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168 changes: 153 additions & 15 deletions docs/opensciws_slides.html
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76 changes: 62 additions & 14 deletions docs/opensciws_website.html
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Expand Up @@ -523,13 +523,6 @@ <h2 class="anchored" data-anchor-id="why-should-we-do-open-science">Why should w
</ul>
</div>
<hr>
<div class="quarto-figure quarto-figure-center">
<figure class="figure">
<p><img src="att/scientists-mostly-hackers.png" class="img-fluid figure-img"></p>
<figcaption class="figure-caption"><a href="https://www.youtube.com/watch?v=zwRdO9_GGhY">Richard McElreath: <em>Science as Amateur Software Development</em></a></figcaption>
</figure>
</div>
<hr>
<p>What are the reasons why science can go wrong?</p>
<hr>
<div class="quarto-figure quarto-figure-center">
Expand All @@ -548,6 +541,13 @@ <h2 class="anchored" data-anchor-id="why-should-we-do-open-science">Why should w
<hr>
<div class="quarto-figure quarto-figure-center">
<figure class="figure">
<p><img src="att/scientists-mostly-hackers.png" class="img-fluid figure-img"></p>
<figcaption class="figure-caption"><a href="https://www.youtube.com/watch?v=zwRdO9_GGhY">Richard McElreath: <em>Science as Amateur Software Development</em></a></figcaption>
</figure>
</div>
<hr>
<div class="quarto-figure quarto-figure-center">
<figure class="figure">
<p><img src="att/skills-to-pay-the-bills.png" class="img-fluid figure-img"></p>
<figcaption class="figure-caption"><a href="https://www.youtube.com/watch?v=zwRdO9_GGhY">source</a></figcaption>
</figure>
Expand All @@ -562,6 +562,9 @@ <h2 class="anchored" data-anchor-id="principles-of-open-science">Principles of O
<figcaption class="figure-caption"><a href="https://www.cos.io/open-science">Center for Open Science</a></figcaption>
</figure>
</div>
<div class="notes">
<p>09:20</p>
</div>
<hr>
</section>
<section id="open-science-lifecycle" class="level2">
Expand Down Expand Up @@ -617,6 +620,9 @@ <h2 class="anchored" data-anchor-id="who-profits-from-open-science">Who profits
<h2 class="anchored" data-anchor-id="what-is-open-science-to-you">What is Open Science to you?</h2>
<p>What do you find interesting, important, or attractive about Open Science?</p>
<p><a href="https://tinyurl.com/opnsci" class="uri">https://tinyurl.com/opnsci</a></p>
<div class="notes">
<p>09:50</p>
</div>
<hr>
</section>
<section id="learning-outcomes" class="level2">
Expand Down Expand Up @@ -905,6 +911,9 @@ <h3 class="anchored" data-anchor-id="reproducibility-et-al.">Reproducibility et
</figure>
</div>
<p><img src="att/reproducibility-ruler.png" class="img-fluid"></p>
<div class="notes">
<p>interesting for student projects</p>
</div>
<hr>
</section>
<section id="the-quality-of-tools" class="level3">
Expand All @@ -929,6 +938,9 @@ <h3 class="anchored" data-anchor-id="why-we-should-test-code">Why we should test
</figure>
</div>
<hr>
<div class="note">
<p>not all our projects have that high stakes</p>
</div>
</section>
<section id="professional-testing" class="level3">
<h3 class="anchored" data-anchor-id="professional-testing">Professional testing</h3>
Expand All @@ -938,6 +950,9 @@ <h3 class="anchored" data-anchor-id="professional-testing">Professional testing<
<figcaption class="figure-caption"><a href="https://www.youtube.com/watch?v=8qzVV7eEiaI&amp;t=396s">source</a></figcaption>
</figure>
</div>
<div class="note">
<p>same is true of industry</p>
</div>
<hr>
</section>
<section id="types-of-tests" class="level3">
Expand Down Expand Up @@ -1002,6 +1017,9 @@ <h3 class="anchored" data-anchor-id="literate-programming">Literate programming<
</div>
</div>
</div>
<div class="notes">
<p>psychological benefit: conversation - helps reasoning - more fun (human) - → ChatBots</p>
</div>
<hr>
</section>
<section id="notebooks" class="level3">
Expand All @@ -1028,6 +1046,13 @@ <h3 class="anchored" data-anchor-id="notebooks">Notebooks</h3>
</div>
<p>→ both work with <a href="https://quarto.org/">Quarto</a></p>
</div>
<div class="notes">
<ul>
<li>who uses notebooks?</li>
<li>which ones?</li>
<li>good for novices &amp; experts</li>
</ul>
</div>
<hr>
</section>
<section id="example-using-nbdev-for-python" class="level3">
Expand All @@ -1041,22 +1066,35 @@ <h3 class="anchored" data-anchor-id="example-using-nbdev-for-python">Example usi
<section id="literate-testing-with-nbdev" class="level3">
<h3 class="anchored" data-anchor-id="literate-testing-with-nbdev">Literate testing with <code>nbdev</code></h3>
<p><img src="att/nbdev-cars-2.png" class="img-fluid"></p>
<div class="notes">
<p>compare with <code>pytest</code>: much easier/natural</p>
</div>
<hr>
</section>
<section id="additional-benefits-of-nbdev" class="level3">
<h3 class="anchored" data-anchor-id="additional-benefits-of-nbdev">Additional benefits of <code>nbdev</code></h3>
<ul>
<li>publishing documentation via Quarto</li>
<li>simple, integrated testing</li>
<li><a href="https://the-turing-way.netlify.app/reproducible-research/ci.html">continuous integration</a></li>
<li>dependency management</li>
<li>publishing code for PyPI and conda</li>
<li>publishing documentation via Quarto</li>
</ul>
<div class="notes">
<ul>
<li>good for novices &amp; experts</li>
<li>covers about 80% of programming setup for free</li>
<li>more about Quarto later</li>
</ul>
</div>
<hr>
</section>
<section id="r-quarto-and-rmarkdown" class="level3">
<h3 class="anchored" data-anchor-id="r-quarto-and-rmarkdown">R: Quarto and RMarkdown</h3>
<p><img src="att/r-literate-programming-quarto.png" class="img-fluid"></p>
<div class="notes">
<p>benefit: visual editor</p>
</div>
<hr>
</section>
</section>
Expand Down Expand Up @@ -1184,6 +1222,17 @@ <h2 class="anchored" data-anchor-id="how-to-share-your-data">How to share your d
</ul></li>
</ul>
</div>
<div class="notes">
<ul>
<li>Excel issues
<ul>
<li>formatting</li>
<li>thousands separators: <code>,</code> vs <code>.</code></li>
<li>date conversion</li>
<li>formulas</li>
</ul></li>
</ul>
</div>
<hr>
</section>
<section id="sharing-social-media-data" class="level2">
Expand Down Expand Up @@ -1211,7 +1260,10 @@ <h2 class="anchored" data-anchor-id="sharing-social-media-data">Sharing social m
<p><a href="https://www.frontiersin.org/articles/10.3389/fdata.2022.971974/full">source</a></p>
</div>
<div class="notes">
<p>paper on incest</p>
<ul>
<li>additional reason: sharing not <strong>considered</strong> (necessary)</li>
<li><strong>ethical</strong> and <strong>privacy</strong>: paper on incest on Twitter</li>
</ul>
</div>
<hr>
</section>
Expand All @@ -1236,11 +1288,7 @@ <h2 class="anchored" data-anchor-id="the-case-of-twitter">The case of Twitter</h
</section>
<section id="data-and-methods-1" class="level2">
<h2 class="anchored" data-anchor-id="data-and-methods-1">Data and methods</h2>
<p>In groups of shared interests and expertise, make a <strong>digital poster</strong> about challenges and possibilities of working with data in your field of study.</p>
<p>For example, this could tackle issues like collecting, publishing, and sharing data.</p>
<p>Try to make it as concrete and constructive as possible.</p>
<p>You have until <strong>14:20 h</strong> to make the poster.</p>
<p>After that, each group will briefly present their poster.</p>
<p>get active: see <a href="https://tinyurl.com/opnsci" class="uri">https://tinyurl.com/opnsci</a></p>
<hr>
<hr>
</section>
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18 changes: 9 additions & 9 deletions docs/search.json
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Expand Up @@ -53,14 +53,14 @@
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Expand Down Expand Up @@ -88,7 +88,7 @@
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Expand Down Expand Up @@ -165,21 +165,21 @@
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"text": "Documenting code\n\nLiterate programming\n\n\n\n\n’Literate programming is a methodology that combines a programming language with a documentation language,\nthereby making programs more robust, more portable, more easily maintained,\nand arguably more fun to write than programs that are written only in a high-level language.\nThe main idea is to treat a program as a piece of literature, addressed to human beings rather than to a computer.\nThe program is also viewed as a hypertext document, rather like the World Wide Web. (Indeed, I used the word WEB for this purpose long before CERN grabbed it!)’\n\nDonald Knuth\n\n\n\n\nsource\n\n\n\n\n\n\npsychological benefit: conversation - helps reasoning - more fun (human) - → ChatBots\n\n\n\n\nNotebooks\n\n\n\nPython\n\n\n\nsource\n\n\n\nR\n\n\n\nsource\n\n\n\n\n→ both work with Quarto\n\n\n\nwho uses notebooks?\nwhich ones?\ngood for novices & experts\n\n\n\n\n\nExample using nbdev for Python\n\nProgramming a deck of cards: https://github.com/fastai/nbdev_cards/\n\n\n\n\n\nLiterate testing with nbdev\n\n\ncompare with pytest: much easier/natural\n\n\n\n\nAdditional benefits of nbdev\n\nsimple, integrated testing\ncontinuous integration\ndependency management\npublishing code for PyPI and conda\npublishing documentation via Quarto\n\n\n\ngood for novices & experts\ncovers about 80% of programming setup for free\nmore about Quarto later\n\n\n\n\n\nR: Quarto and RMarkdown\n\n\nbenefit: visual editor"
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Expand Down Expand Up @@ -214,14 +214,14 @@
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"text": "How to share your data\n\nTuring Way tutorial\n\nStep 1: Select what data you want to share; eg.:\n\nethical concerns\ncommercial concerns\n\nStep 2: Choose a data repository or other sharing platform\n\noverview: re3data, NIH, FAIRsharing\nexamples: Zenodo, Dryad\n\nStep 3: Choose a licence and link to your paper and code; e.g.:\n\nCreative Commons\nOpen Data Commons\n\nStep 4: Upload your data and documentation\n\ngood file organisation\nappropriate file formats (e.g. csv &gt; xlsx)"
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Expand All @@ -235,7 +235,7 @@
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