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access/UCloud.html

@@ -200,7 +200,7 @@ <h3 class="anchored" data-anchor-id="step-2"><strong>Step 2</strong></h3>
 <p>For this example, we select Sandbox_workshop.</p>
 <div class="quarto-figure quarto-figure-center">
 <figure class="figure">
-<p><a href="../images/workspace.png" class="lightbox" data-gallery="quarto-lightbox-gallery-1" data-glightbox="description: .lightbox-desc-1" title="Dashboard: your workspace"><img src="../images/workspace.png" class="black-box img-fluid figure-img" alt="Screenshot of your dashboard"></a></p>
+<p><a href="../images/workspace.png" class="lightbox" data-glightbox="description: .lightbox-desc-1" data-gallery="quarto-lightbox-gallery-1" title="Dashboard: your workspace"><img src="../images/workspace.png" class="black-box img-fluid figure-img" alt="Screenshot of your dashboard"></a></p>
 <figcaption>Dashboard: your workspace</figcaption>
 </figure>
 </div>
@@ -233,7 +233,7 @@ <h3 class="anchored" data-anchor-id="step-3"><strong>Step 3</strong></h3>
 <p>Then click on Apps in the left panel to investigate what tools and environments you can use (green circle). The easiest way to find Sandbox resources is to search via the toolbar (red circle). In this example, we’ll select the Genomics Sandbox (which will bring you to the submission screen).</p>
 <div class="quarto-figure quarto-figure-center">
 <figure class="figure">
-<p><a href="../images/apps.png" class="lightbox" data-gallery="quarto-lightbox-gallery-2" data-glightbox="description: .lightbox-desc-2" title="Dashboard: all apps"><img src="../images/apps.png" class="black-box img-fluid figure-img" alt="Screenshot of apps dashboard"></a></p>
+<p><a href="../images/apps.png" class="lightbox" data-glightbox="description: .lightbox-desc-2" data-gallery="quarto-lightbox-gallery-2" title="Dashboard: all apps"><img src="../images/apps.png" class="black-box img-fluid figure-img" alt="Screenshot of apps dashboard"></a></p>
 <figcaption>Dashboard: all apps</figcaption>
 </figure>
 </div>
@@ -256,7 +256,7 @@ <h3 class="anchored" data-anchor-id="step-4"><strong>Step 4</strong></h3>
 <p>Click on the app button to get into the settings window. First, we recommend reading the documentation of the app (highlighted in green). Then, you can configure the app as shown below, or be provided with a configuration file made available in a workshop’s project folders (<em>import parameters</em>) which will take care of everything for you.</p>
 <div class="quarto-figure quarto-figure-center">
 <figure class="figure">
-<p><a href="../images/configure_NGS.png" class="lightbox" data-gallery="quarto-lightbox-gallery-3" data-glightbox="description: .lightbox-desc-3" title="Dashboard jobs: configuration step"><img src="../images/configure_NGS.png" class="black-box img-fluid figure-img" alt="Screenshot of how to configure your job"></a></p>
+<p><a href="../images/configure_NGS.png" class="lightbox" data-glightbox="description: .lightbox-desc-3" data-gallery="quarto-lightbox-gallery-3" title="Dashboard jobs: configuration step"><img src="../images/configure_NGS.png" class="black-box img-fluid figure-img" alt="Screenshot of how to configure your job"></a></p>
 <figcaption>Dashboard jobs: configuration step</figcaption>
 </figure>
 </div>
@@ -290,7 +290,7 @@ <h3 class="anchored" data-anchor-id="step-5"><strong>Step 5</strong></h3>
 <p>Wait to go through the queue. When the session starts, the timer begins to count down. In a couple of minutes, you should be able to open the interface through the button (green circle) in a new window (refresh the window if needed).</p>
 <div class="quarto-figure quarto-figure-center">
 <figure class="figure">
-<p><a href="../images/running_NGS.png" class="lightbox" data-gallery="quarto-lightbox-gallery-4" data-glightbox="description: .lightbox-desc-4" title="Dashboard jobs: running the app"><img src="../images/running_NGS.png" class="black-box img-fluid figure-img" alt="Screenshot of dashboard running app"></a></p>
+<p><a href="../images/running_NGS.png" class="lightbox" data-glightbox="description: .lightbox-desc-4" data-gallery="quarto-lightbox-gallery-4" title="Dashboard jobs: running the app"><img src="../images/running_NGS.png" class="black-box img-fluid figure-img" alt="Screenshot of dashboard running app"></a></p>
 <figcaption>Dashboard jobs: running the app</figcaption>
 </figure>
 </div>
@@ -301,14 +301,14 @@ <h3 class="anchored" data-anchor-id="step-6"><strong>Step 6</strong></h3>
 <p>If you are testing the genomic app, your interface should look like in the image below. Different apps might use other development environments. In this case, you will be working from <a href="https://jupyter.org/">JupyterLab</a>. You can open Jupyter Notebooks (yellow square), R studio (blue square) or a terminal (black square) among others. In this case, #1 and #2 have all the software and packages that you will need pre-installed (this is not the case with Python 3 to the left).</p>
 <div class="quarto-figure quarto-figure-center">
 <figure class="figure">
-<p><a href="../images/interface_jupyterlab.png" class="lightbox" data-gallery="quarto-lightbox-gallery-5" data-glightbox="description: .lightbox-desc-5" title="JupyterLab interface: running the app"><img src="../images/interface_jupyterlab.png" class="black-box img-fluid figure-img" alt="Screenshot of JupyterLab interface"></a></p>
+<p><a href="../images/interface_jupyterlab.png" class="lightbox" data-glightbox="description: .lightbox-desc-5" data-gallery="quarto-lightbox-gallery-5" title="JupyterLab interface: running the app"><img src="../images/interface_jupyterlab.png" class="black-box img-fluid figure-img" alt="Screenshot of JupyterLab interface"></a></p>
 <figcaption>JupyterLab interface: running the app</figcaption>
 </figure>
 </div>
 <p>You can navigate through the different folders and start running the Python notebooks (pink arrow).</p>
 <div class="quarto-figure quarto-figure-center">
 <figure class="figure">
-<p><a href="../images/openning_notebook.png" class="lightbox" data-gallery="quarto-lightbox-gallery-6" data-glightbox="description: .lightbox-desc-6" title="JupyterLab interface: openning notebook"><img src="../images/openning_notebook.png" class="black-box img-fluid figure-img" alt="Screenshot of Jupyter Notebook"></a></p>
+<p><a href="../images/openning_notebook.png" class="lightbox" data-glightbox="description: .lightbox-desc-6" data-gallery="quarto-lightbox-gallery-6" title="JupyterLab interface: openning notebook"><img src="../images/openning_notebook.png" class="black-box img-fluid figure-img" alt="Screenshot of Jupyter Notebook"></a></p>
 <figcaption>JupyterLab interface: openning notebook</figcaption>
 </figure>
 </div>
@@ -897,7 +897,7 @@ <h3 class="anchored" data-anchor-id="step-6"><strong>Step 6</strong></h3>
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 </script>
 </div> <!-- /content -->
-<script>var lightboxQuarto = GLightbox({"descPosition":"bottom","openEffect":"zoom","closeEffect":"zoom","selector":".lightbox","loop":false});
+<script>var lightboxQuarto = GLightbox({"descPosition":"bottom","loop":false,"closeEffect":"zoom","selector":".lightbox","openEffect":"zoom"});
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index.html

@@ -132,6 +132,26 @@
 
 
 
+<style>
+  body {
+    position: relative;
+  }
+
+  .background-overlay {
+    position: absolute;
+    top: 0;
+    left: 0;
+    width: 150%;
+    height: 100%;
+    background-image: url("https://international.au.dk/fileadmin/ingen_mappe_valgt/Next-Generation_Sequencing.jpg");
+    background-size: cover;
+    background-repeat: no-repeat;
+    opacity: 0.2; /* Adjust the opacity for transparency */
+  }
+</style>
+<div class="background-overlay">
+
+</div>
 <section id="introduction-to-next-generation-sequencing-data" class="level1 centered">
 <h1 class="centered">Introduction to Next Generation Sequencing data</h1>
 <div style="text-align: center;">
@@ -156,29 +176,27 @@ <h2 class="anchored" data-anchor-id="compiled-exercises">Compiled exercises</h2>
 </section>
 <section id="course-overview" class="level1">
 <h1>Course overview</h1>
-<div class="callout callout-style-default callout-note callout-titled" title="">
+<div class="callout callout-style-default callout-note callout-titled" title="overview">
 <div class="callout-header d-flex align-content-center">
 <div class="callout-icon-container">
 <i class="callout-icon"></i>
 </div>
 <div class="callout-title-container flex-fill">
-Note
+overview
 </div>
 </div>
 <div class="callout-body-container callout-body">
 <p>After the course, you will have knowledge of bioinformatics methods for analyzing genomes using NGS data, including knowledge of the existing types of genome data, how the different types of data can be displayed and analyzed, the current methods for genome assembly and analysis, their accuracy and how they can be used. The course will enable you to devise and run a project that makes use of NGS data.</p>
 <ul>
-<li><strong>Prerequisites:</strong> This is an introductory course that needs a basic understanding of the biology behind sequencing, and not necessarily programming experience (though this would help!).</li>
-</ul>
-<p>-<strong>Syllabus:</strong> - Describe key challenges in the analysis of NGS data</p>
-<pre><code>- Explain the theoretical foundation for methods that use NGS for assembly and analysis of genomes
-
-- Discuss the bioinformatic methods for genome analysis and hypothesize what drives the outcome of the methods
-
-- Review original literature within the subjects and relate the discussed topics to analysis scenarios
-
-- Apply bioinformatics tools within the selected application areas and reflect on the results, formulating your own conclusion in the proposed tasks</code></pre>
+<li><p><strong>Prerequisites:</strong> This is an introductory course that needs a basic understanding of the biology behind sequencing, and not necessarily programming experience (though this would help!).</p></li>
+<li><p><strong>Syllabus:</strong></p>
 <ul>
+<li><p>Describe key challenges in the analysis of NGS data</p></li>
+<li><p>Explain the theoretical foundation for methods that use NGS for assembly and analysis of genomes</p></li>
+<li><p>Discuss the bioinformatic methods for genome analysis and hypothesize what drives the outcome of the methods</p></li>
+<li><p>Review original literature within the subjects and relate the discussed topics to analysis scenarios</p></li>
+<li><p>Apply bioinformatics tools within the selected application areas and reflect on the results, formulating your own conclusion in the proposed tasks</p></li>
+</ul></li>
 <li><p><strong>Time:</strong> 20 hours (for reading through the code, executing it, answering questions). The material fits 4-5 days lessons.</p></li>
 <li><p><strong>Supporting Materials:</strong></p>
 <ul>