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exercises/compute_environment/index.html

@@ -445,8 +445,8 @@ <h1 class="title">Compute environment</h1>
 <div class="sourceCode" id="cb1"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="fu">mkdir</span> <span class="at">-p</span> /proj/naiss2023-22-1084/users/YOURUSERNAME</span>
 <span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a><span class="bu">cd</span> /proj/naiss2023-22-1084/users/YOURUSERNAME</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 <p>All computations should be run on a compute node. You can request an <a href="https://www.uppmax.uu.se/support/faq/running-jobs-faq/how-can-i-run-interactively-on-a-compute-node/">interactive session</a> with the <code>interactive</code> command. For example, to request an eight hour job on 4 cores, run</p>
-<div class="sourceCode" id="cb2"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="ex">interactive</span> <span class="at">-A</span> naiss2023-22-1084 <span class="at">--cores</span> 4 <span class="dt">\</span></span>
-<span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a>   <span class="at">--partition</span> core <span class="at">--time</span> 08:00:00 <span class="dt">\</span></span>
+<div class="sourceCode" id="cb2"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="ex">interactive</span> <span class="at">-A</span> naiss2023-22-1084 <span class="at">-n</span> 4 <span class="dt">\</span></span>
+<span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a>   <span class="at">--time</span> 08:00:00 <span class="dt">\</span></span>
 <span id="cb2-3"><a href="#cb2-3" aria-hidden="true" tabindex="-1"></a>   <span class="at">--reservation</span><span class="op">=</span>naiss2023-22-1084</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
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exercises/datasets/monkeyflowers.html

@@ -380,7 +380,7 @@ <h1 class="title">Monkeyflowers dataset</h1>
 </header><!-- markdownlint-disable MD041 --><!-- markdownlint-disable MD041 --><!-- markdownlint-enable MD041 --><!-- markdownlint-disable MD041 --><!-- markdownlint-enable MD041 --><!-- markdownlint-enable MD041 --><div>
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-<figure class="figure"><p><a href="https://www.science.org/cms/10.1126/science.365.6456.854/asset/db271bee-8914-4712-9965-dcf1615b6a43/assets/graphic/365_854_f1.jpeg" class="lightbox" title="The allure of monkeyflowers (DOI: 10.1126/science.365.6456.854)" data-gallery="quarto-lightbox-gallery-1"><img src="https://www.science.org/cms/10.1126/science.365.6456.854/asset/db271bee-8914-4712-9965-dcf1615b6a43/assets/graphic/365_854_f1.jpeg" class="img-fluid figure-img" alt="The allure of monkeyflowers (DOI: 10.1126/science.365.6456.854)"></a></p>
+<figure class="figure"><p><a href="https://www.science.org/cms/10.1126/science.365.6456.854/asset/db271bee-8914-4712-9965-dcf1615b6a43/assets/graphic/365_854_f1.jpeg" class="lightbox" data-gallery="quarto-lightbox-gallery-1" title="The allure of monkeyflowers (DOI: 10.1126/science.365.6456.854)"><img src="https://www.science.org/cms/10.1126/science.365.6456.854/asset/db271bee-8914-4712-9965-dcf1615b6a43/assets/graphic/365_854_f1.jpeg" class="img-fluid figure-img" alt="The allure of monkeyflowers (DOI: 10.1126/science.365.6456.854)"></a></p>
 </figure>
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@@ -391,13 +391,13 @@ <h1 class="title">Monkeyflowers dataset</h1>
 <p>Recently, <span class="citation" data-cites="stankowski_WidespreadSelectionGene_2019">Stankowski et al. (<a href="#ref-stankowski_WidespreadSelectionGene_2019" role="doc-biblioref">2019</a>)</span> used the monkeyflower system to investigate what forces affect the genomic landscape. <span class="citation" data-cites="burri_InterpretingDifferentiationLandscapes_2017">Burri (<a href="#ref-burri_InterpretingDifferentiationLandscapes_2017" role="doc-biblioref">2017</a>)</span> has suggested that background selection (BGS) is one of the main causes for correlations between genomic landscapes, and that one way to study this phenomenon is to look at closely related taxa. This is one of the objectives of the <span class="citation" data-cites="stankowski_WidespreadSelectionGene_2019">Stankowski et al. (<a href="#ref-stankowski_WidespreadSelectionGene_2019" role="doc-biblioref">2019</a>)</span> paper.</p>
 <p>They performed whole-genome resequencing of 37 individuals from 7 subspecies and 2 ecotypes of <em>Mimulus aurantiacus</em> and its sister taxon <em>M. clevelandii</em> (<a href="#fig-evolutionary-relationship">Figure&nbsp;1</a>), all sampled in California (<a href="#fig-monkeyflower-sampling-location">Figure&nbsp;2</a>).</p>
 <div id="fig-evolutionary-relationship" class="quarto-figure quarto-figure-center anchored">
-<figure class="figure"><p><a href="assets/images/stankowski-2019-fig1A.png" class="lightbox" title="Evolutionary relationships across the radiation" data-gallery="quarto-lightbox-gallery-2"><img src="assets/images/stankowski-2019-fig1A.png" class="img-fluid figure-img"></a></p>
+<figure class="figure"><p><a href="assets/images/stankowski-2019-fig1A.png" class="lightbox" data-gallery="quarto-lightbox-gallery-2" title="Evolutionary relationships across the radiation"><img src="assets/images/stankowski-2019-fig1A.png" class="img-fluid figure-img"></a></p>
 <figcaption class="figure-caption">Figure&nbsp;1: Evolutionary relationships across the radiation</figcaption></figure>
 </div>
 
 <div class="no-row-height column-margin column-container"><div class="">
 <div id="fig-monkeyflower-sampling-location" class="quarto-figure quarto-figure-center anchored">
-<figure class="figure"><p><a href="../../slides/simulation/assets/images/stankowski-2019-figs2.jpg" class="lightbox" title="Sampling locations" data-gallery="quarto-lightbox-gallery-3"><img src="../../slides/simulation/assets/images/stankowski-2019-figs2.jpg" class="img-fluid figure-img"></a></p>
+<figure class="figure"><p><a href="../../slides/simulation/assets/images/stankowski-2019-figs2.jpg" class="lightbox" data-gallery="quarto-lightbox-gallery-3" title="Sampling locations"><img src="../../slides/simulation/assets/images/stankowski-2019-figs2.jpg" class="img-fluid figure-img"></a></p>
 <figcaption class="figure-caption">Figure&nbsp;2: Sampling locations</figcaption></figure>
 </div>
 </div></div><p>Genomewide statistics, such as diversity (<span class="math inline">\(\pi\)</span>), divergence (<span class="math inline">\(d_{XY}\)</span>) and differentiation <span class="math inline">\(F_{ST}\)</span>, were calculated within and between taxa to generate genomic diversity landscapes. The landscapes were highly similar across taxa, and local variation in genomic features, such as gene density and recombination rate, was predictive of variation in landscape patterns. These features suggest the influence of selection, in particular BGS.</p>
@@ -413,7 +413,7 @@ <h1 class="title">Monkeyflowers dataset</h1>
 </ol>
 <p><a href="#fig-slim-simulations">Figure&nbsp;3</a> shows typical results of the simulations.</p>
 <div id="fig-slim-simulations" class="quarto-figure quarto-figure-center anchored">
-<figure class="figure"><p><a href="../../slides/simulation/assets/images/stankowski-2019-fig7.png" class="lightbox" title="Genomic landscapes simulated under different divergence histories." data-gallery="quarto-lightbox-gallery-4"><img src="../../slides/simulation/assets/images/stankowski-2019-fig7.png" class="img-fluid figure-img"></a></p>
+<figure class="figure"><p><a href="../../slides/simulation/assets/images/stankowski-2019-fig7.png" class="lightbox" data-gallery="quarto-lightbox-gallery-4" title="Genomic landscapes simulated under different divergence histories."><img src="../../slides/simulation/assets/images/stankowski-2019-fig7.png" class="img-fluid figure-img"></a></p>
 <figcaption class="figure-caption">Figure&nbsp;3: Genomic landscapes simulated under different divergence histories.</figcaption></figure>
 </div>
 <p>In conclusion, the authors found that although BGS plays a role, it does not sufficiently explain all observations, and that other aspects of natural selection (such as rapid adaptation) are responsible for the similarities between genomic landscapes.</p>
@@ -760,7 +760,7 @@ <h1 class="title">Monkeyflowers dataset</h1>
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