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access/UCloud.html

@@ -235,7 +235,7 @@ <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>
@@ -268,7 +268,7 @@ <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>
@@ -291,7 +291,7 @@ <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>
@@ -325,7 +325,7 @@ <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>
@@ -336,14 +336,14 @@ <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>
@@ -932,7 +932,7 @@ <h3 class="anchored" data-anchor-id="step-6"><strong>Step 6</strong></h3>
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 </script>
 </div> <!-- /content -->
-<script>var lightboxQuarto = GLightbox({"selector":".lightbox","closeEffect":"zoom","openEffect":"zoom","descPosition":"bottom","loop":false});
+<script>var lightboxQuarto = GLightbox({"descPosition":"bottom","closeEffect":"zoom","selector":".lightbox","openEffect":"zoom","loop":false});
 window.onload = () => {
   lightboxQuarto.on('slide_before_load', (data) => {
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cards/JenniferBartell.html

@@ -193,7 +193,7 @@ <h1 class="title">Jennifer Bartell</h1>
 
 <p><img src="jennie.jpg" class="img-fluid" width="300"></p>
 <p><a href="https://dk.linkedin.com/in/jagbartell"><img src="LinkedIN.png" class="img-fluid" width="50"></a> <a href="mailto:[email protected]?subject=Test"><img src="Outlook.png" class="img-fluid" width="50"></a> <a href="https://heads.ku.dk/"><img src="mapPin.png" class="img-fluid" width="50"></a></p>
-<p>Jenifer is the Sandbox project coordinator, beyond being also a data scientist. She is based at the university of Copenhagen. Jennifer has a long experience in bacterial genomics and metabolomics, transcriptomics and pathway analysis.</p>
+<p>Jennifer (Jennie) is the Sandbox project manager from the Center for Health Data Science at the University of Copenhagen. Jennie has a broad background in computational systems biology, bioinformatics, and health data modeling. Her PhD and postdoc work also included high throughput phenotyping and long read sequencing of bacterial strain libraries, so she can also speak ‘wet lab’ with experimentalists interested in gaining data science skills. In addition to project management, she’s developing ‘HPC lab’ content and is knowledgable about research data management. She has been deeply involved in the synthetic health data arm of the project, which has turned into a collaborative research project between her, Anders Krogh, Martin Boegsted, and Jan Trzaskowski with a 4 year data science grant from the NNF.</p>
 
 
 

contact/contact.html

@@ -265,7 +265,7 @@ <h1 class="title">Contact the Sandbox</h1>
 <tbody>
 <tr class="odd">
 <td>Jennifer Bartell</td>
-<td>Project Coordinator, Data Scientist</td>
+<td>Project Manager, Data Scientist</td>
 <td>Center for Health Data Science, KU</td>
 <td>Anders Krogh</td>
 </tr>
@@ -314,7 +314,7 @@ <h1 class="title">Contact the Sandbox</h1>
 
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-<div class="g-col-1" data-index="0" data-listing-file-modified-sort="1715255509736" data-listing-reading-time-sort="1" data-listing-word-count-sort="47">
+<div class="g-col-1" data-index="0" data-listing-file-modified-sort="1715334472110" data-listing-reading-time-sort="1" data-listing-word-count-sort="47">
 <a href="../cards/AlbaMartinez.html" class="quarto-grid-link">
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@@ -329,7 +329,7 @@ <h5 class="no-anchor card-title listing-title">
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-<div class="g-col-1" data-index="1" data-listing-file-modified-sort="1715255509736" data-listing-reading-time-sort="1" data-listing-word-count-sort="38">
+<div class="g-col-1" data-index="1" data-listing-file-modified-sort="1715334472110" data-listing-reading-time-sort="1" data-listing-word-count-sort="38">
 <a href="../cards/JacobHansen.html" class="quarto-grid-link">
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@@ -344,7 +344,7 @@ <h5 class="no-anchor card-title listing-title">
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-<div class="g-col-1" data-index="2" data-listing-file-modified-sort="1715255509736" data-listing-reading-time-sort="1" data-listing-word-count-sort="41">
+<div class="g-col-1" data-index="2" data-listing-file-modified-sort="1715334472110" data-listing-reading-time-sort="1" data-listing-word-count-sort="41">
 <a href="../cards/JakobSkelmose.html" class="quarto-grid-link">
 <div class="quarto-grid-item card h-100 card-left">
 <p class="card-img-top"><img src="../cards/jaKob.jpg" style="height: 300px;"  class="thumbnail-image card-img"/></p>
@@ -359,7 +359,7 @@ <h5 class="no-anchor card-title listing-title">
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-<div class="g-col-1" data-index="3" data-listing-file-modified-sort="1715255509736" data-listing-reading-time-sort="1" data-listing-word-count-sort="43">
+<div class="g-col-1" data-index="3" data-listing-file-modified-sort="1715334472110" data-listing-reading-time-sort="1" data-listing-word-count-sort="133">
 <a href="../cards/JenniferBartell.html" class="quarto-grid-link">
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@@ -374,7 +374,7 @@ <h5 class="no-anchor card-title listing-title">
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-<div class="g-col-1" data-index="4" data-listing-file-modified-sort="1715255509736" data-listing-reading-time-sort="1" data-listing-word-count-sort="53">
+<div class="g-col-1" data-index="4" data-listing-file-modified-sort="1715334472110" data-listing-reading-time-sort="1" data-listing-word-count-sort="53">
 <a href="../cards/SamueleSoraggi.html" class="quarto-grid-link">
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datasets/datapolicy.html

@@ -195,7 +195,7 @@ <h1 class="title">Data policy</h1>
     <div>
     <div class="quarto-title-meta-heading">Modified</div>
     <div class="quarto-title-meta-contents">
-      <p class="date-modified">May 9, 2024</p>
+      <p class="date-modified">May 10, 2024</p>
     </div>
   </div>
 

datasets/synthdata.html

@@ -199,7 +199,7 @@ <h1 class="title">Synthetic data</h1>
     <div>
     <div class="quarto-title-meta-heading">Modified</div>
     <div class="quarto-title-meta-contents">
-      <p class="date-modified">May 9, 2024</p>
+      <p class="date-modified">May 10, 2024</p>
     </div>
   </div>
 

modules/index.html

@@ -190,7 +190,7 @@ <h1 class="title">Training modules</h1>
     <div>
     <div class="quarto-title-meta-heading">Modified</div>
     <div class="quarto-title-meta-contents">
-      <p class="date-modified">May 9, 2024</p>
+      <p class="date-modified">May 10, 2024</p>
     </div>
   </div>