updating module 2 & 3 for publication

DamLabResources · Dec 19, 2024 · 48ec37c · 48ec37c
1 parent af03089
commit 48ec37c
Show file tree

Hide file tree

Showing 51 changed files with 3,065 additions and 125 deletions.
diff --git a/_bblearn/Module02/Module02_lab.html b/_bblearn/Module02/Module02_lab.html
@@ -63,7 +63,7 @@
     <link rel="index" title="Index" href="../../genindex.html" />
     <link rel="search" title="Search" href="../../search.html" />
     <link rel="next" title="Module 3: DataFrames" href="../../content/Module03/Module03_book.html" />
-    <link rel="prev" title="Dilution calculations" href="../../content/Module02/dilution_calculations.html" />
+    <link rel="prev" title="Walkthrough" href="Module02_walkthrough_SOLUTION.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
   </head>
@@ -191,15 +191,15 @@
 </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">
+<li class="toctree-l2"><a class="reference internal" href="../../content/Module02/dilution_calculations.html">Molarity Calculations</a></li>
 <li class="toctree-l2"><a class="reference internal" href="Module02_walkthrough_SOLUTION.html">Walkthrough</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../../content/Module02/nanopore_description.html">Nanopore Sequencing</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../../content/Module02/dilution_calculations.html">Dilution calculations</a></li>
 <li class="toctree-l2 current active"><a class="current reference internal" href="#">Lab</a></li>
 
 
 </ul>
 </li>
 <li class="toctree-l1 has-children"><a class="reference internal" href="../../content/Module03/Module03_book.html">Module 3: DataFrames</a><input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-3"><i class="fa-solid fa-chevron-down"></i></label><ul>
+<li class="toctree-l2"><a class="reference internal" href="../../content/Module03/spreadsheet_organization.html">Spreadsheet Organization</a></li>
 <li class="toctree-l2"><a class="reference internal" href="../Module03/Module03_walkthrough_SOLUTION.html">Walkthrough</a></li>
 
 <li class="toctree-l2"><a class="reference internal" href="../Module03/Module03_lab.html">Lab</a></li>
@@ -247,6 +247,14 @@
 <li class="toctree-l2"><a class="reference internal" href="../Module10/Module10_walkthrough_SOLUTION.html">Walkthrough</a></li>
 <li class="toctree-l2"><a class="reference internal" href="../Module10/Module10_lab.html">Lab</a></li>
 
+</ul>
+</li>
+</ul>
+<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/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>
 </li>
 </ul>
@@ -431,7 +439,7 @@ <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 COIVD-19 sequencing.
+<p>In this lab, we will delve into the exciting world of viral sample preparation for nanopore sequencing for COVID-19 sequencing.
 Specifically, we will be comparing the yield of two different RT-PCR methods: the Paragon system and the PacBio system.</p>
 <p>Before we can sequence our samples, we need to make sure that we have a sufficient amount of DNA to work with.
 This means calculating the appropriate dilutions of our samples to ensure that we have enough material to generate accurate and reliable results.</p>
@@ -799,12 +807,12 @@ <h2>Submission<a class="headerlink" href="#submission" title="Link to this headi
 
 <div class="prev-next-area">
     <a class="left-prev"
-       href="../../content/Module02/dilution_calculations.html"
+       href="Module02_walkthrough_SOLUTION.html"
        title="previous page">
       <i class="fa-solid fa-angle-left"></i>
       <div class="prev-next-info">
         <p class="prev-next-subtitle">previous</p>
-        <p class="prev-next-title">Dilution calculations</p>
+        <p class="prev-next-title">Walkthrough</p>
       </div>
     </a>
     <a class="right-next"

diff --git a/_bblearn/Module02/Module02_walkthrough_SOLUTION.html b/_bblearn/Module02/Module02_walkthrough_SOLUTION.html
@@ -62,8 +62,8 @@
     <link rel="canonical" href="https://damlabresources.github.io/quantitative-reasoning-in-biology/_bblearn/Module02/Module02_walkthrough_SOLUTION.html" />
     <link rel="index" title="Index" href="../../genindex.html" />
     <link rel="search" title="Search" href="../../search.html" />
-    <link rel="next" title="Nanopore Sequencing" href="../../content/Module02/nanopore_description.html" />
-    <link rel="prev" title="Module 2: Simple calculations" href="../../content/Module02/Module02_book.html" />
+    <link rel="next" title="Lab" href="Module02_lab.html" />
+    <link rel="prev" title="Molarity Calculations" href="../../content/Module02/dilution_calculations.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
   </head>
@@ -191,15 +191,15 @@
 </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">
+<li class="toctree-l2"><a class="reference internal" href="../../content/Module02/dilution_calculations.html">Molarity Calculations</a></li>
 <li class="toctree-l2 current active"><a class="current reference internal" href="#">Walkthrough</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../../content/Module02/nanopore_description.html">Nanopore Sequencing</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../../content/Module02/dilution_calculations.html">Dilution calculations</a></li>
 <li class="toctree-l2"><a class="reference internal" href="Module02_lab.html">Lab</a></li>
 
 
 </ul>
 </li>
 <li class="toctree-l1 has-children"><a class="reference internal" href="../../content/Module03/Module03_book.html">Module 3: DataFrames</a><input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-3"><i class="fa-solid fa-chevron-down"></i></label><ul>
+<li class="toctree-l2"><a class="reference internal" href="../../content/Module03/spreadsheet_organization.html">Spreadsheet Organization</a></li>
 <li class="toctree-l2"><a class="reference internal" href="../Module03/Module03_walkthrough_SOLUTION.html">Walkthrough</a></li>
 
 <li class="toctree-l2"><a class="reference internal" href="../Module03/Module03_lab.html">Lab</a></li>
@@ -247,6 +247,14 @@
 <li class="toctree-l2"><a class="reference internal" href="../Module10/Module10_walkthrough_SOLUTION.html">Walkthrough</a></li>
 <li class="toctree-l2"><a class="reference internal" href="../Module10/Module10_lab.html">Lab</a></li>
 
+</ul>
+</li>
+</ul>
+<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/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>
 </li>
 </ul>
@@ -816,20 +824,20 @@ <h2>Conclusion<a class="headerlink" href="#conclusion" title="Link to this headi
 
 <div class="prev-next-area">
     <a class="left-prev"
-       href="../../content/Module02/Module02_book.html"
+       href="../../content/Module02/dilution_calculations.html"
        title="previous page">
       <i class="fa-solid fa-angle-left"></i>
       <div class="prev-next-info">
         <p class="prev-next-subtitle">previous</p>
-        <p class="prev-next-title">Module 2: Simple calculations</p>
+        <p class="prev-next-title">Molarity Calculations</p>
       </div>
     </a>
     <a class="right-next"
-       href="../../content/Module02/nanopore_description.html"
+       href="Module02_lab.html"
        title="next page">
       <div class="prev-next-info">
         <p class="prev-next-subtitle">next</p>
-        <p class="prev-next-title">Nanopore Sequencing</p>
+        <p class="prev-next-title">Lab</p>
       </div>
       <i class="fa-solid fa-angle-right"></i>
     </a>

diff --git a/_bblearn/Module03/Module03_lab.html b/_bblearn/Module03/Module03_lab.html
@@ -191,15 +191,15 @@
 </ul>
 </li>
 <li class="toctree-l1 has-children"><a class="reference internal" href="../../content/Module02/Module02_book.html">Module 2: Simple calculations</a><input 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>
+<li class="toctree-l2"><a class="reference internal" href="../../content/Module02/dilution_calculations.html">Molarity Calculations</a></li>
 <li class="toctree-l2"><a class="reference internal" href="../Module02/Module02_walkthrough_SOLUTION.html">Walkthrough</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../../content/Module02/nanopore_description.html">Nanopore Sequencing</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../../content/Module02/dilution_calculations.html">Dilution calculations</a></li>
 <li class="toctree-l2"><a class="reference internal" href="../Module02/Module02_lab.html">Lab</a></li>
 
 
 </ul>
 </li>
 <li class="toctree-l1 current active has-children"><a class="reference internal" href="../../content/Module03/Module03_book.html">Module 3: DataFrames</a><input checked="" class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-3"><i class="fa-solid fa-chevron-down"></i></label><ul class="current">
+<li class="toctree-l2"><a class="reference internal" href="../../content/Module03/spreadsheet_organization.html">Spreadsheet Organization</a></li>
 <li class="toctree-l2"><a class="reference internal" href="Module03_walkthrough_SOLUTION.html">Walkthrough</a></li>
 
 <li class="toctree-l2 current active"><a class="current reference internal" href="#">Lab</a></li>
@@ -247,6 +247,14 @@
 <li class="toctree-l2"><a class="reference internal" href="../Module10/Module10_walkthrough_SOLUTION.html">Walkthrough</a></li>
 <li class="toctree-l2"><a class="reference internal" href="../Module10/Module10_lab.html">Lab</a></li>
 
+</ul>
+</li>
+</ul>
+<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/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>
 </li>
 </ul>

diff --git a/_bblearn/Module03/Module03_walkthrough_SOLUTION.html b/_bblearn/Module03/Module03_walkthrough_SOLUTION.html
@@ -63,7 +63,7 @@
     <link rel="index" title="Index" href="../../genindex.html" />
     <link rel="search" title="Search" href="../../search.html" />
     <link rel="next" title="Lab" href="Module03_lab.html" />
-    <link rel="prev" title="Module 3: DataFrames" href="../../content/Module03/Module03_book.html" />
+    <link rel="prev" title="Spreadsheet Organization" href="../../content/Module03/spreadsheet_organization.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
   </head>
@@ -191,15 +191,15 @@
 </ul>
 </li>
 <li class="toctree-l1 has-children"><a class="reference internal" href="../../content/Module02/Module02_book.html">Module 2: Simple calculations</a><input 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>
+<li class="toctree-l2"><a class="reference internal" href="../../content/Module02/dilution_calculations.html">Molarity Calculations</a></li>
 <li class="toctree-l2"><a class="reference internal" href="../Module02/Module02_walkthrough_SOLUTION.html">Walkthrough</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../../content/Module02/nanopore_description.html">Nanopore Sequencing</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../../content/Module02/dilution_calculations.html">Dilution calculations</a></li>
 <li class="toctree-l2"><a class="reference internal" href="../Module02/Module02_lab.html">Lab</a></li>
 
 
 </ul>
 </li>
 <li class="toctree-l1 current active has-children"><a class="reference internal" href="../../content/Module03/Module03_book.html">Module 3: DataFrames</a><input checked="" class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-3"><i class="fa-solid fa-chevron-down"></i></label><ul class="current">
+<li class="toctree-l2"><a class="reference internal" href="../../content/Module03/spreadsheet_organization.html">Spreadsheet Organization</a></li>
 <li class="toctree-l2 current active"><a class="current reference internal" href="#">Walkthrough</a></li>
 
 <li class="toctree-l2"><a class="reference internal" href="Module03_lab.html">Lab</a></li>
@@ -247,6 +247,14 @@
 <li class="toctree-l2"><a class="reference internal" href="../Module10/Module10_walkthrough_SOLUTION.html">Walkthrough</a></li>
 <li class="toctree-l2"><a class="reference internal" href="../Module10/Module10_lab.html">Lab</a></li>
 
+</ul>
+</li>
+</ul>
+<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/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>
 </li>
 </ul>
@@ -2487,12 +2495,12 @@ <h1>Conclusion<a class="headerlink" href="#conclusion" title="Link to this headi
 
 <div class="prev-next-area">
     <a class="left-prev"
-       href="../../content/Module03/Module03_book.html"
+       href="../../content/Module03/spreadsheet_organization.html"
        title="previous page">
       <i class="fa-solid fa-angle-left"></i>
       <div class="prev-next-info">
         <p class="prev-next-subtitle">previous</p>
-        <p class="prev-next-title">Module 3: DataFrames</p>
+        <p class="prev-next-title">Spreadsheet Organization</p>
       </div>
     </a>
     <a class="right-next"

diff --git a/_bblearn/Module04/Module04_lab.html b/_bblearn/Module04/Module04_lab.html
@@ -191,15 +191,15 @@
 </ul>
 </li>
 <li class="toctree-l1 has-children"><a class="reference internal" href="../../content/Module02/Module02_book.html">Module 2: Simple calculations</a><input 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>
+<li class="toctree-l2"><a class="reference internal" href="../../content/Module02/dilution_calculations.html">Molarity Calculations</a></li>
 <li class="toctree-l2"><a class="reference internal" href="../Module02/Module02_walkthrough_SOLUTION.html">Walkthrough</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../../content/Module02/nanopore_description.html">Nanopore Sequencing</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../../content/Module02/dilution_calculations.html">Dilution calculations</a></li>
 <li class="toctree-l2"><a class="reference internal" href="../Module02/Module02_lab.html">Lab</a></li>
 
 
 </ul>
 </li>
 <li class="toctree-l1 has-children"><a class="reference internal" href="../../content/Module03/Module03_book.html">Module 3: DataFrames</a><input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-3"><i class="fa-solid fa-chevron-down"></i></label><ul>
+<li class="toctree-l2"><a class="reference internal" href="../../content/Module03/spreadsheet_organization.html">Spreadsheet Organization</a></li>
 <li class="toctree-l2"><a class="reference internal" href="../Module03/Module03_walkthrough_SOLUTION.html">Walkthrough</a></li>
 
 <li class="toctree-l2"><a class="reference internal" href="../Module03/Module03_lab.html">Lab</a></li>
@@ -247,6 +247,14 @@
 <li class="toctree-l2"><a class="reference internal" href="../Module10/Module10_walkthrough_SOLUTION.html">Walkthrough</a></li>
 <li class="toctree-l2"><a class="reference internal" href="../Module10/Module10_lab.html">Lab</a></li>
 
+</ul>
+</li>
+</ul>
+<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/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>
 </li>
 </ul>