Updating for launch

_bblearn/Module02/Module02_lab.html

@@ -118,7 +118,7 @@
 
 
   <div class="bd-header-announcement container-fluid bd-header-announcement">
-    <div class="bd-header-announcement__content">Work in progress!</div>
+    <div class="bd-header-announcement__content">Welcome Spring 2025 Students!</div>
   </div>
 
 
@@ -186,8 +186,8 @@
 <p aria-level="2" class="caption" role="heading"><span class="caption-text">Part 1 : Hello World</span></p>
 <ul class="current nav bd-sidenav">
 <li class="toctree-l1 has-children"><a class="reference internal" href="../../content/Module01/Module01_book.html">Module 1: Hello World</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-1"><i class="fa-solid fa-chevron-down"></i></label><ul>
-<li class="toctree-l2"><a class="reference internal" href="../../content/Module01/Module01_walkthrough.html">Walkthrough</a></li>
 <li class="toctree-l2"><a class="reference internal" href="../../content/Module01/notebook_actions.html">Notebook basics</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../../content/Module01/Module01_walkthrough.html">Walkthrough</a></li>
 </ul>
 </li>
 <li class="toctree-l1 current active has-children"><a class="reference internal" href="../../content/Module02/Module02_book.html">Module 2: Simple calculations</a><input checked="" class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-2"><i class="fa-solid fa-chevron-down"></i></label><ul class="current">
@@ -253,6 +253,7 @@
 <p aria-level="2" class="caption" role="heading"><span class="caption-text">Extra</span></p>
 <ul class="nav bd-sidenav">
 <li class="toctree-l1 has-children"><a class="reference internal" href="../../content/misc/resources.html">Resources</a><input class="toctree-checkbox" id="toctree-checkbox-11" name="toctree-checkbox-11" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-11"><i class="fa-solid fa-chevron-down"></i></label><ul>
+<li class="toctree-l2"><a class="reference internal" href="../../content/faq.html">Frequently Asked Questions</a></li>
 <li class="toctree-l2"><a class="reference internal" href="../../content/changelog.html">Change Log</a></li>
 <li class="toctree-l2"><a class="reference internal" href="../../content/misc/works_cited.html">Works Cited</a></li>
 </ul>
@@ -418,10 +419,7 @@ <h2> Contents </h2>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#q5-which-samples-are-usable">Q5: Which samples are <em>usable</em>?</a></li>
 </ul>
 </li>
-<li class="toc-h1 nav-item toc-entry"><a class="reference internal nav-link" href="#conclusion">Conclusion</a><ul class="visible nav section-nav flex-column">
-<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#submission">Submission</a></li>
-</ul>
-</li>
+<li class="toc-h1 nav-item toc-entry"><a class="reference internal nav-link" href="#conclusion">Conclusion</a></li>
 </ul>
 
             </nav>
@@ -436,7 +434,6 @@ <h2> Contents </h2>
 
   <section class="tex2jax_ignore mathjax_ignore" id="lab">
 <h1>Lab<a class="headerlink" href="#lab" title="Link to this heading">#</a></h1>
-<p>Remember, all labs are due at 11:59 PM (Philadelphia time) on the Sunday of each instructional week.</p>
 <section id="introduction">
 <h2>Introduction<a class="headerlink" href="#introduction" title="Link to this heading">#</a></h2>
 <p>In this lab, we will delve into the exciting world of viral sample preparation for nanopore sequencing for COVID-19 sequencing.
@@ -473,25 +470,6 @@ <h1>Protocol Evaluation<a class="headerlink" href="#protocol-evaluation" title="
 <p>In this lab, you will work through a basic exercise in evaluating the yield of the <em>Paragon</em> and <em>PacBio</em> systems.</p>
 <section id="q1-extract-the-relevant-information-from-the-text-above">
 <h2>Q1: Extract the relevant information from the text above<a class="headerlink" href="#q1-extract-the-relevant-information-from-the-text-above" title="Link to this heading">#</a></h2>
-<table class="table">
-<thead>
-<tr class="row-odd"><th class="head"><p></p></th>
-<th class="head"><p></p></th>
-</tr>
-</thead>
-<tbody>
-<tr class="row-even"><td><p>Points</p></td>
-<td><p>2</p></td>
-</tr>
-<tr class="row-odd"><td><p>Public Checks</p></td>
-<td><p>2</p></td>
-</tr>
-<tr class="row-even"><td><p>Hidden Tests</p></td>
-<td><p>0</p></td>
-</tr>
-</tbody>
-</table>
-<p><em>Points:</em> 2</p>
 <div class="cell docutils container">
 <div class="cell_input docutils container">
 <div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># It is often useful to define all of your variables at the beginning.</span>
@@ -520,24 +498,6 @@ <h2>Q2: Calculate the molecular weight of each template<a class="headerlink" hre
 In order to accurately compare the yield of each method, it is important to know the molecular weight of the templates being used.
 Therefore, as a part of this lab, we need to calculate the molecular weight of each template.
 This will allow us to accurately compare the yield of each method and understand how the different characteristics of each method may impact the overall results.</p>
-<table class="table">
-<thead>
-<tr class="row-odd"><th class="head"><p></p></th>
-<th class="head"><p></p></th>
-</tr>
-</thead>
-<tbody>
-<tr class="row-even"><td><p>Points</p></td>
-<td><p>2</p></td>
-</tr>
-<tr class="row-odd"><td><p>Public Checks</p></td>
-<td><p>4</p></td>
-</tr>
-<tr class="row-even"><td><p>Hidden Tests</p></td>
-<td><p>0</p></td>
-</tr>
-</tbody>
-</table>
 <p><em>Feeling stuck?</em></p>
 <p>Try doing it on <strong>paper</strong> first.</p>
 <p><em>Points:</em> 4</p>
@@ -590,24 +550,6 @@ <h2>Q2: Calculate the molecular weight of each template<a class="headerlink" hre
 </section>
 <section id="q3-what-is-the-molarity-of-each-paragon-sample">
 <h2>Q3: What is the <em>molarity</em> of each <em>Paragon</em> sample?<a class="headerlink" href="#q3-what-is-the-molarity-of-each-paragon-sample" title="Link to this heading">#</a></h2>
-<table class="table">
-<thead>
-<tr class="row-odd"><th class="head"><p></p></th>
-<th class="head"><p></p></th>
-</tr>
-</thead>
-<tbody>
-<tr class="row-even"><td><p>Points</p></td>
-<td><p>4</p></td>
-</tr>
-<tr class="row-odd"><td><p>Public Checks</p></td>
-<td><p>4</p></td>
-</tr>
-<tr class="row-even"><td><p>Hidden Tests</p></td>
-<td><p>2</p></td>
-</tr>
-</tbody>
-</table>
 <p><em>Feeling stuck?</em></p>
 <p>Try doing it on <strong>paper</strong> first.</p>
 <p>A typical molarity for this protocol is between 50 and 500 fmols/ul.</p>
@@ -703,25 +645,6 @@ <h2>Q5: Which samples are <em>usable</em>?<a class="headerlink" href="#q5-which-
 As stated in the protocol, you need to provide 200 fmoles of DNA in 10 ul of dH20.
 Based on the yield data that you calculated for the fresh and degraded PacBio and Paragon samples, you will need to determine which samples have a concentration of DNA that meets or exceeds this requirement.
 In other words, you will need to determine which samples are usable for the sequencing protocol based on their DNA concentration.</p>
-<table class="table">
-<thead>
-<tr class="row-odd"><th class="head"><p></p></th>
-<th class="head"><p></p></th>
-</tr>
-</thead>
-<tbody>
-<tr class="row-even"><td><p>Points</p></td>
-<td><p>6</p></td>
-</tr>
-<tr class="row-odd"><td><p>Public Checks</p></td>
-<td><p>1</p></td>
-</tr>
-<tr class="row-even"><td><p>Hidden Tests</p></td>
-<td><p>4</p></td>
-</tr>
-</tbody>
-</table>
-<p><em>Points:</em> 6</p>
 <div class="cell docutils container">
 <div class="cell_input docutils container">
 <div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># Do the necessary calculations in this cell or the create more above.</span>
@@ -760,20 +683,6 @@ <h1>Conclusion<a class="headerlink" href="#conclusion" title="Link to this headi
 This is just the beginning of your journey with Python and data analysis.
 Keep up the great work as we continue to expand on these techniques and explore more complicated results in future assignments.</p>
 <hr class="docutils" />
-<section id="submission">
-<h2>Submission<a class="headerlink" href="#submission" title="Link to this heading">#</a></h2>
-<p>Check:</p>
-<ul class="simple">
-<li><p>That all tables and graphs are rendered properly.</p></li>
-<li><p>Code completes without errors by using <code class="docutils literal notranslate"><span class="pre">Restart</span> <span class="pre">&amp;</span> <span class="pre">Run</span> <span class="pre">All</span></code>.</p></li>
-<li><p>All checks <strong>pass</strong>.</p></li>
-<li><p>Excess code cells and print statments have been removed to create a <em>clean</em> submission.</p></li>
-</ul>
-<p>Remember, as this is a lab, there are hidden tests that you will be evaluated against.
-Just because all checks pass does not mean everything is correct.
-Double-check your work!</p>
-<p>Then save the notebook and the <code class="docutils literal notranslate"><span class="pre">File</span></code> -&gt; <code class="docutils literal notranslate"><span class="pre">Download</span></code> -&gt; <code class="docutils literal notranslate"><span class="pre">Download</span> <span class="pre">.ipynb</span></code>. Upload this file to BBLearn.</p>
-</section>
 </section>
 
     <script type="text/x-thebe-config">
@@ -853,10 +762,7 @@ <h2>Submission<a class="headerlink" href="#submission" title="Link to this headi
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#q5-which-samples-are-usable">Q5: Which samples are <em>usable</em>?</a></li>
 </ul>
 </li>
-<li class="toc-h1 nav-item toc-entry"><a class="reference internal nav-link" href="#conclusion">Conclusion</a><ul class="visible nav section-nav flex-column">
-<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#submission">Submission</a></li>
-</ul>
-</li>
+<li class="toc-h1 nav-item toc-entry"><a class="reference internal nav-link" href="#conclusion">Conclusion</a></li>
 </ul>
 
   </nav></div>

_bblearn/Module02/Module02_walkthrough_SOLUTION.html

@@ -118,7 +118,7 @@
 
 
   <div class="bd-header-announcement container-fluid bd-header-announcement">
-    <div class="bd-header-announcement__content">Work in progress!</div>
+    <div class="bd-header-announcement__content">Welcome Spring 2025 Students!</div>
   </div>
 
 
@@ -186,8 +186,8 @@
 <p aria-level="2" class="caption" role="heading"><span class="caption-text">Part 1 : Hello World</span></p>
 <ul class="current nav bd-sidenav">
 <li class="toctree-l1 has-children"><a class="reference internal" href="../../content/Module01/Module01_book.html">Module 1: Hello World</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-1"><i class="fa-solid fa-chevron-down"></i></label><ul>
-<li class="toctree-l2"><a class="reference internal" href="../../content/Module01/Module01_walkthrough.html">Walkthrough</a></li>
 <li class="toctree-l2"><a class="reference internal" href="../../content/Module01/notebook_actions.html">Notebook basics</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../../content/Module01/Module01_walkthrough.html">Walkthrough</a></li>
 </ul>
 </li>
 <li class="toctree-l1 current active has-children"><a class="reference internal" href="../../content/Module02/Module02_book.html">Module 2: Simple calculations</a><input checked="" class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-2"><i class="fa-solid fa-chevron-down"></i></label><ul class="current">
@@ -253,6 +253,7 @@
 <p aria-level="2" class="caption" role="heading"><span class="caption-text">Extra</span></p>
 <ul class="nav bd-sidenav">
 <li class="toctree-l1 has-children"><a class="reference internal" href="../../content/misc/resources.html">Resources</a><input class="toctree-checkbox" id="toctree-checkbox-11" name="toctree-checkbox-11" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-11"><i class="fa-solid fa-chevron-down"></i></label><ul>
+<li class="toctree-l2"><a class="reference internal" href="../../content/faq.html">Frequently Asked Questions</a></li>
 <li class="toctree-l2"><a class="reference internal" href="../../content/changelog.html">Change Log</a></li>
 <li class="toctree-l2"><a class="reference internal" href="../../content/misc/works_cited.html">Works Cited</a></li>
 </ul>
@@ -433,7 +434,6 @@ <h2> Contents </h2>
 
   <section class="tex2jax_ignore mathjax_ignore" id="walkthrough">
 <h1>Walkthrough<a class="headerlink" href="#walkthrough" title="Link to this heading">#</a></h1>
-<p>Remember, all assignments are due before the weekly synchronous session.</p>
 <section id="learning-objectives">
 <h2>Learning Objectives<a class="headerlink" href="#learning-objectives" title="Link to this heading">#</a></h2>
 <p>At the end of this learning activity you will be able to:</p>