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diff --git a/.nojekyll b/.nojekyll
@@ -1 +1 @@
-43520d99
+6ae30520
diff --git a/TeachingModule/AnalysisMSData_FragPipe.html b/TeachingModule/AnalysisMSData_FragPipe.html
@@ -194,20 +194,20 @@ <h2 id="toc-title">On this page</h2>
 <div class="question">
 <p>What is FTP, and what is its functionality?</p>
 </div>
-<p>For downloading the data, we will use the <strong>Proteomics Sandbox Application</strong> on UCloud. This platform allows us to access the necessary storage capacity as well as the computational power required to execute this process.</p>
-<p>The <strong>Proteomics Sandbox Application</strong> is a virtual environment that includes multiple software tools, including <strong>FragPipe</strong> for analyzing proteomics data.</p>
-<p>You can find the <strong>Proteomics Sandbox Application</strong> on UCloud <a href="https://cloud.sdu.dk/app/jobs/create?app=proteomics">here</a>.</p>
+<p>To download the data, we will use the <strong>Proteomics Sandbox Application</strong> on UCloud. This platform provides the necessary storage capacity and computational power to perform this process.</p>
+<p>The <strong>Proteomics Sandbox Application</strong> is a virtual environment that includes various software tools, such as <strong>FragPipe</strong>, for analyzing proteomics data.</p>
 <p>First, we will download the data for the sample files to be used in <strong>FragPipe</strong>. Then, we will launch <strong>FragPipe</strong> to run the first analysis of the data. Before doing so, we have some questions regarding <strong>FragPipe</strong> and its usability:</p>
 <div class="question">
 <p>What is FragPipe, and what are its applications?</p>
 </div>
 <div class="question">
-<p>If FragPipe were not used for this part of the teaching module, which alternative software tools could be employed? Please provide a few examples.</p>
+<p>If FragPipe was not used for this part of the teaching module, which alternative software tools could be employed? Please provide a few examples.</p>
 </div>
 <div class="question">
 <p>What are the benefits of using FragPipe?</p>
 </div>
 <p>Now that we know what we want to do and why, it is time to start the <strong>Proteomics Sandbox</strong> application, or job. Simple analyses in <strong>FragPipe</strong> may only require 8 GB of RAM, while large-scale or complex analyses may require 24 GB of memory or more (<a href="https://fragpipe.nesvilab.org/docs/tutorial_fragpipe.html#:~:text=FragPipe%20runs%20on%20Windows%20and,24%20GB%20memory%20or%20more.">FragPipe Documentation</a>), which is why we will allocate 24 GB for this exercise.</p>
+<p>You can access the <strong>Proteomics Sandbox Application</strong> on UCloud <a href="https://cloud.sdu.dk/app/jobs/create?app=proteomics&amp;version=Oct2024">here</a>.</p>
 <p>In UCloud, the settings should look like this:</p>
 <div class="quarto-figure quarto-figure-center">
 <figure class="figure">
@@ -252,7 +252,19 @@ <h4 class="anchored" data-anchor-id="download-data-from-the-paper">Download Data
 <div class="question">
 <p>Please locate the address.</p>
 </div>
-<p>Click on the “Dataset FTP location” link.</p>
+<div class="callout callout-style-default callout-tip callout-titled">
+<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">
+Tip
+</div>
+</div>
+<div class="callout-body-container callout-body">
+<p>Click on the <strong>Dataset FTP location</strong> link.</p>
+</div>
+</div>
 <div class="question">
 <p>We now have access to the data stored on the FTP server. Please provide a brief description of the contents of the folder on the FTP server.</p>
 </div>
@@ -262,7 +274,22 @@ <h4 class="anchored" data-anchor-id="download-data-from-the-paper">Download Data
 <span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a><span class="ex">https://storage.jpostdb.org/JPST000265/HJOSLO2U_QEHF_20150318_TMT_pool3_300ugIPG37-49_7of15ul_fr01.raw</span></span>
 <span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a><span class="ex">https://storage.jpostdb.org/JPST000265/HJOSLO2U_QEHF_20150322_TMT_pool4_300ugIPG37-49_7of15ul_fr01.raw</span></span>
 <span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a><span class="ex">https://storage.jpostdb.org/JPST000265/HJOSLO2U_QEHF_20150329_TMT_pool5_300ugIPG37-49_7of15ul_fr01.raw</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
-<p>(You can also download this list <a href="https://github.com/hds-sandbox/proteomics-sandbox/blob/webpage/TeachingModule/urls.txt">here</a>).</p>
+<div class="callout callout-style-default callout-tip callout-titled">
+<div class="callout-header d-flex align-content-center" data-bs-toggle="collapse" data-bs-target=".callout-3-contents" aria-controls="callout-3" aria-expanded="false" aria-label="Toggle callout">
+<div class="callout-icon-container">
+<i class="callout-icon"></i>
+</div>
+<div class="callout-title-container flex-fill">
+Tip to Download of Data
+</div>
+<div class="callout-btn-toggle d-inline-block border-0 py-1 ps-1 pe-0 float-end"><i class="callout-toggle"></i></div>
+</div>
+<div id="callout-3" class="callout-3-contents callout-collapse collapse">
+<div class="callout-body-container callout-body">
+<p>You can also download this list <a href="https://github.com/hds-sandbox/proteomics-sandbox/blob/webpage/TeachingModule/urls.txt">here</a>.</p>
+</div>
+</div>
+</div>
 <div class="callout callout-style-default callout-note callout-titled">
 <div class="callout-header d-flex align-content-center">
 <div class="callout-icon-container">

diff --git a/colabfold.html b/colabfold.html
@@ -156,7 +156,7 @@ <h1 class="title">ColabFold</h1>
     <div>
     <div class="quarto-title-meta-heading">Modified</div>
     <div class="quarto-title-meta-contents">
-      <p class="date-modified">November 12, 2024</p>
+      <p class="date-modified">November 19, 2024</p>
     </div>
   </div>
 

diff --git a/coursematerials.html b/coursematerials.html
@@ -6,7 +6,7 @@
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
-<meta name="dcterms.date" content="2024-11-12">
+<meta name="dcterms.date" content="2024-11-19">
 
 <title>Course Materials – Clinical Proteomics</title>
 <style>
@@ -163,7 +163,7 @@ <h1 class="title">Course Materials</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">November 12, 2024</p>
+      <p class="date">November 19, 2024</p>
     </div>
   </div>
 

diff --git a/fragpipe.html b/fragpipe.html
@@ -6,7 +6,7 @@
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
-<meta name="dcterms.date" content="2024-11-12">
+<meta name="dcterms.date" content="2024-11-19">
 
 <title>FragPipe – Clinical Proteomics</title>
 <style>
@@ -156,7 +156,7 @@ <h1 class="title">FragPipe</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">November 12, 2024</p>
+      <p class="date">November 19, 2024</p>
     </div>
   </div>
 

diff --git a/gettingstarted.html b/gettingstarted.html
@@ -6,7 +6,7 @@
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
-<meta name="dcterms.date" content="2024-11-12">
+<meta name="dcterms.date" content="2024-11-19">
 
 <title>Getting Started – Clinical Proteomics</title>
 <style>
@@ -165,7 +165,7 @@ <h1 class="title">Getting Started</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">November 12, 2024</p>
+      <p class="date">November 19, 2024</p>
     </div>
   </div>
 

diff --git a/index.html b/index.html
@@ -156,7 +156,7 @@ <h1 class="title">Clinical Proteomics</h1>
     <div>
     <div class="quarto-title-meta-heading">Modified</div>
     <div class="quarto-title-meta-contents">
-      <p class="date-modified">November 12, 2024</p>
+      <p class="date-modified">November 19, 2024</p>
     </div>
   </div>
 

diff --git a/sdrf.html b/sdrf.html
@@ -7,7 +7,7 @@
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
 <meta name="author" content="Lev Levitsky">
-<meta name="dcterms.date" content="2024-11-12">
+<meta name="dcterms.date" content="2024-11-19">
 
 <title>Breast Cancer Proteomics Module: SDRF – Clinical Proteomics</title>
 <style>
@@ -164,7 +164,7 @@ <h1 class="title">Breast Cancer Proteomics Module: SDRF</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">November 12, 2024</p>
+      <p class="date">November 19, 2024</p>
     </div>
   </div>
 

diff --git a/search.json b/search.json
diff --git a/setup.html b/setup.html
@@ -6,7 +6,7 @@
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
-<meta name="dcterms.date" content="2024-11-12">
+<meta name="dcterms.date" content="2024-11-19">
 
 <title>Setup – Clinical Proteomics</title>
 <style>
@@ -159,7 +159,7 @@ <h1 class="title">Setup</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">November 12, 2024</p>
+      <p class="date">November 19, 2024</p>
     </div>
   </div>
 

diff --git a/sitemap.xml b/sitemap.xml
@@ -2,54 +2,54 @@
 <urlset xmlns="http://www.sitemaps.org/schemas/sitemap/0.9">
   <url>
     <loc>https://hds-sandbox.github.io/proteomics-sandbox/Create SDRF.html</loc>
-    <lastmod>2024-11-12T14:14:32.582Z</lastmod>
+    <lastmod>2024-11-19T08:36:12.050Z</lastmod>
   </url>
   <url>
     <loc>https://hds-sandbox.github.io/proteomics-sandbox/coursematerials.html</loc>
-    <lastmod>2024-11-12T14:14:32.582Z</lastmod>
+    <lastmod>2024-11-19T08:36:12.054Z</lastmod>
   </url>
   <url>
     <loc>https://hds-sandbox.github.io/proteomics-sandbox/contributors.html</loc>
-    <lastmod>2024-11-12T14:14:32.582Z</lastmod>
+    <lastmod>2024-11-19T08:36:12.054Z</lastmod>
   </url>
   <url>
     <loc>https://hds-sandbox.github.io/proteomics-sandbox/teachingmodule.html</loc>
-    <lastmod>2024-11-12T14:14:32.626Z</lastmod>
+    <lastmod>2024-11-19T08:36:12.098Z</lastmod>
   </url>
   <url>
     <loc>https://hds-sandbox.github.io/proteomics-sandbox/colabfold.html</loc>
-    <lastmod>2024-11-12T14:14:32.582Z</lastmod>
+    <lastmod>2024-11-19T08:36:12.054Z</lastmod>
   </url>
   <url>
     <loc>https://hds-sandbox.github.io/proteomics-sandbox/TeachingModule/AnalysisMSData_FragPipe.html</loc>
-    <lastmod>2024-11-12T14:14:32.582Z</lastmod>
+    <lastmod>2024-11-19T08:36:12.050Z</lastmod>
   </url>
   <url>
     <loc>https://hds-sandbox.github.io/proteomics-sandbox/TeachingModule/Preliminarywork.html</loc>
-    <lastmod>2024-11-12T14:14:32.582Z</lastmod>
+    <lastmod>2024-11-19T08:36:12.050Z</lastmod>
   </url>
   <url>
     <loc>https://hds-sandbox.github.io/proteomics-sandbox/TeachingModule/DataScreening_Multivariate.html</loc>
-    <lastmod>2024-11-12T14:14:32.582Z</lastmod>
+    <lastmod>2024-11-19T08:36:12.050Z</lastmod>
   </url>
   <url>
     <loc>https://hds-sandbox.github.io/proteomics-sandbox/sdrf.html</loc>
-    <lastmod>2024-11-12T14:14:32.626Z</lastmod>
+    <lastmod>2024-11-19T08:36:12.094Z</lastmod>
   </url>
   <url>
     <loc>https://hds-sandbox.github.io/proteomics-sandbox/fragpipe.html</loc>
-    <lastmod>2024-11-12T14:14:32.582Z</lastmod>
+    <lastmod>2024-11-19T08:36:12.054Z</lastmod>
   </url>
   <url>
     <loc>https://hds-sandbox.github.io/proteomics-sandbox/setup.html</loc>
-    <lastmod>2024-11-12T14:14:32.626Z</lastmod>
+    <lastmod>2024-11-19T08:36:12.098Z</lastmod>
   </url>
   <url>
     <loc>https://hds-sandbox.github.io/proteomics-sandbox/index.html</loc>
-    <lastmod>2024-11-12T14:14:32.622Z</lastmod>
+    <lastmod>2024-11-19T08:36:12.090Z</lastmod>
   </url>
   <url>
     <loc>https://hds-sandbox.github.io/proteomics-sandbox/gettingstarted.html</loc>
-    <lastmod>2024-11-12T14:14:32.582Z</lastmod>
+    <lastmod>2024-11-19T08:36:12.054Z</lastmod>
   </url>
 </urlset>
diff --git a/teachingmodule.html b/teachingmodule.html
@@ -7,7 +7,7 @@
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
 <meta name="author" content="Jacob Fredegaard Hansen">
-<meta name="dcterms.date" content="2024-11-12">
+<meta name="dcterms.date" content="2024-11-19">
 
 <title>Breast Cancer Proteomics Module – Clinical Proteomics</title>
 <style>
@@ -211,7 +211,7 @@ <h1 class="title">Breast Cancer Proteomics Module</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">November 12, 2024</p>
+      <p class="date">November 19, 2024</p>
     </div>
   </div>
 
@@ -681,20 +681,20 @@ <h2 class="anchored" data-anchor-id="part-2-analysis-of-ms-data-using-fragpipe">
 <div class="question">
 <p>What is FTP, and what is its functionality?</p>
 </div>
-<p>For downloading the data, we will use the <strong>Proteomics Sandbox Application</strong> on UCloud. This platform allows us to access the necessary storage capacity as well as the computational power required to execute this process.</p>
-<p>The <strong>Proteomics Sandbox Application</strong> is a virtual environment that includes multiple software tools, including <strong>FragPipe</strong> for analyzing proteomics data.</p>
-<p>You can find the <strong>Proteomics Sandbox Application</strong> on UCloud <a href="https://cloud.sdu.dk/app/jobs/create?app=proteomics">here</a>.</p>
+<p>To download the data, we will use the <strong>Proteomics Sandbox Application</strong> on UCloud. This platform provides the necessary storage capacity and computational power to perform this process.</p>
+<p>The <strong>Proteomics Sandbox Application</strong> is a virtual environment that includes various software tools, such as <strong>FragPipe</strong>, for analyzing proteomics data.</p>
 <p>First, we will download the data for the sample files to be used in <strong>FragPipe</strong>. Then, we will launch <strong>FragPipe</strong> to run the first analysis of the data. Before doing so, we have some questions regarding <strong>FragPipe</strong> and its usability:</p>
 <div class="question">
 <p>What is FragPipe, and what are its applications?</p>
 </div>
 <div class="question">
-<p>If FragPipe were not used for this part of the teaching module, which alternative software tools could be employed? Please provide a few examples.</p>
+<p>If FragPipe was not used for this part of the teaching module, which alternative software tools could be employed? Please provide a few examples.</p>
 </div>
 <div class="question">
 <p>What are the benefits of using FragPipe?</p>
 </div>
 <p>Now that we know what we want to do and why, it is time to start the <strong>Proteomics Sandbox</strong> application, or job. Simple analyses in <strong>FragPipe</strong> may only require 8 GB of RAM, while large-scale or complex analyses may require 24 GB of memory or more (<a href="https://fragpipe.nesvilab.org/docs/tutorial_fragpipe.html#:~:text=FragPipe%20runs%20on%20Windows%20and,24%20GB%20memory%20or%20more.">FragPipe Documentation</a>), which is why we will allocate 24 GB for this exercise.</p>
+<p>You can access the <strong>Proteomics Sandbox Application</strong> on UCloud <a href="https://cloud.sdu.dk/app/jobs/create?app=proteomics&amp;version=Oct2024">here</a>.</p>
 <p>In UCloud, the settings should look like this:</p>
 <div class="quarto-figure quarto-figure-center">
 <figure class="figure">
@@ -739,7 +739,19 @@ <h4 class="anchored" data-anchor-id="download-data-from-the-paper">Download Data
 <div class="question">
 <p>Please locate the address.</p>
 </div>
-<p>Click on the “Dataset FTP location” link.</p>
+<div class="callout callout-style-default callout-tip callout-titled">
+<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">
+Tip
+</div>
+</div>
+<div class="callout-body-container callout-body">
+<p>Click on the <strong>Dataset FTP location</strong> link.</p>
+</div>
+</div>
 <div class="question">
 <p>We now have access to the data stored on the FTP server. Please provide a brief description of the contents of the folder on the FTP server.</p>
 </div>
@@ -750,7 +762,22 @@ <h4 class="anchored" data-anchor-id="download-data-from-the-paper">Download Data
 <span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a><span class="ex">https://storage.jpostdb.org/JPST000265/HJOSLO2U_QEHF_20150322_TMT_pool4_300ugIPG37-49_7of15ul_fr01.raw</span></span>
 <span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a><span class="ex">https://storage.jpostdb.org/JPST000265/HJOSLO2U_QEHF_20150329_TMT_pool5_300ugIPG37-49_7of15ul_fr01.raw</span></span>
 <span id="cb1-6"><a href="#cb1-6" aria-hidden="true" tabindex="-1"></a></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
-<p>(You can also download this list <a href="https://github.com/hds-sandbox/proteomics-sandbox/blob/webpage/TeachingModule/urls.txt">here</a>).</p>
+<div class="callout callout-style-default callout-tip callout-titled">
+<div class="callout-header d-flex align-content-center" data-bs-toggle="collapse" data-bs-target=".callout-7-contents" aria-controls="callout-7" aria-expanded="false" aria-label="Toggle callout">
+<div class="callout-icon-container">
+<i class="callout-icon"></i>
+</div>
+<div class="callout-title-container flex-fill">
+Tip to Download of Data
+</div>
+<div class="callout-btn-toggle d-inline-block border-0 py-1 ps-1 pe-0 float-end"><i class="callout-toggle"></i></div>
+</div>
+<div id="callout-7" class="callout-7-contents callout-collapse collapse">
+<div class="callout-body-container callout-body">
+<p>You can also download this list <a href="https://github.com/hds-sandbox/proteomics-sandbox/blob/webpage/TeachingModule/urls.txt">here</a>.</p>
+</div>
+</div>
+</div>
 <div class="callout callout-style-default callout-note callout-titled">
 <div class="callout-header d-flex align-content-center">
 <div class="callout-icon-container">