
</section></section>
<section id="what-kind-of-practices-andor-tools-we-need-to-apply-for-creating-better-research-software" class="title-slide slide level1 center" data-background-color="#67032F">
<h1>What kind of practices and/or tools we need to apply for creating better research software?</h1>
<ul>
<li class="fragment">Capturing computational environments.</li>
<li class="fragment">Version controlling and publishing our code.</li>
</ul>
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<section id="what-kind-of-practices-andor-tools-we-need-to-apply-for-creating-better-research-software-1" class="title-slide slide level1 center" data-background-color="#67032F">
<h1>What kind of practices and/or tools we need to apply for creating better research software?</h1>
<ul>
<li class="fragment">Document the code for your users.</li>
<li class="fragment">Software could need maintenance.</li>
</ul>
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