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-# Table of contents
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-## Table of contents
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-:::: { .columns }
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-::: { .column .center width="33%"}
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-<br>
-Section 1
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-::: { .column .center width="33%"}
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-Section 2
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-Resources
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-<!-- Insert section 'Quarto basics' -->
+<!-- Insert section 'Main slides' -->
+</section>
+<section id="acknowledgments" class="slide level2">
+<h2>Acknowledgments</h2>
+<p>This presentation is strongly inspired by the chapter <a href="https://book.the-turing-way.org/communication/dif-articles/software.html"><strong><em>Software papers</em></strong></a> of the online book <a href="https://book.the-turing-way.org/"><strong>The Turing Way</strong></a>.</p>
+<p><br></p>
+<div class="quarto-figure quarto-figure-center">
+<figure>
+<p><img data-src="images/logo-turing-way.png" class="quarto-figure quarto-figure-center" style="width:20.0%"></p>
+</figure>
+</div>
+<p><br></p>
+<blockquote>
+<p>The Turing Way Community (2021) <em>The Turing Way: A handbook for reproducible, ethical and collaborative research</em>. Zenodo. <a href="https://doi.org/10.5281/zenodo.3233853" class="uri">https://doi.org/10.5281/zenodo.3233853</a>.</p>
+</blockquote>
+</section>
+<section id="what-is-a-software-paper" class="slide level2">
+<h2>What is a software paper?</h2>
+<div class="columns">
+<div class="column" style="width:50%;">
+<ul>
+<li>Share a new piece of software with the research community</li>
+<li>Close to traditional method papers</li>
+<li>Shorter than traditional articles (between 2 and 10 pages)</li>
+<li>Focus on describing the software and its use</li>
+</ul>
+</div><div class="column" style="width:5%;">
+
+</div><div class="column" style="width:45%;">
+
+</div></div>
+</section>
+<section id="what-is-a-software-paper-1" class="slide level2">
+<h2>What is a software paper?</h2>
+<div class="columns">
+<div class="column" style="width:50%;">
+<ul>
+<li>Share a new piece of software with the research community</li>
+<li>Close to traditional method papers</li>
+<li>Shorter than traditional articles (between 2 and 10 pages)</li>
+<li>Focus on describing the software and its use</li>
+</ul>
+<p><br></p>
+<p><strong><em>But wait! What does this have to do with the data?</em></strong></p>
+</div><div class="column" style="width:5%;">
+
+</div><div class="column" style="width:45%;">
+
+</div></div>
+</section>
+<section id="what-is-a-software-paper-2" class="slide level2">
+<h2>What is a software paper?</h2>
+<div class="columns">
+<div class="column" style="width:50%;">
+<ul>
+<li>Share a new piece of software with the research community</li>
+<li>Close to traditional method papers</li>
+<li>Shorter than traditional articles (between 2 and 10 pages)</li>
+<li>Focus on describing the software and its use</li>
+</ul>
+<p><br></p>
+<p><strong><em>But wait! What does this have to do with the data?</em></strong></p>
+</div><div class="column" style="width:5%;">
+
+</div><div class="column" style="width:45%;">
+<p><img data-src="images/pipeline-1.png"></p>
+<p><br></p>
+<p><i class="fa-solid fa-circle-right" aria-label="circle-right"></i> &nbsp;Software paper about <strong>your pipeline</strong></p>
+</div></div>
+</section>
+<section id="what-is-a-software-paper-3" class="slide level2">
+<h2>What is a software paper?</h2>
+<div class="columns">
+<div class="column" style="width:50%;">
+<ul>
+<li>Share a new piece of software with the research community</li>
+<li>Close to traditional method papers</li>
+<li>Shorter than traditional articles (between 2 and 10 pages)</li>
+<li>Focus on describing the software and its use</li>
+</ul>
+<p><br></p>
+<p><strong><em>But wait! What does this have to do with the data?</em></strong></p>
+</div><div class="column" style="width:5%;">
+
+</div><div class="column" style="width:45%;">
+<p><img data-src="images/pipeline-2.png"></p>
+<p><br></p>
+<p><i class="fa-solid fa-circle-right" aria-label="circle-right"></i> &nbsp;Software paper about <strong>a tool to access data</strong></p>
+</div></div>
+</section>
+<section id="what-is-a-software-paper-4" class="slide level2">
+<h2>What is a software paper?</h2>
+<div class="columns">
+<div class="column" style="width:50%;">
+<ul>
+<li>Share a new piece of software with the research community</li>
+<li>Close to traditional method papers</li>
+<li>Shorter than traditional articles (between 2 and 10 pages)</li>
+<li>Focus on describing the software and its use</li>
+</ul>
+<p><br></p>
+<p><strong><em>But wait! What does this have to do with the data?</em></strong></p>
+</div><div class="column" style="width:5%;">
+
+</div><div class="column" style="width:45%;">
+<p><img data-src="images/pipeline-3.png"></p>
+<p><br></p>
+<p><i class="fa-solid fa-circle-right" aria-label="circle-right"></i> &nbsp;Software paper about <strong>a tool to add new data</strong></p>
+</div></div>
+</section>
+<section id="software-papers---examples" class="slide level2">
+<h2>Software papers - Examples</h2>
+<div class="columns">
+<div class="column" style="width:50%;">
+<p><a href="https://besjournals.onlinelibrary.wiley.com/doi/10.1111/2041-210X.13910"><img data-src="images/mee-screenshot-1.png"></a></p>
+</div><div class="column" style="width:50%;">
+<p><a href="https://besjournals.onlinelibrary.wiley.com/doi/10.1111/2041-210X.13868"><img data-src="images/mee-screenshot-6.png"></a></p>
+</div></div>
+<div class="columns">
+<div class="column" style="width:50%;">
+<p><a href="https://besjournals.onlinelibrary.wiley.com/doi/10.1111/2041-210X.14213"><img data-src="images/mee-screenshot-3.png"></a></p>
+</div><div class="column" style="width:50%;">
+<p><a href="https://besjournals.onlinelibrary.wiley.com/doi/10.1111/2041-210X.13779"><img data-src="images/mee-screenshot-4.png"></a></p>
+</div></div>
+</section>
+<section id="software-paper---why" class="slide level2">
+<h2>Software paper - Why?</h2>
+<ul>
+<li>Advertise your code to an interested audience</li>
+<li>Increase the visibility of your code and community</li>
+<li>Improve your software through peer-review</li>
+</ul>
+</section>
+<section id="in-which-journals" class="slide level2">
+<h2>In which journals?</h2>
+<ul>
+<li>Methods in Ecology and Evolution &nbsp;&nbsp;<a href="https://besjournals.onlinelibrary.wiley.com/journal/2041210x"><i class="fa-solid fa-up-right-from-square fa-xs" aria-label="up-right-from-square"></i></a></li>
+<li>Journal of Open Source Software (JOSS) &nbsp;&nbsp;<a href="https://joss.theoj.org/"><i class="fa-solid fa-up-right-from-square fa-xs" aria-label="up-right-from-square"></i></a></li>
+<li>Journal of Open Research Software (JORS) &nbsp;&nbsp;<a href="https://openresearchsoftware.metajnl.com/"><i class="fa-solid fa-up-right-from-square fa-xs" aria-label="up-right-from-square"></i></a></li>
+<li>BMC Bioinformatics &nbsp;&nbsp;<a href="https://bmcbioinformatics.biomedcentral.com/"><i class="fa-solid fa-up-right-from-square fa-xs" aria-label="up-right-from-square"></i></a></li>
+<li>PeerJ &nbsp;&nbsp;<a href="https://peerj.com/about/publications/#PeerJ"><i class="fa-solid fa-up-right-from-square fa-xs" aria-label="up-right-from-square"></i></a></li>
+<li>PLOS Computational Biology: Software &nbsp;&nbsp;<a href="https://collections.plos.org/collection/software/"><i class="fa-solid fa-up-right-from-square fa-xs" aria-label="up-right-from-square"></i></a></li>
+<li>PLOS ONE &nbsp;&nbsp;<a href="https://journals.plos.org/plosone/"><i class="fa-solid fa-up-right-from-square fa-xs" aria-label="up-right-from-square"></i></a></li>
+<li>…</li>
+</ul>
+</section>
+<section id="zoom-on-joss" class="slide level2">
+<h2>Zoom on JOSS</h2>
+<p>Feedback on publishing in <strong>Journal of Open Source Software</strong> (JOSS)</p>
+<div class="columns">
+<div class="column" style="width:50%;">
+<p><img data-src="images/chessboard-repo.png" style="width:80.0%"></p>
+</div><div class="column" style="width:50%;">
+<p><img data-src="images/chessboard-paper.png" style="width:60.0%"></p>
+</div></div>
+<div class="columns">
+<div class="column" style="width:50%;">
+<div class="small">
+<p><a href="https://github.com/frbcesab/chessboard/" class="uri">https://github.com/frbcesab/chessboard/</a></p>
+</div>
+</div><div class="column" style="width:50%;">
+<div class="small">
+<p><a href="https://joss.theoj.org/papers/10.21105/joss.05753" class="uri">https://joss.theoj.org/papers/10.21105/joss.05753</a></p>
+</div>
+</div></div>
 </section>
-<section id="introduction" class="title-slide slide level1 center">
-<h1>Introduction</h1>
-<p>Coming soon…</p>
+<section id="thanks" class="title-slide slide level1 center">
+<h1>Thanks!</h1>
 <div class="quarto-auto-generated-content">
 <p><img src="images/logo-affiliation.png" class="slide-logo"></p>
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