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           <i aria-hidden="true" class="icon" data-feather="eye"></i> Learner View <i data-feather="chevron-down"></i>
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     <div id="flush-collapsecurrent" class="accordion-collapse collapse show" aria-labelledby="flush-headingcurrent" data-bs-parent="#accordionFlushcurrent">
       <div class="accordion-body">
         <ul><li><a href="#introduction">Introduction</a></li>
@@ -212,7 +212,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
 <li><a href="#structuring-data-in-spreadsheets">Structuring data in spreadsheets</a></li>
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     <div class="accordion-header" id="flush-heading4">
         <a href="03-ncbi-sra.html">3. Examining Data on the NCBI SRA Database</a>
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@@ -262,10 +262,10 @@ <h2 class="accordion-header" id="flush-headingTwelve">
               </div>
             </div>
             <hr class="half-width resources"><a href="aio.html">See all in one page</a>
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+
 
             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
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             </div>
           </div><!-- /div.accordion -->
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@@ -286,18 +286,18 @@ <h2 class="accordion-header" id="flush-headingTwelve">
           Home
         </a>
         <a class="chapter-link float-end" href="02-project-planning.html" rel="next">
-          Next: Planning for NGS... 
+          Next: Planning for NGS...
           <i aria-hidden="true" class="small-arrow" data-feather="arrow-right"></i>
         </a>
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Data Tidiness</h1>
         <p>Last updated on 2023-06-14 |
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/episodes/01-tidiness.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
-        
-        
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+
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           <button role="button" aria-pressed="false" tabindex="0" id="expand-code" class="pull-right" data-expand="Expand All Solutions " data-collapse="Collapse All Solutions "> Expand All Solutions <i aria-hidden="true" data-feather="plus"></i></button>
         </div>
@@ -330,8 +330,8 @@ <h3 class="card-title">Objectives</h3>
 </div>
 </div>
 </div>
-<section id="introduction"><h2 class="section-heading">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
-</h2>
+<section><h2 class="section-heading" id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
+<a class="anchor" aria-label="anchor" href="#introduction"></a></h2>
 <hr class="half-width"><p>When we think about the data for a sequencing project, we often start
 by thinking about the sequencing data that we get back from the
 sequencing center. However, equally or more important is the data you’ve
@@ -358,7 +358,7 @@ <h3 class="callout-title">Discussion<a class="anchor" aria-label="anchor" href="
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <p>Types of files and information you have generated:</p>
 <ul><li>Spreadsheet or tabular data with the data from your experiment and
@@ -379,8 +379,8 @@ <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 <p>All of the data and information just discussed can be considered
 metadata, i.e. data about the data. We want to follow a few guidelines
 for metadata.</p>
-</section><section id="notes"><h2 class="section-heading">Notes<a class="anchor" aria-label="anchor" href="#notes"></a>
-</h2>
+</section><section><h2 class="section-heading" id="notes">Notes<a class="anchor" aria-label="anchor" href="#notes"></a>
+<a class="anchor" aria-label="anchor" href="#notes"></a></h2>
 <hr class="half-width"><p>Notes about your experiment, including how you prepared your samples
 for sequencing, should be in your lab notebook, whether that’s a
 physical lab notebook or electronic lab notebook. For guidelines on good
@@ -409,8 +409,8 @@ <h3 class="callout-title">Unique identifiers<a class="anchor" aria-label="anchor
 </div>
 </div>
 </div>
-</section><section id="data-about-the-experiment"><h2 class="section-heading">Data about the experiment<a class="anchor" aria-label="anchor" href="#data-about-the-experiment"></a>
-</h2>
+</section><section><h2 class="section-heading" id="data-about-the-experiment">Data about the experiment<a class="anchor" aria-label="anchor" href="#data-about-the-experiment"></a>
+<a class="anchor" aria-label="anchor" href="#data-about-the-experiment"></a></h2>
 <hr class="half-width"><p>Data about the experiment is usually collected in spreadsheets, like
 Excel.</p>
 <p>What type of data to collect depends on your experiment and there are
@@ -435,8 +435,8 @@ <h3 class="callout-title">Metadata standards<a class="anchor" aria-label="anchor
 </div>
 </div>
 </div>
-</section><section id="structuring-data-in-spreadsheets"><h2 class="section-heading">Structuring data in spreadsheets<a class="anchor" aria-label="anchor" href="#structuring-data-in-spreadsheets"></a>
-</h2>
+</section><section><h2 class="section-heading" id="structuring-data-in-spreadsheets">Structuring data in spreadsheets<a class="anchor" aria-label="anchor" href="#structuring-data-in-spreadsheets"></a>
+<a class="anchor" aria-label="anchor" href="#structuring-data-in-spreadsheets"></a></h2>
 <hr class="half-width"><p>Regardless of the type of data you’re collecting, there are standard
 ways to enter that data into the spreadsheet to make it easier to
 analyze later. We often enter data in a way that makes it easy for us as
@@ -487,7 +487,7 @@ <h3 class="callout-title">Discussion<a class="anchor" aria-label="anchor" href="
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 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <p>A full set of types of issues with spreadsheet data is at the <a href="https://www.datacarpentry.org/spreadsheet-ecology-lesson/02-common-mistakes/" class="external-link">Data
 Carpentry Ecology spreadsheet lesson</a>. Not all are present in this
@@ -547,7 +547,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
           Home
         </a>
         <a class="chapter-link float-end" href="02-project-planning.html" rel="next">
-          Next: Planning for NGS... 
+          Next: Planning for NGS...
           <i aria-hidden="true" class="small-arrow" data-feather="arrow-right"></i>
         </a>
       </div>
@@ -558,18 +558,18 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
       		<footer class="row footer mx-md-3"><hr><div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/episodes/01-tidiness.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/datacarpentry/organization-genomics/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/datacarpentry/organization-genomics/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/datacarpentry/organization-genomics/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:team@carpentries.org">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
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         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
-        
+
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
         <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
 			</div>
@@ -594,7 +594,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://datacarpentry.github.io/organization-genomics/01-tidiness.html",
   "dateCreated": "2015-03-24",
   "dateModified": "2023-06-14",
-  "datePublished": "2024-07-02"
+  "datePublished": "2024-07-09"
 }
 
   </script><script>
diff --git a/02-project-planning.html b/02-project-planning.html
index fd4d1a59..99c66e20 100644
--- a/02-project-planning.html
+++ b/02-project-planning.html
@@ -46,7 +46,7 @@
             </li>
           </ul></li>
       </div>
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       <div class="dropdown" id="instructor-dropdown">
         <button class="btn btn-secondary dropdown-toggle bordered-button" type="button" id="dropdownMenu1" data-bs-toggle="dropdown" aria-expanded="false">
           <i aria-hidden="true" class="icon" data-feather="eye"></i> Learner View <i data-feather="chevron-down"></i>
@@ -170,7 +170,7 @@ <h2 class="accordion-header" id="flush-headingNine">
                 </div><!--/div.accordion-flush-->
               </div><!--div.sidenav-view-selector -->
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           <div class="accordion accordion-flush" id="accordionFlush11">
@@ -189,7 +189,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading1">
         <a href="index.html">Summary and Setup</a>
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 <li><a href="#summary">Summary</a></li>
         </ul></div><!--/div.accordion-body-->
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     <div class="accordion-header" id="flush-heading4">
         <a href="03-ncbi-sra.html">3. Examining Data on the NCBI SRA Database</a>
     </div><!--/div.accordion-header-->
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 </div><!--/div.accordion-flush-->
 
@@ -262,10 +262,10 @@ <h2 class="accordion-header" id="flush-headingTwelve">
               </div>
             </div>
             <hr class="half-width resources"><a href="aio.html">See all in one page</a>
-            
+
 
             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
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             </div>
           </div><!-- /div.accordion -->
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@@ -286,18 +286,18 @@ <h2 class="accordion-header" id="flush-headingTwelve">
           Previous: Data Tidiness
         </a>
         <a class="chapter-link float-end" href="03-ncbi-sra.html" rel="next">
-          Next: Examining Data on... 
+          Next: Examining Data on...
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         </a>
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Planning for NGS Projects</h1>
         <p>Last updated on 2024-04-04 |
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/episodes/02-project-planning.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
-        
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           <button role="button" aria-pressed="false" tabindex="0" id="expand-code" class="pull-right" data-expand="Expand All Solutions " data-collapse="Collapse All Solutions "> Expand All Solutions <i aria-hidden="true" data-feather="plus"></i></button>
         </div>
@@ -358,8 +358,8 @@ <h3 class="callout-title">Discussion<a class="anchor" aria-label="anchor" href="
 </div>
 </div>
 </div>
-<section id="sending-samples-to-the-facility"><h2 class="section-heading">Sending samples to the facility<a class="anchor" aria-label="anchor" href="#sending-samples-to-the-facility"></a>
-</h2>
+<section><h2 class="section-heading" id="sending-samples-to-the-facility">Sending samples to the facility<a class="anchor" aria-label="anchor" href="#sending-samples-to-the-facility"></a>
+<a class="anchor" aria-label="anchor" href="#sending-samples-to-the-facility"></a></h2>
 <hr class="half-width"><p>The first step in sending your sample for sequencing will be to
 complete a form documenting the metadata for the facility. Take a look
 at the following example submission spreadsheet.</p>
@@ -388,7 +388,7 @@ <h3 class="callout-title">Exercise<a class="anchor" aria-label="anchor" href="#e
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
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 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <p>Errors:</p>
 <ul><li>Sequential order of well_position changes</li>
@@ -416,8 +416,8 @@ <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </div>
 </div>
 </div>
-</section><section id="retrieving-sample-sequencing-data-from-the-facility"><h2 class="section-heading">Retrieving sample sequencing data from the facility<a class="anchor" aria-label="anchor" href="#retrieving-sample-sequencing-data-from-the-facility"></a>
-</h2>
+</section><section><h2 class="section-heading" id="retrieving-sample-sequencing-data-from-the-facility">Retrieving sample sequencing data from the facility<a class="anchor" aria-label="anchor" href="#retrieving-sample-sequencing-data-from-the-facility"></a>
+<a class="anchor" aria-label="anchor" href="#retrieving-sample-sequencing-data-from-the-facility"></a></h2>
 <hr class="half-width"><p>When the data come back from the sequencing facility, you will
 receive some documentation (metadata) as well as the sequence files
 themselves. Download and examine the following example file - here
@@ -450,7 +450,7 @@ <h3 class="callout-title">Exercise<a class="anchor" aria-label="anchor" href="#e
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <ol style="list-style-type: decimal"><li>Samples are organized by sample_id</li>
 <li>To relate filenames use the sample_id, and do a VLOOKUP on
@@ -469,8 +469,8 @@ <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </div>
 </div>
 </div>
-</section><section id="storing-data"><h2 class="section-heading">Storing data<a class="anchor" aria-label="anchor" href="#storing-data"></a>
-</h2>
+</section><section><h2 class="section-heading" id="storing-data">Storing data<a class="anchor" aria-label="anchor" href="#storing-data"></a>
+<a class="anchor" aria-label="anchor" href="#storing-data"></a></h2>
 <hr class="half-width"><p>The raw data you get back from the sequencing center is the
 foundation of your sequencing analysis. You need to keep this data, so
 that you can always come back to it if there are any questions or you
@@ -505,8 +505,8 @@ <h4 id="some-data-storage-solutions">Some data storage solutions<a class="anchor
 to Cloud Computing for Genomics”</a>.</p>
 </div>
 </div>
-</section><section id="summary"><h2 class="section-heading">Summary<a class="anchor" aria-label="anchor" href="#summary"></a>
-</h2>
+</section><section><h2 class="section-heading" id="summary">Summary<a class="anchor" aria-label="anchor" href="#summary"></a>
+<a class="anchor" aria-label="anchor" href="#summary"></a></h2>
 <hr class="half-width"><p>Before analysis of data has begun, there are already many potential
 areas for errors and omissions. Keeping organized and keeping a critical
 eye can help catch mistakes.</p>
@@ -561,7 +561,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
           Previous: Data Tidiness
         </a>
         <a class="chapter-link float-end" href="03-ncbi-sra.html" rel="next">
-          Next: Examining Data on... 
+          Next: Examining Data on...
           <i aria-hidden="true" class="small-arrow" data-feather="arrow-right"></i>
         </a>
       </div>
@@ -572,18 +572,18 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
       		<footer class="row footer mx-md-3"><hr><div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/episodes/02-project-planning.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/datacarpentry/organization-genomics/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/datacarpentry/organization-genomics/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/datacarpentry/organization-genomics/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:team@carpentries.org">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
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         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
-        
+
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
         <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
 			</div>
@@ -608,7 +608,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://datacarpentry.github.io/organization-genomics/02-project-planning.html",
   "dateCreated": "2015-03-24",
   "dateModified": "2024-04-04",
-  "datePublished": "2024-07-02"
+  "datePublished": "2024-07-09"
 }
 
   </script><script>
diff --git a/03-ncbi-sra.html b/03-ncbi-sra.html
index 7fe2551d..b7a301f5 100644
--- a/03-ncbi-sra.html
+++ b/03-ncbi-sra.html
@@ -46,7 +46,7 @@
             </li>
           </ul></li>
       </div>
-      
+
       <div class="dropdown" id="instructor-dropdown">
         <button class="btn btn-secondary dropdown-toggle bordered-button" type="button" id="dropdownMenu1" data-bs-toggle="dropdown" aria-expanded="false">
           <i aria-hidden="true" class="icon" data-feather="eye"></i> Learner View <i data-feather="chevron-down"></i>
@@ -170,7 +170,7 @@ <h2 class="accordion-header" id="flush-headingNine">
                 </div><!--/div.accordion-flush-->
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             <hr class="half-width resources"><a href="aio.html">See all in one page</a>
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             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
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       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Examining Data on the NCBI SRA Database</h1>
         <p>Last updated on 2023-11-20 |
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/episodes/03-ncbi-sra.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
-        
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         </div>
@@ -345,8 +345,8 @@ <h3 class="card-title">Objectives</h3>
 (SRA)</a> is the database we will be using for this lesson, but the
 EMBL-EBI’s Nucleotide Archive (ENA) is also useful. The general
 processes are similar for any database.</p>
-<section id="accessing-the-original-archived-data"><h2 class="section-heading">Accessing the original archived data<a class="anchor" aria-label="anchor" href="#accessing-the-original-archived-data"></a>
-</h2>
+<section><h2 class="section-heading" id="accessing-the-original-archived-data">Accessing the original archived data<a class="anchor" aria-label="anchor" href="#accessing-the-original-archived-data"></a>
+<a class="anchor" aria-label="anchor" href="#accessing-the-original-archived-data"></a></h2>
 <hr class="half-width"><p>The <a href="https://www.datacarpentry.org/organization-genomics/data" class="external-link">sequencing
 dataset (from Tenaillon, <em>et al.</em> 2016) adapted for this
 lesson</a> was obtained from the <a href="https://www.ncbi.nlm.nih.gov/sra" class="external-link">NCBI Sequence Read Archive</a>,
@@ -470,7 +470,7 @@ <h3 class="callout-title">Discussion<a class="anchor" aria-label="anchor" href="
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-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
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 <div class="accordion-body">
 <ol style="list-style-type: decimal"><li>Escherichia coli B str. REL606 shown under the “organism” column.
 This is a tricky question because the column labeled “strain” actually
@@ -496,8 +496,8 @@ <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 changes. If you were to save this file, make sure you save it as a
 text-based <code>.csv</code> file format.</p>
 </div>
-</section><section id="downloading-a-few-sequencing-files-embl-ebi"><h2 class="section-heading">Downloading a few sequencing files: EMBL-EBI<a class="anchor" aria-label="anchor" href="#downloading-a-few-sequencing-files-embl-ebi"></a>
-</h2>
+</section><section><h2 class="section-heading" id="downloading-a-few-sequencing-files-embl-ebi">Downloading a few sequencing files: EMBL-EBI<a class="anchor" aria-label="anchor" href="#downloading-a-few-sequencing-files-embl-ebi"></a>
+<a class="anchor" aria-label="anchor" href="#downloading-a-few-sequencing-files-embl-ebi"></a></h2>
 <hr class="half-width"><p>The SRA does not support direct download of fastq files from its
 webpage. However, the <a href="https://www.ebi.ac.uk/ena/browser/home" class="external-link">European Nucleotide
 Archive</a> does. Let’s see how we can get a download link to a file we
@@ -515,8 +515,8 @@ <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 this way. For that, the NCBI has made a software package called the
 <code>sra-toolkit</code>. However, for a couple files, it’s often easier
 to go through the ENA.</p>
-</section><section id="where-to-learn-more"><h2 class="section-heading">Where to learn more<a class="anchor" aria-label="anchor" href="#where-to-learn-more"></a>
-</h2>
+</section><section><h2 class="section-heading" id="where-to-learn-more">Where to learn more<a class="anchor" aria-label="anchor" href="#where-to-learn-more"></a>
+<a class="anchor" aria-label="anchor" href="#where-to-learn-more"></a></h2>
 <hr class="half-width"><div class="section level3">
 <h3 id="about-the-sequence-read-archive">About the Sequence Read Archive<a class="anchor" aria-label="anchor" href="#about-the-sequence-read-archive"></a></h3>
 <ul><li>You can learn more about the SRA by reading the <a href="https://www.ncbi.nlm.nih.gov/Traces/sra/" class="external-link">SRA
@@ -526,8 +526,8 @@ <h3 id="about-the-sequence-read-archive">About the Sequence Read Archive<a class
 Toolkit</a>
 </li>
 </ul></div>
-</section><section id="references"><h2 class="section-heading">References<a class="anchor" aria-label="anchor" href="#references"></a>
-</h2>
+</section><section><h2 class="section-heading" id="references">References<a class="anchor" aria-label="anchor" href="#references"></a>
+<a class="anchor" aria-label="anchor" href="#references"></a></h2>
 <hr class="half-width"><p>Tenaillon O, Barrick JE, Ribeck N, Deatherage DE, Blanchard JL,
 Dasgupta A, Wu GC, Wielgoss S, Cruveiller S, Médigue C, Schneider D,
 Lenski RE. Tempo and mode of genome evolution in a 50,000-generation
@@ -571,18 +571,18 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
       		<footer class="row footer mx-md-3"><hr><div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/episodes/03-ncbi-sra.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/datacarpentry/organization-genomics/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/datacarpentry/organization-genomics/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/datacarpentry/organization-genomics/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:team@carpentries.org">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
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+
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@@ -607,7 +607,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://datacarpentry.github.io/organization-genomics/03-ncbi-sra.html",
   "dateCreated": "2015-03-24",
   "dateModified": "2023-11-20",
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+  "datePublished": "2024-07-09"
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   </script><script>
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+++ b/404.html
@@ -46,7 +46,7 @@
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     </div>
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 </div>
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               </div>
             </div>
             <hr class="half-width resources"><a href="https://datacarpentry.github.io/organization-genomics/aio.html" class="external-link">See all in one page</a>
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             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
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         <h1>Page not found</h1>
         
-<section id="our-apologies"><h2 class="section-heading">Our apologies!<a class="anchor" aria-label="anchor" href="#our-apologies"></a>
-</h2>
+<section><h2 class="section-heading" id="our-apologies">Our apologies!<a class="anchor" aria-label="anchor" href="#our-apologies"></a>
+<a class="anchor" aria-label="anchor" href="#our-apologies"></a></h2>
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@@ -297,18 +297,18 @@ <h1>Page not found</h1>
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         <p>
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         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/README.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/datacarpentry/organization-genomics/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/datacarpentry/organization-genomics/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/datacarpentry/organization-genomics/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:team@carpentries.org">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
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 			<div class="col-md-6">
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         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
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+
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
         <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
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@@ -332,8 +332,8 @@ <h1>Page not found</h1>
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   "identifier": "https://datacarpentry.github.io/organization-genomics/404.html",
   "dateCreated": "2015-03-24",
-  "dateModified": "2024-07-02",
-  "datePublished": "2024-07-02"
+  "dateModified": "2024-07-09",
+  "datePublished": "2024-07-09"
 }
 
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index 2bdc5093..587d3d65 100644
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@@ -46,7 +46,7 @@
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         <a href="index.html">Summary and Setup</a>
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@@ -198,7 +198,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
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         <a href="01-tidiness.html">1. Data Tidiness</a>
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             <hr class="half-width resources"><a href="aio.html">See all in one page</a>
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@@ -279,11 +279,11 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Contributor Code of Conduct</h1>
         <p>Last updated on 2023-05-02 |
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+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/CODE_OF_CONDUCT.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
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@@ -322,18 +322,18 @@ <h1>Contributor Code of Conduct</h1>
       		<footer class="row footer mx-md-3"><hr><div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
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+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/CODE_OF_CONDUCT.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/datacarpentry/organization-genomics/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/datacarpentry/organization-genomics/" class="external-link">Source</a></p>
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 			<div class="col-md-6">
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 			</div>
@@ -358,7 +358,7 @@ <h1>Contributor Code of Conduct</h1>
   "identifier": "https://datacarpentry.github.io/organization-genomics/CODE_OF_CONDUCT.html",
   "dateCreated": "2015-03-24",
   "dateModified": "2023-05-02",
-  "datePublished": "2024-07-02"
+  "datePublished": "2024-07-09"
 }
 
   </script><script>
diff --git a/LICENSE.html b/LICENSE.html
index 59c1aeaf..d591e458 100644
--- a/LICENSE.html
+++ b/LICENSE.html
@@ -46,7 +46,7 @@
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         <a href="index.html">Summary and Setup</a>
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 </div><!--/div.accordion-flush-->
 
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         <a href="03-ncbi-sra.html">3. Examining Data on the NCBI SRA Database</a>
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             <hr class="half-width resources"><a href="aio.html">See all in one page</a>
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@@ -279,19 +279,19 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Licenses</h1>
         <p>Last updated on 2023-05-02 |
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/LICENSE.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
-        
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-        
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+
+
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           <button role="button" aria-pressed="false" tabindex="0" id="expand-code" class="pull-right" data-expand="Expand All Solutions " data-collapse="Collapse All Solutions "> Expand All Solutions <i aria-hidden="true" data-feather="plus"></i></button>
         </div>
 
         
 
-<section id="instructional-material"><h2 class="section-heading">Instructional Material<a class="anchor" aria-label="anchor" href="#instructional-material"></a>
-</h2>
+<section><h2 class="section-heading" id="instructional-material">Instructional Material<a class="anchor" aria-label="anchor" href="#instructional-material"></a>
+<a class="anchor" aria-label="anchor" href="#instructional-material"></a></h2>
 <hr class="half-width"><p>All Carpentries (Software Carpentry, Data Carpentry, and Library
 Carpentry) instructional material is made available under the <a href="https://creativecommons.org/licenses/by/4.0/" class="external-link">Creative Commons
 Attribution license</a>. The following is a human-readable summary of
@@ -324,8 +324,8 @@ <h1>Licenses</h1>
 permissions necessary for your intended use. For example, other rights
 such as publicity, privacy, or moral rights may limit how you use the
 material.</li>
-</ul></section><section id="software"><h2 class="section-heading">Software<a class="anchor" aria-label="anchor" href="#software"></a>
-</h2>
+</ul></section><section><h2 class="section-heading" id="software">Software<a class="anchor" aria-label="anchor" href="#software"></a>
+<a class="anchor" aria-label="anchor" href="#software"></a></h2>
 <hr class="half-width"><p>Except where otherwise noted, the example programs and other software
 provided by The Carpentries are made available under the <a href="https://opensource.org" class="external-link">OSI</a>-approved <a href="https://opensource.org/licenses/mit-license.html" class="external-link">MIT
 license</a>.</p>
@@ -345,8 +345,8 @@ <h1>Licenses</h1>
 CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
 TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
 SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.</p>
-</section><section id="trademark"><h2 class="section-heading">Trademark<a class="anchor" aria-label="anchor" href="#trademark"></a>
-</h2>
+</section><section><h2 class="section-heading" id="trademark">Trademark<a class="anchor" aria-label="anchor" href="#trademark"></a>
+<a class="anchor" aria-label="anchor" href="#trademark"></a></h2>
 <hr class="half-width"><p>“The Carpentries”, “Software Carpentry”, “Data Carpentry”, and
 “Library Carpentry” and their respective logos are registered trademarks
 of <a href="https://communityin.org/" class="external-link">Community Initiatives</a>.</p>
@@ -373,18 +373,18 @@ <h1>Licenses</h1>
       		<footer class="row footer mx-md-3"><hr><div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/LICENSE.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/datacarpentry/organization-genomics/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/datacarpentry/organization-genomics/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/datacarpentry/organization-genomics/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:team@carpentries.org">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
-        
+
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
         <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
 			</div>
@@ -409,7 +409,7 @@ <h1>Licenses</h1>
   "identifier": "https://datacarpentry.github.io/organization-genomics/LICENSE.html",
   "dateCreated": "2015-03-24",
   "dateModified": "2023-05-02",
-  "datePublished": "2024-07-02"
+  "datePublished": "2024-07-09"
 }
 
   </script><script>
diff --git a/aio.html b/aio.html
index eba96bc6..1fda361c 100644
--- a/aio.html
+++ b/aio.html
@@ -65,7 +65,7 @@
           </ul>
 </li>
       </div>
-      
+
       <div class="dropdown" id="instructor-dropdown">
         <button class="btn btn-secondary dropdown-toggle bordered-button" type="button" id="dropdownMenu1" data-bs-toggle="dropdown" aria-expanded="false">
           <i aria-hidden="true" class="icon" data-feather="eye"></i> Learner View <i data-feather="chevron-down"></i>
@@ -204,7 +204,7 @@ <h2 class="accordion-header" id="flush-headingNine">
 <!--div.sidenav-view-selector -->
             </div>
 <!--/div.col -->
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+
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 </div>
 <!--/div.mobile-row -->
@@ -226,7 +226,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         <a href="index.html">Summary and Setup</a>
     </div>
 <!--/div.accordion-header-->
-        
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 <!--/div.accordion-item-->
 </div>
@@ -238,7 +238,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         <a href="01-tidiness.html">1. Data Tidiness</a>
     </div>
 <!--/div.accordion-header-->
-        
+
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 <!--/div.accordion-item-->
 </div>
@@ -250,7 +250,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         <a href="02-project-planning.html">2. Planning for NGS Projects</a>
     </div>
 <!--/div.accordion-header-->
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 <!--/div.accordion-item-->
 </div>
@@ -262,7 +262,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         <a href="03-ncbi-sra.html">3. Examining Data on the NCBI SRA Database</a>
     </div>
 <!--/div.accordion-header-->
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+
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 <!--/div.accordion-item-->
 </div>
@@ -301,11 +301,11 @@ <h2 class="accordion-header" id="flush-headingTwelve">
             </div>
             <hr class="half-width resources">
 <a href="aio.html">See all in one page</a>
-            
+
 
             <hr class="d-none d-sm-block d-md-none">
 <div class="d-grid gap-1">
-            
+
             </div>
           </div>
 <!-- /div.accordion -->
@@ -326,7 +326,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
 <section id="aio-01-tidiness"><p>Content from <a href="01-tidiness.html">Data Tidiness</a></p>
 <hr>
 <p>Last updated on 2023-06-14 |
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/episodes/01-tidiness.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <div class="text-end">
           <button role="button" aria-pressed="false" tabindex="0" id="expand-code" class="pull-right" data-expand="Expand All Solutions " data-collapse="Collapse All Solutions "> Expand All Solutions <i aria-hidden="true" data-feather="plus"></i></button>
@@ -361,7 +361,8 @@ <h3 class="card-title">Objectives</h3>
 </div>
 </div>
 </div>
-<section id="introduction"><h2 class="section-heading">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
+<section><h2 class="section-heading" id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
+<a class="anchor" aria-label="anchor" href="#introduction"></a>
 </h2>
 <hr class="half-width">
 <p>When we think about the data for a sequencing project, we often start
@@ -390,7 +391,7 @@ <h3 class="callout-title">Discussion<a class="anchor" aria-label="anchor" href="
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <p>Types of files and information you have generated:</p>
 <ul>
@@ -413,7 +414,8 @@ <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 <p>All of the data and information just discussed can be considered
 metadata, i.e. data about the data. We want to follow a few guidelines
 for metadata.</p>
-</section><section id="notes"><h2 class="section-heading">Notes<a class="anchor" aria-label="anchor" href="#notes"></a>
+</section><section><h2 class="section-heading" id="notes">Notes<a class="anchor" aria-label="anchor" href="#notes"></a>
+<a class="anchor" aria-label="anchor" href="#notes"></a>
 </h2>
 <hr class="half-width">
 <p>Notes about your experiment, including how you prepared your samples
@@ -444,7 +446,8 @@ <h3 class="callout-title">Unique identifiers<a class="anchor" aria-label="anchor
 </div>
 </div>
 </div>
-</section><section id="data-about-the-experiment"><h2 class="section-heading">Data about the experiment<a class="anchor" aria-label="anchor" href="#data-about-the-experiment"></a>
+</section><section><h2 class="section-heading" id="data-about-the-experiment">Data about the experiment<a class="anchor" aria-label="anchor" href="#data-about-the-experiment"></a>
+<a class="anchor" aria-label="anchor" href="#data-about-the-experiment"></a>
 </h2>
 <hr class="half-width">
 <p>Data about the experiment is usually collected in spreadsheets, like
@@ -471,7 +474,8 @@ <h3 class="callout-title">Metadata standards<a class="anchor" aria-label="anchor
 </div>
 </div>
 </div>
-</section><section id="structuring-data-in-spreadsheets"><h2 class="section-heading">Structuring data in spreadsheets<a class="anchor" aria-label="anchor" href="#structuring-data-in-spreadsheets"></a>
+</section><section><h2 class="section-heading" id="structuring-data-in-spreadsheets">Structuring data in spreadsheets<a class="anchor" aria-label="anchor" href="#structuring-data-in-spreadsheets"></a>
+<a class="anchor" aria-label="anchor" href="#structuring-data-in-spreadsheets"></a>
 </h2>
 <hr class="half-width">
 <p>Regardless of the type of data you’re collecting, there are standard
@@ -526,7 +530,7 @@ <h3 class="callout-title">Discussion<a class="anchor" aria-label="anchor" href="
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <p>A full set of types of issues with spreadsheet data is at the <a href="https://www.datacarpentry.org/spreadsheet-ecology-lesson/02-common-mistakes/" class="external-link">Data
 Carpentry Ecology spreadsheet lesson</a>. Not all are present in this
@@ -580,7 +584,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
 </section></section><section id="aio-02-project-planning"><p>Content from <a href="02-project-planning.html">Planning for NGS Projects</a></p>
 <hr>
 <p>Last updated on 2024-04-04 |
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/episodes/02-project-planning.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <div class="text-end">
           <button role="button" aria-pressed="false" tabindex="0" id="expand-code" class="pull-right" data-expand="Expand All Solutions " data-collapse="Collapse All Solutions "> Expand All Solutions <i aria-hidden="true" data-feather="plus"></i></button>
@@ -643,7 +647,8 @@ <h3 class="callout-title">Discussion<a class="anchor" aria-label="anchor" href="
 </div>
 </div>
 </div>
-<section id="sending-samples-to-the-facility"><h2 class="section-heading">Sending samples to the facility<a class="anchor" aria-label="anchor" href="#sending-samples-to-the-facility"></a>
+<section><h2 class="section-heading" id="sending-samples-to-the-facility">Sending samples to the facility<a class="anchor" aria-label="anchor" href="#sending-samples-to-the-facility"></a>
+<a class="anchor" aria-label="anchor" href="#sending-samples-to-the-facility"></a>
 </h2>
 <hr class="half-width">
 <p>The first step in sending your sample for sequencing will be to
@@ -676,7 +681,7 @@ <h3 class="callout-title">Exercise<a class="anchor" aria-label="anchor" href="#e
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <p>Errors:</p>
 <ul>
@@ -712,7 +717,8 @@ <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </div>
 </div>
 </div>
-</section><section id="retrieving-sample-sequencing-data-from-the-facility"><h2 class="section-heading">Retrieving sample sequencing data from the facility<a class="anchor" aria-label="anchor" href="#retrieving-sample-sequencing-data-from-the-facility"></a>
+</section><section><h2 class="section-heading" id="retrieving-sample-sequencing-data-from-the-facility">Retrieving sample sequencing data from the facility<a class="anchor" aria-label="anchor" href="#retrieving-sample-sequencing-data-from-the-facility"></a>
+<a class="anchor" aria-label="anchor" href="#retrieving-sample-sequencing-data-from-the-facility"></a>
 </h2>
 <hr class="half-width">
 <p>When the data come back from the sequencing facility, you will
@@ -751,7 +757,7 @@ <h3 class="callout-title">Exercise<a class="anchor" aria-label="anchor" href="#e
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <ol style="list-style-type: decimal">
 <li>Samples are organized by sample_id</li>
@@ -772,7 +778,8 @@ <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </div>
 </div>
 </div>
-</section><section id="storing-data"><h2 class="section-heading">Storing data<a class="anchor" aria-label="anchor" href="#storing-data"></a>
+</section><section><h2 class="section-heading" id="storing-data">Storing data<a class="anchor" aria-label="anchor" href="#storing-data"></a>
+<a class="anchor" aria-label="anchor" href="#storing-data"></a>
 </h2>
 <hr class="half-width">
 <p>The raw data you get back from the sequencing center is the
@@ -813,7 +820,8 @@ <h4 id="some-data-storage-solutions">Some data storage solutions<a class="anchor
 to Cloud Computing for Genomics”</a>.</p>
 </div>
 </div>
-</section><section id="summary"><h2 class="section-heading">Summary<a class="anchor" aria-label="anchor" href="#summary"></a>
+</section><section><h2 class="section-heading" id="summary">Summary<a class="anchor" aria-label="anchor" href="#summary"></a>
+<a class="anchor" aria-label="anchor" href="#summary"></a>
 </h2>
 <hr class="half-width">
 <p>Before analysis of data has begun, there are already many potential
@@ -863,7 +871,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
 </section></section><section id="aio-03-ncbi-sra"><p>Content from <a href="03-ncbi-sra.html">Examining Data on the NCBI SRA Database</a></p>
 <hr>
 <p>Last updated on 2023-11-20 |
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/episodes/03-ncbi-sra.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <div class="text-end">
           <button role="button" aria-pressed="false" tabindex="0" id="expand-code" class="pull-right" data-expand="Expand All Solutions " data-collapse="Collapse All Solutions "> Expand All Solutions <i aria-hidden="true" data-feather="plus"></i></button>
@@ -913,7 +921,8 @@ <h3 class="card-title">Objectives</h3>
 (SRA)</a> is the database we will be using for this lesson, but the
 EMBL-EBI’s Nucleotide Archive (ENA) is also useful. The general
 processes are similar for any database.</p>
-<section id="accessing-the-original-archived-data"><h2 class="section-heading">Accessing the original archived data<a class="anchor" aria-label="anchor" href="#accessing-the-original-archived-data"></a>
+<section><h2 class="section-heading" id="accessing-the-original-archived-data">Accessing the original archived data<a class="anchor" aria-label="anchor" href="#accessing-the-original-archived-data"></a>
+<a class="anchor" aria-label="anchor" href="#accessing-the-original-archived-data"></a>
 </h2>
 <hr class="half-width">
 <p>The <a href="https://www.datacarpentry.org/organization-genomics/data" class="external-link">sequencing
@@ -1048,7 +1057,7 @@ <h3 class="callout-title">Discussion<a class="anchor" aria-label="anchor" href="
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <ol style="list-style-type: decimal">
 <li>Escherichia coli B str. REL606 shown under the “organism” column.
@@ -1076,7 +1085,8 @@ <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 changes. If you were to save this file, make sure you save it as a
 text-based <code>.csv</code> file format.</p>
 </div>
-</section><section id="downloading-a-few-sequencing-files-embl-ebi"><h2 class="section-heading">Downloading a few sequencing files: EMBL-EBI<a class="anchor" aria-label="anchor" href="#downloading-a-few-sequencing-files-embl-ebi"></a>
+</section><section><h2 class="section-heading" id="downloading-a-few-sequencing-files-embl-ebi">Downloading a few sequencing files: EMBL-EBI<a class="anchor" aria-label="anchor" href="#downloading-a-few-sequencing-files-embl-ebi"></a>
+<a class="anchor" aria-label="anchor" href="#downloading-a-few-sequencing-files-embl-ebi"></a>
 </h2>
 <hr class="half-width">
 <p>The SRA does not support direct download of fastq files from its
@@ -1098,7 +1108,8 @@ <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 this way. For that, the NCBI has made a software package called the
 <code>sra-toolkit</code>. However, for a couple files, it’s often easier
 to go through the ENA.</p>
-</section><section id="where-to-learn-more"><h2 class="section-heading">Where to learn more<a class="anchor" aria-label="anchor" href="#where-to-learn-more"></a>
+</section><section><h2 class="section-heading" id="where-to-learn-more">Where to learn more<a class="anchor" aria-label="anchor" href="#where-to-learn-more"></a>
+<a class="anchor" aria-label="anchor" href="#where-to-learn-more"></a>
 </h2>
 <hr class="half-width">
 <div class="section level3">
@@ -1113,7 +1124,8 @@ <h3 id="about-the-sequence-read-archive">About the Sequence Read Archive<a class
 </li>
 </ul>
 </div>
-</section><section id="references"><h2 class="section-heading">References<a class="anchor" aria-label="anchor" href="#references"></a>
+</section><section><h2 class="section-heading" id="references">References<a class="anchor" aria-label="anchor" href="#references"></a>
+<a class="anchor" aria-label="anchor" href="#references"></a>
 </h2>
 <hr class="half-width">
 <p>Tenaillon O, Barrick JE, Ribeck N, Deatherage DE, Blanchard JL,
@@ -1150,18 +1162,18 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
 <div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/README.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/datacarpentry/organization-genomics/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/datacarpentry/organization-genomics/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/datacarpentry/organization-genomics/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:team@carpentries.org">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
-        
+
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
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 			<div class="col-md-6">
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 			</div>
 			<div class="col-md-6">
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-        
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@@ -250,7 +250,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         <a href="02-project-planning.html">2. Planning for NGS Projects</a>
     </div>
 <!--/div.accordion-header-->
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 <!--/div.accordion-item-->
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@@ -262,7 +262,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         <a href="03-ncbi-sra.html">3. Examining Data on the NCBI SRA Database</a>
     </div>
 <!--/div.accordion-header-->
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             </div>
             <hr class="half-width resources">
 <a href="aio.html">See all in one page</a>
-            
+
 
             <hr class="d-none d-sm-block d-md-none">
 <div class="d-grid gap-1">
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           </div>
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@@ -324,15 +324,18 @@ <h2 class="accordion-header" id="flush-headingTwelve">
         <h1>Instructor Notes</h1>
         
 
-<section id="instructor-notes"><h2 class="section-heading">Instructor notes<a class="anchor" aria-label="anchor" href="#instructor-notes"></a>
+<section><h2 class="section-heading" id="instructor-notes">Instructor notes<a class="anchor" aria-label="anchor" href="#instructor-notes"></a>
+<a class="anchor" aria-label="anchor" href="#instructor-notes"></a>
 </h2>
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+<hr class="half-width"></section><section><h2 class="section-heading" id="lesson-motivation-and-learning-objectives">Lesson motivation and learning objectives<a class="anchor" aria-label="anchor" href="#lesson-motivation-and-learning-objectives"></a>
+<a class="anchor" aria-label="anchor" href="#lesson-motivation-and-learning-objectives"></a>
 </h2>
 <hr class="half-width">
 <p>The purpose of this lesson is <em>not</em> to teach how to do data
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 do some data cleaning and quality control in a spreadsheet program.</p>
-</section><section id="lesson-design"><h2 class="section-heading">Lesson design<a class="anchor" aria-label="anchor" href="#lesson-design"></a>
+</section><section><h2 class="section-heading" id="lesson-design">Lesson design<a class="anchor" aria-label="anchor" href="#lesson-design"></a>
+<a class="anchor" aria-label="anchor" href="#lesson-design"></a>
 </h2>
 <hr class="half-width">
 <div class="section level4">
@@ -399,7 +402,8 @@ <h4 id="concluding-points">Concluding points<a class="anchor" aria-label="anchor
 analyses as we’ll see in the rest of the workshop.</li>
 </ul>
 </div>
-</section><section id="working-with-participants-level-of-expertise"><h2 class="section-heading">Working with participants’ level of expertise<a class="anchor" aria-label="anchor" href="#working-with-participants-level-of-expertise"></a>
+</section><section><h2 class="section-heading" id="working-with-participants-level-of-expertise">Working with participants’ level of expertise<a class="anchor" aria-label="anchor" href="#working-with-participants-level-of-expertise"></a>
+<a class="anchor" aria-label="anchor" href="#working-with-participants-level-of-expertise"></a>
 </h2>
 <hr class="half-width">
 <p>Learners may be taking this lesson for many reasons - they may be
@@ -447,14 +451,16 @@ <h4 id="data-tidiness-1">
 survey, then present the range of answers during the class. It can also
 be helpful for instructors and helpers to share what they work on.</p>
 </div>
-</section><section id="technical-tips-and-tricks"><h2 class="section-heading">Technical tips and tricks<a class="anchor" aria-label="anchor" href="#technical-tips-and-tricks"></a>
+</section><section><h2 class="section-heading" id="technical-tips-and-tricks">Technical tips and tricks<a class="anchor" aria-label="anchor" href="#technical-tips-and-tricks"></a>
+<a class="anchor" aria-label="anchor" href="#technical-tips-and-tricks"></a>
 </h2>
 <hr class="half-width">
 <p>Provide information on setting up your environment for learners to
 view your live coding (increasing text size, changing text color, etc),
 as well as general recommendations for working with coding tools to best
 suit the learning environment.</p>
-</section><section id="common-problems"><h2 class="section-heading">Common problems<a class="anchor" aria-label="anchor" href="#common-problems"></a>
+</section><section><h2 class="section-heading" id="common-problems">Common problems<a class="anchor" aria-label="anchor" href="#common-problems"></a>
+<a class="anchor" aria-label="anchor" href="#common-problems"></a>
 </h2>
 <hr class="half-width">
 <div class="section level4">
@@ -492,18 +498,18 @@ <h4 id="people-are-not-interactive-or-responsive-on-the-exercises">People are no
 <div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/README.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/datacarpentry/organization-genomics/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/datacarpentry/organization-genomics/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/datacarpentry/organization-genomics/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:team@carpentries.org">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
-        
+
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
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@@ -528,8 +534,8 @@ <h4 id="people-are-not-interactive-or-responsive-on-the-exercises">People are no
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   "dateCreated": "2015-03-24",
-  "dateModified": "2024-07-02",
-  "datePublished": "2024-07-02"
+  "dateModified": "2024-07-09",
+  "datePublished": "2024-07-09"
 }
 
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diff --git a/instructor/01-tidiness.html b/instructor/01-tidiness.html
index 8c89875d..4132522c 100644
--- a/instructor/01-tidiness.html
+++ b/instructor/01-tidiness.html
@@ -46,7 +46,7 @@
             </li>
           </ul></li>
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-      
+
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           <i aria-hidden="true" class="icon" data-feather="eye"></i> Instructor View <i data-feather="chevron-down"></i>
@@ -170,7 +170,7 @@ <h2 class="accordion-header" id="flush-headingNine">
                 </div><!--/div.accordion-flush-->
               </div><!--div.sidenav-view-selector -->
             </div><!--/div.col -->
-      
+
             <hr></div><!--/div.mobile-row -->
 
           <div class="accordion accordion-flush" id="accordionFlush11">
@@ -189,7 +189,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading1">
         <a href="index.html">Summary and Schedule</a>
     </div><!--/div.accordion-header-->
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+
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@@ -203,7 +203,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         </span>
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+
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@@ -212,7 +212,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
 <li><a href="#structuring-data-in-spreadsheets">Structuring data in spreadsheets</a></li>
         </ul></div><!--/div.accordion-body-->
     </div><!--/div.accordion-collapse-->
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 </div><!--/div.accordion-flush-->
 
@@ -221,7 +221,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
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         <a href="02-project-planning.html">2. Planning for NGS Projects</a>
     </div><!--/div.accordion-header-->
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+
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 </div><!--/div.accordion-flush-->
 
@@ -230,7 +230,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading4">
         <a href="03-ncbi-sra.html">3. Examining Data on the NCBI SRA Database</a>
     </div><!--/div.accordion-header-->
-        
+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -262,10 +262,10 @@ <h2 class="accordion-header" id="flush-headingTwelve">
               </div>
             </div>
             <hr class="half-width resources"><a href="../instructor/aio.html">See all in one page</a>
-            
+
 
             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
-            
+
             </div>
           </div><!-- /div.accordion -->
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@@ -286,20 +286,20 @@ <h2 class="accordion-header" id="flush-headingTwelve">
           Home
         </a>
         <a class="chapter-link float-end" href="../instructor/02-project-planning.html" rel="next">
-          Next: Planning for NGS... 
+          Next: Planning for NGS...
           <i aria-hidden="true" class="small-arrow" data-feather="arrow-right"></i>
         </a>
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Data Tidiness</h1>
         <p>Last updated on 2023-06-14 |
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/episodes/01-tidiness.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
-        
-        
-        
+
+
+
         <p>Estimated time: <i aria-hidden="true" data-feather="clock"></i> 30 minutes</p>
-        
+
         <div class="text-end">
           <button role="button" aria-pressed="false" tabindex="0" id="expand-code" class="pull-right" data-expand="Expand All Solutions " data-collapse="Collapse All Solutions "> Expand All Solutions <i aria-hidden="true" data-feather="plus"></i></button>
         </div>
@@ -332,8 +332,8 @@ <h3 class="card-title">Objectives</h3>
 </div>
 </div>
 </div>
-<section id="introduction"><h2 class="section-heading">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
-</h2>
+<section><h2 class="section-heading" id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
+<a class="anchor" aria-label="anchor" href="#introduction"></a></h2>
 <hr class="half-width"><p>When we think about the data for a sequencing project, we often start
 by thinking about the sequencing data that we get back from the
 sequencing center. However, equally or more important is the data you’ve
@@ -360,7 +360,7 @@ <h3 class="callout-title">Discussion<a class="anchor" aria-label="anchor" href="
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 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <p>Types of files and information you have generated:</p>
 <ul><li>Spreadsheet or tabular data with the data from your experiment and
@@ -381,8 +381,8 @@ <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 <p>All of the data and information just discussed can be considered
 metadata, i.e. data about the data. We want to follow a few guidelines
 for metadata.</p>
-</section><section id="notes"><h2 class="section-heading">Notes<a class="anchor" aria-label="anchor" href="#notes"></a>
-</h2>
+</section><section><h2 class="section-heading" id="notes">Notes<a class="anchor" aria-label="anchor" href="#notes"></a>
+<a class="anchor" aria-label="anchor" href="#notes"></a></h2>
 <hr class="half-width"><p>Notes about your experiment, including how you prepared your samples
 for sequencing, should be in your lab notebook, whether that’s a
 physical lab notebook or electronic lab notebook. For guidelines on good
@@ -411,8 +411,8 @@ <h3 class="callout-title">Unique identifiers<a class="anchor" aria-label="anchor
 </div>
 </div>
 </div>
-</section><section id="data-about-the-experiment"><h2 class="section-heading">Data about the experiment<a class="anchor" aria-label="anchor" href="#data-about-the-experiment"></a>
-</h2>
+</section><section><h2 class="section-heading" id="data-about-the-experiment">Data about the experiment<a class="anchor" aria-label="anchor" href="#data-about-the-experiment"></a>
+<a class="anchor" aria-label="anchor" href="#data-about-the-experiment"></a></h2>
 <hr class="half-width"><p>Data about the experiment is usually collected in spreadsheets, like
 Excel.</p>
 <p>What type of data to collect depends on your experiment and there are
@@ -437,8 +437,8 @@ <h3 class="callout-title">Metadata standards<a class="anchor" aria-label="anchor
 </div>
 </div>
 </div>
-</section><section id="structuring-data-in-spreadsheets"><h2 class="section-heading">Structuring data in spreadsheets<a class="anchor" aria-label="anchor" href="#structuring-data-in-spreadsheets"></a>
-</h2>
+</section><section><h2 class="section-heading" id="structuring-data-in-spreadsheets">Structuring data in spreadsheets<a class="anchor" aria-label="anchor" href="#structuring-data-in-spreadsheets"></a>
+<a class="anchor" aria-label="anchor" href="#structuring-data-in-spreadsheets"></a></h2>
 <hr class="half-width"><p>Regardless of the type of data you’re collecting, there are standard
 ways to enter that data into the spreadsheet to make it easier to
 analyze later. We often enter data in a way that makes it easy for us as
@@ -489,7 +489,7 @@ <h3 class="callout-title">Discussion<a class="anchor" aria-label="anchor" href="
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 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <p>A full set of types of issues with spreadsheet data is at the <a href="https://www.datacarpentry.org/spreadsheet-ecology-lesson/02-common-mistakes/" class="external-link">Data
 Carpentry Ecology spreadsheet lesson</a>. Not all are present in this
@@ -549,7 +549,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
           Home
         </a>
         <a class="chapter-link float-end" href="../instructor/02-project-planning.html" rel="next">
-          Next: Planning for NGS... 
+          Next: Planning for NGS...
           <i aria-hidden="true" class="small-arrow" data-feather="arrow-right"></i>
         </a>
       </div>
@@ -560,18 +560,18 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
       		<footer class="row footer mx-md-3"><hr><div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/episodes/01-tidiness.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/datacarpentry/organization-genomics/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/datacarpentry/organization-genomics/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/datacarpentry/organization-genomics/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:team@carpentries.org">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
-        
+
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
         <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
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@@ -596,7 +596,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
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   "dateCreated": "2015-03-24",
   "dateModified": "2023-06-14",
-  "datePublished": "2024-07-02"
+  "datePublished": "2024-07-09"
 }
 
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diff --git a/instructor/02-project-planning.html b/instructor/02-project-planning.html
index 824a64a3..af54bcef 100644
--- a/instructor/02-project-planning.html
+++ b/instructor/02-project-planning.html
@@ -46,7 +46,7 @@
             </li>
           </ul></li>
       </div>
-      
+
       <div class="dropdown" id="instructor-dropdown">
         <button class="btn btn-secondary dropdown-toggle bordered-button" type="button" id="dropdownMenu1" data-bs-toggle="dropdown" aria-expanded="false">
           <i aria-hidden="true" class="icon" data-feather="eye"></i> Instructor View <i data-feather="chevron-down"></i>
@@ -170,7 +170,7 @@ <h2 class="accordion-header" id="flush-headingNine">
                 </div><!--/div.accordion-flush-->
               </div><!--div.sidenav-view-selector -->
             </div><!--/div.col -->
-      
+
             <hr></div><!--/div.mobile-row -->
 
           <div class="accordion accordion-flush" id="accordionFlush11">
@@ -189,7 +189,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading1">
         <a href="index.html">Summary and Schedule</a>
     </div><!--/div.accordion-header-->
-        
+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -198,7 +198,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading2">
         <a href="01-tidiness.html">1. Data Tidiness</a>
     </div><!--/div.accordion-header-->
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 </div><!--/div.accordion-flush-->
 
@@ -212,7 +212,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         </span>
       </button>
     </div><!--/div.accordion-header-->
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+
     <div id="flush-collapsecurrent" class="accordion-collapse collapse show" aria-labelledby="flush-headingcurrent" data-bs-parent="#accordionFlushcurrent">
       <div class="accordion-body">
         <ul><li><a href="#sending-samples-to-the-facility">Sending samples to the facility</a></li>
@@ -221,7 +221,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
 <li><a href="#summary">Summary</a></li>
         </ul></div><!--/div.accordion-body-->
     </div><!--/div.accordion-collapse-->
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@@ -230,7 +230,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading4">
         <a href="03-ncbi-sra.html">3. Examining Data on the NCBI SRA Database</a>
     </div><!--/div.accordion-header-->
-        
+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -262,10 +262,10 @@ <h2 class="accordion-header" id="flush-headingTwelve">
               </div>
             </div>
             <hr class="half-width resources"><a href="../instructor/aio.html">See all in one page</a>
-            
+
 
             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
-            
+
             </div>
           </div><!-- /div.accordion -->
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@@ -286,20 +286,20 @@ <h2 class="accordion-header" id="flush-headingTwelve">
           Previous: Data Tidiness
         </a>
         <a class="chapter-link float-end" href="../instructor/03-ncbi-sra.html" rel="next">
-          Next: Examining Data on... 
+          Next: Examining Data on...
           <i aria-hidden="true" class="small-arrow" data-feather="arrow-right"></i>
         </a>
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Planning for NGS Projects</h1>
         <p>Last updated on 2024-04-04 |
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/episodes/02-project-planning.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
-        
-        
-        
+
+
+
         <p>Estimated time: <i aria-hidden="true" data-feather="clock"></i> 30 minutes</p>
-        
+
         <div class="text-end">
           <button role="button" aria-pressed="false" tabindex="0" id="expand-code" class="pull-right" data-expand="Expand All Solutions " data-collapse="Collapse All Solutions "> Expand All Solutions <i aria-hidden="true" data-feather="plus"></i></button>
         </div>
@@ -360,8 +360,8 @@ <h3 class="callout-title">Discussion<a class="anchor" aria-label="anchor" href="
 </div>
 </div>
 </div>
-<section id="sending-samples-to-the-facility"><h2 class="section-heading">Sending samples to the facility<a class="anchor" aria-label="anchor" href="#sending-samples-to-the-facility"></a>
-</h2>
+<section><h2 class="section-heading" id="sending-samples-to-the-facility">Sending samples to the facility<a class="anchor" aria-label="anchor" href="#sending-samples-to-the-facility"></a>
+<a class="anchor" aria-label="anchor" href="#sending-samples-to-the-facility"></a></h2>
 <hr class="half-width"><p>The first step in sending your sample for sequencing will be to
 complete a form documenting the metadata for the facility. Take a look
 at the following example submission spreadsheet.</p>
@@ -390,7 +390,7 @@ <h3 class="callout-title">Exercise<a class="anchor" aria-label="anchor" href="#e
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
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 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
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 <div class="accordion-body">
 <p>Errors:</p>
 <ul><li>Sequential order of well_position changes</li>
@@ -418,8 +418,8 @@ <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </div>
 </div>
 </div>
-</section><section id="retrieving-sample-sequencing-data-from-the-facility"><h2 class="section-heading">Retrieving sample sequencing data from the facility<a class="anchor" aria-label="anchor" href="#retrieving-sample-sequencing-data-from-the-facility"></a>
-</h2>
+</section><section><h2 class="section-heading" id="retrieving-sample-sequencing-data-from-the-facility">Retrieving sample sequencing data from the facility<a class="anchor" aria-label="anchor" href="#retrieving-sample-sequencing-data-from-the-facility"></a>
+<a class="anchor" aria-label="anchor" href="#retrieving-sample-sequencing-data-from-the-facility"></a></h2>
 <hr class="half-width"><p>When the data come back from the sequencing facility, you will
 receive some documentation (metadata) as well as the sequence files
 themselves. Download and examine the following example file - here
@@ -452,7 +452,7 @@ <h3 class="callout-title">Exercise<a class="anchor" aria-label="anchor" href="#e
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <ol style="list-style-type: decimal"><li>Samples are organized by sample_id</li>
 <li>To relate filenames use the sample_id, and do a VLOOKUP on
@@ -471,8 +471,8 @@ <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </div>
 </div>
 </div>
-</section><section id="storing-data"><h2 class="section-heading">Storing data<a class="anchor" aria-label="anchor" href="#storing-data"></a>
-</h2>
+</section><section><h2 class="section-heading" id="storing-data">Storing data<a class="anchor" aria-label="anchor" href="#storing-data"></a>
+<a class="anchor" aria-label="anchor" href="#storing-data"></a></h2>
 <hr class="half-width"><p>The raw data you get back from the sequencing center is the
 foundation of your sequencing analysis. You need to keep this data, so
 that you can always come back to it if there are any questions or you
@@ -507,8 +507,8 @@ <h4 id="some-data-storage-solutions">Some data storage solutions<a class="anchor
 to Cloud Computing for Genomics”</a>.</p>
 </div>
 </div>
-</section><section id="summary"><h2 class="section-heading">Summary<a class="anchor" aria-label="anchor" href="#summary"></a>
-</h2>
+</section><section><h2 class="section-heading" id="summary">Summary<a class="anchor" aria-label="anchor" href="#summary"></a>
+<a class="anchor" aria-label="anchor" href="#summary"></a></h2>
 <hr class="half-width"><p>Before analysis of data has begun, there are already many potential
 areas for errors and omissions. Keeping organized and keeping a critical
 eye can help catch mistakes.</p>
@@ -563,7 +563,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
           Previous: Data Tidiness
         </a>
         <a class="chapter-link float-end" href="../instructor/03-ncbi-sra.html" rel="next">
-          Next: Examining Data on... 
+          Next: Examining Data on...
           <i aria-hidden="true" class="small-arrow" data-feather="arrow-right"></i>
         </a>
       </div>
@@ -574,18 +574,18 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
       		<footer class="row footer mx-md-3"><hr><div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/episodes/02-project-planning.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/datacarpentry/organization-genomics/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/datacarpentry/organization-genomics/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/datacarpentry/organization-genomics/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:team@carpentries.org">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
-        
+
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
         <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
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   "dateCreated": "2015-03-24",
   "dateModified": "2024-04-04",
-  "datePublished": "2024-07-02"
+  "datePublished": "2024-07-09"
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diff --git a/instructor/03-ncbi-sra.html b/instructor/03-ncbi-sra.html
index 540e581c..d5033e43 100644
--- a/instructor/03-ncbi-sra.html
+++ b/instructor/03-ncbi-sra.html
@@ -46,7 +46,7 @@
             </li>
           </ul></li>
       </div>
-      
+
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           <i aria-hidden="true" class="icon" data-feather="eye"></i> Instructor View <i data-feather="chevron-down"></i>
@@ -170,7 +170,7 @@ <h2 class="accordion-header" id="flush-headingNine">
                 </div><!--/div.accordion-flush-->
               </div><!--div.sidenav-view-selector -->
             </div><!--/div.col -->
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           <div class="accordion accordion-flush" id="accordionFlush11">
@@ -189,7 +189,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading1">
         <a href="index.html">Summary and Schedule</a>
     </div><!--/div.accordion-header-->
-        
+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -198,7 +198,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading2">
         <a href="01-tidiness.html">1. Data Tidiness</a>
     </div><!--/div.accordion-header-->
-        
+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -207,7 +207,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading3">
         <a href="02-project-planning.html">2. Planning for NGS Projects</a>
     </div><!--/div.accordion-header-->
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 </div><!--/div.accordion-flush-->
 
@@ -221,7 +221,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         </span>
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     </div><!--/div.accordion-header-->
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       <div class="accordion-body">
         <ul><li><a href="#accessing-the-original-archived-data">Accessing the original archived data</a></li>
@@ -230,7 +230,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
 <li><a href="#references">References</a></li>
         </ul></div><!--/div.accordion-body-->
     </div><!--/div.accordion-collapse-->
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+
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 </div><!--/div.accordion-flush-->
 
@@ -262,10 +262,10 @@ <h2 class="accordion-header" id="flush-headingTwelve">
               </div>
             </div>
             <hr class="half-width resources"><a href="../instructor/aio.html">See all in one page</a>
-            
+
 
             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
-            
+
             </div>
           </div><!-- /div.accordion -->
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@@ -293,13 +293,13 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Examining Data on the NCBI SRA Database</h1>
         <p>Last updated on 2023-11-20 |
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/episodes/03-ncbi-sra.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
-        
-        
-        
+
+
+
         <p>Estimated time: <i aria-hidden="true" data-feather="clock"></i> 30 minutes</p>
-        
+
         <div class="text-end">
           <button role="button" aria-pressed="false" tabindex="0" id="expand-code" class="pull-right" data-expand="Expand All Solutions " data-collapse="Collapse All Solutions "> Expand All Solutions <i aria-hidden="true" data-feather="plus"></i></button>
         </div>
@@ -347,8 +347,8 @@ <h3 class="card-title">Objectives</h3>
 (SRA)</a> is the database we will be using for this lesson, but the
 EMBL-EBI’s Nucleotide Archive (ENA) is also useful. The general
 processes are similar for any database.</p>
-<section id="accessing-the-original-archived-data"><h2 class="section-heading">Accessing the original archived data<a class="anchor" aria-label="anchor" href="#accessing-the-original-archived-data"></a>
-</h2>
+<section><h2 class="section-heading" id="accessing-the-original-archived-data">Accessing the original archived data<a class="anchor" aria-label="anchor" href="#accessing-the-original-archived-data"></a>
+<a class="anchor" aria-label="anchor" href="#accessing-the-original-archived-data"></a></h2>
 <hr class="half-width"><p>The <a href="https://www.datacarpentry.org/organization-genomics/data" class="external-link">sequencing
 dataset (from Tenaillon, <em>et al.</em> 2016) adapted for this
 lesson</a> was obtained from the <a href="https://www.ncbi.nlm.nih.gov/sra" class="external-link">NCBI Sequence Read Archive</a>,
@@ -472,7 +472,7 @@ <h3 class="callout-title">Discussion<a class="anchor" aria-label="anchor" href="
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   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <ol style="list-style-type: decimal"><li>Escherichia coli B str. REL606 shown under the “organism” column.
 This is a tricky question because the column labeled “strain” actually
@@ -498,8 +498,8 @@ <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 changes. If you were to save this file, make sure you save it as a
 text-based <code>.csv</code> file format.</p>
 </div>
-</section><section id="downloading-a-few-sequencing-files-embl-ebi"><h2 class="section-heading">Downloading a few sequencing files: EMBL-EBI<a class="anchor" aria-label="anchor" href="#downloading-a-few-sequencing-files-embl-ebi"></a>
-</h2>
+</section><section><h2 class="section-heading" id="downloading-a-few-sequencing-files-embl-ebi">Downloading a few sequencing files: EMBL-EBI<a class="anchor" aria-label="anchor" href="#downloading-a-few-sequencing-files-embl-ebi"></a>
+<a class="anchor" aria-label="anchor" href="#downloading-a-few-sequencing-files-embl-ebi"></a></h2>
 <hr class="half-width"><p>The SRA does not support direct download of fastq files from its
 webpage. However, the <a href="https://www.ebi.ac.uk/ena/browser/home" class="external-link">European Nucleotide
 Archive</a> does. Let’s see how we can get a download link to a file we
@@ -517,8 +517,8 @@ <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 this way. For that, the NCBI has made a software package called the
 <code>sra-toolkit</code>. However, for a couple files, it’s often easier
 to go through the ENA.</p>
-</section><section id="where-to-learn-more"><h2 class="section-heading">Where to learn more<a class="anchor" aria-label="anchor" href="#where-to-learn-more"></a>
-</h2>
+</section><section><h2 class="section-heading" id="where-to-learn-more">Where to learn more<a class="anchor" aria-label="anchor" href="#where-to-learn-more"></a>
+<a class="anchor" aria-label="anchor" href="#where-to-learn-more"></a></h2>
 <hr class="half-width"><div class="section level3">
 <h3 id="about-the-sequence-read-archive">About the Sequence Read Archive<a class="anchor" aria-label="anchor" href="#about-the-sequence-read-archive"></a></h3>
 <ul><li>You can learn more about the SRA by reading the <a href="https://www.ncbi.nlm.nih.gov/Traces/sra/" class="external-link">SRA
@@ -528,8 +528,8 @@ <h3 id="about-the-sequence-read-archive">About the Sequence Read Archive<a class
 Toolkit</a>
 </li>
 </ul></div>
-</section><section id="references"><h2 class="section-heading">References<a class="anchor" aria-label="anchor" href="#references"></a>
-</h2>
+</section><section><h2 class="section-heading" id="references">References<a class="anchor" aria-label="anchor" href="#references"></a>
+<a class="anchor" aria-label="anchor" href="#references"></a></h2>
 <hr class="half-width"><p>Tenaillon O, Barrick JE, Ribeck N, Deatherage DE, Blanchard JL,
 Dasgupta A, Wu GC, Wielgoss S, Cruveiller S, Médigue C, Schneider D,
 Lenski RE. Tempo and mode of genome evolution in a 50,000-generation
@@ -573,18 +573,18 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
       		<footer class="row footer mx-md-3"><hr><div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
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+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/episodes/03-ncbi-sra.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/datacarpentry/organization-genomics/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/datacarpentry/organization-genomics/" class="external-link">Source</a></p>
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 			<div class="col-md-6">
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 			</div>
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   "dateCreated": "2015-03-24",
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+  "datePublished": "2024-07-09"
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diff --git a/instructor/404.html b/instructor/404.html
index ae830187..5e80904f 100644
--- a/instructor/404.html
+++ b/instructor/404.html
@@ -46,7 +46,7 @@
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           </ul></li>
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-      
+
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           <div class="accordion accordion-flush" id="accordionFlush11">
@@ -191,7 +191,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         <a href="https://datacarpentry.github.io/organization-genomics/index.html" class="external-link">Summary and Setup</a>
     </div>
 <!--/div.accordion-header-->
-        
+
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 <!--/div.accordion-item-->
 </div>
@@ -202,7 +202,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         <a href="https://datacarpentry.github.io/organization-genomics/01-tidiness.html" class="external-link">1. Data Tidiness</a>
     </div>
 <!--/div.accordion-header-->
-        
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 <!--/div.accordion-item-->
 </div>
@@ -213,7 +213,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         <a href="https://datacarpentry.github.io/organization-genomics/02-project-planning.html" class="external-link">2. Planning for NGS Projects</a>
     </div>
 <!--/div.accordion-header-->
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@@ -224,7 +224,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         <a href="https://datacarpentry.github.io/organization-genomics/03-ncbi-sra.html" class="external-link">3. Examining Data on the NCBI SRA Database</a>
     </div>
 <!--/div.accordion-header-->
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@@ -258,10 +258,10 @@ <h2 class="accordion-header" id="flush-headingTwelve">
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@@ -274,8 +274,8 @@ <h2 class="accordion-header" id="flush-headingTwelve">
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-<section id="our-apologies"><h2 class="section-heading">Our apologies!<a class="anchor" aria-label="anchor" href="#our-apologies"></a>
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+<section><h2 class="section-heading" id="our-apologies">Our apologies!<a class="anchor" aria-label="anchor" href="#our-apologies"></a>
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@@ -297,18 +297,18 @@ <h1>Page not found</h1>
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   "identifier": "https://datacarpentry.github.io/organization-genomics/instructor/404.html",
   "dateCreated": "2015-03-24",
-  "dateModified": "2024-07-02",
-  "datePublished": "2024-07-02"
+  "dateModified": "2024-07-09",
+  "datePublished": "2024-07-09"
 }
 
   </script><script>
diff --git a/instructor/CODE_OF_CONDUCT.html b/instructor/CODE_OF_CONDUCT.html
index 5b892fff..f0058d0d 100644
--- a/instructor/CODE_OF_CONDUCT.html
+++ b/instructor/CODE_OF_CONDUCT.html
@@ -46,7 +46,7 @@
             </li>
           </ul></li>
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-      
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@@ -170,7 +170,7 @@ <h2 class="accordion-header" id="flush-headingNine">
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         <a href="index.html">Summary and Schedule</a>
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@@ -198,7 +198,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
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         <a href="01-tidiness.html">1. Data Tidiness</a>
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@@ -207,7 +207,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
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@@ -216,7 +216,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
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     </div><!--/div.accordion-header-->
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@@ -248,10 +248,10 @@ <h2 class="accordion-header" id="flush-headingTwelve">
               </div>
             </div>
             <hr class="half-width resources"><a href="../instructor/aio.html">See all in one page</a>
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             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
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@@ -279,13 +279,13 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Contributor Code of Conduct</h1>
         <p>Last updated on 2023-05-02 |
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/CODE_OF_CONDUCT.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
-        
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         </div>
@@ -324,18 +324,18 @@ <h1>Contributor Code of Conduct</h1>
       		<footer class="row footer mx-md-3"><hr><div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/CODE_OF_CONDUCT.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/datacarpentry/organization-genomics/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
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 				<p><a href="https://github.com/datacarpentry/organization-genomics/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:team@carpentries.org">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
-        
+
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
         <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
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diff --git a/instructor/LICENSE.html b/instructor/LICENSE.html
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+++ b/instructor/LICENSE.html
@@ -46,7 +46,7 @@
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@@ -170,7 +170,7 @@ <h2 class="accordion-header" id="flush-headingNine">
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               </div><!--div.sidenav-view-selector -->
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           <div class="accordion accordion-flush" id="accordionFlush11">
@@ -189,7 +189,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
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         <a href="index.html">Summary and Schedule</a>
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@@ -198,7 +198,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
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@@ -216,7 +216,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
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         <a href="03-ncbi-sra.html">3. Examining Data on the NCBI SRA Database</a>
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@@ -248,10 +248,10 @@ <h2 class="accordion-header" id="flush-headingTwelve">
               </div>
             </div>
             <hr class="half-width resources"><a href="../instructor/aio.html">See all in one page</a>
-            
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             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
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@@ -279,21 +279,21 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Licenses</h1>
         <p>Last updated on 2023-05-02 |
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/LICENSE.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
-        
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         </div>
 
         
 
-<section id="instructional-material"><h2 class="section-heading">Instructional Material<a class="anchor" aria-label="anchor" href="#instructional-material"></a>
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+<section><h2 class="section-heading" id="instructional-material">Instructional Material<a class="anchor" aria-label="anchor" href="#instructional-material"></a>
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 <hr class="half-width"><p>All Carpentries (Software Carpentry, Data Carpentry, and Library
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@@ -326,8 +326,8 @@ <h1>Licenses</h1>
 permissions necessary for your intended use. For example, other rights
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 material.</li>
-</ul></section><section id="software"><h2 class="section-heading">Software<a class="anchor" aria-label="anchor" href="#software"></a>
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 <hr class="half-width"><p>Except where otherwise noted, the example programs and other software
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 license</a>.</p>
@@ -347,8 +347,8 @@ <h1>Licenses</h1>
 CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
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+</section><section><h2 class="section-heading" id="trademark">Trademark<a class="anchor" aria-label="anchor" href="#trademark"></a>
+<a class="anchor" aria-label="anchor" href="#trademark"></a></h2>
 <hr class="half-width"><p>“The Carpentries”, “Software Carpentry”, “Data Carpentry”, and
 “Library Carpentry” and their respective logos are registered trademarks
 of <a href="https://communityin.org/" class="external-link">Community Initiatives</a>.</p>
@@ -375,18 +375,18 @@ <h1>Licenses</h1>
       		<footer class="row footer mx-md-3"><hr><div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/LICENSE.md" class="external-link">Edit on GitHub</a>
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+
 	
         | <a href="https://github.com/datacarpentry/organization-genomics/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
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 				<p><a href="https://github.com/datacarpentry/organization-genomics/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:team@carpentries.org">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
-        
+
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
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@@ -411,7 +411,7 @@ <h1>Licenses</h1>
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diff --git a/instructor/aio.html b/instructor/aio.html
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@@ -207,7 +207,7 @@ <h2 class="accordion-header" id="flush-headingNine">
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@@ -332,7 +332,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
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 <hr>
 <p>Last updated on 2023-06-14 |
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/episodes/01-tidiness.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <p>Estimated time: <i aria-hidden="true" data-feather="clock"></i> 30 minutes</p>
 <div class="text-end">
@@ -368,7 +368,8 @@ <h3 class="card-title">Objectives</h3>
 </div>
 </div>
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+<section><h2 class="section-heading" id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
+<a class="anchor" aria-label="anchor" href="#introduction"></a>
 </h2>
 <hr class="half-width">
 <p>When we think about the data for a sequencing project, we often start
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 <p>Types of files and information you have generated:</p>
 <ul>
@@ -420,7 +421,8 @@ <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 <p>All of the data and information just discussed can be considered
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 for metadata.</p>
-</section><section id="notes"><h2 class="section-heading">Notes<a class="anchor" aria-label="anchor" href="#notes"></a>
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 </h2>
 <hr class="half-width">
 <p>Notes about your experiment, including how you prepared your samples
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 </h2>
 <hr class="half-width">
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 </div>
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-</section><section id="structuring-data-in-spreadsheets"><h2 class="section-heading">Structuring data in spreadsheets<a class="anchor" aria-label="anchor" href="#structuring-data-in-spreadsheets"></a>
+</section><section><h2 class="section-heading" id="structuring-data-in-spreadsheets">Structuring data in spreadsheets<a class="anchor" aria-label="anchor" href="#structuring-data-in-spreadsheets"></a>
+<a class="anchor" aria-label="anchor" href="#structuring-data-in-spreadsheets"></a>
 </h2>
 <hr class="half-width">
 <p>Regardless of the type of data you’re collecting, there are standard
@@ -533,7 +537,7 @@ <h3 class="callout-title">Discussion<a class="anchor" aria-label="anchor" href="
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+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <p>A full set of types of issues with spreadsheet data is at the <a href="https://www.datacarpentry.org/spreadsheet-ecology-lesson/02-common-mistakes/" class="external-link">Data
 Carpentry Ecology spreadsheet lesson</a>. Not all are present in this
@@ -587,7 +591,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
 </section></section><section id="aio-02-project-planning"><p>Content from <a href="02-project-planning.html">Planning for NGS Projects</a></p>
 <hr>
 <p>Last updated on 2024-04-04 |
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/episodes/02-project-planning.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <p>Estimated time: <i aria-hidden="true" data-feather="clock"></i> 30 minutes</p>
 <div class="text-end">
@@ -651,7 +655,8 @@ <h3 class="callout-title">Discussion<a class="anchor" aria-label="anchor" href="
 </div>
 </div>
 </div>
-<section id="sending-samples-to-the-facility"><h2 class="section-heading">Sending samples to the facility<a class="anchor" aria-label="anchor" href="#sending-samples-to-the-facility"></a>
+<section><h2 class="section-heading" id="sending-samples-to-the-facility">Sending samples to the facility<a class="anchor" aria-label="anchor" href="#sending-samples-to-the-facility"></a>
+<a class="anchor" aria-label="anchor" href="#sending-samples-to-the-facility"></a>
 </h2>
 <hr class="half-width">
 <p>The first step in sending your sample for sequencing will be to
@@ -684,7 +689,7 @@ <h3 class="callout-title">Exercise<a class="anchor" aria-label="anchor" href="#e
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 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <p>Errors:</p>
 <ul>
@@ -720,7 +725,8 @@ <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </div>
 </div>
 </div>
-</section><section id="retrieving-sample-sequencing-data-from-the-facility"><h2 class="section-heading">Retrieving sample sequencing data from the facility<a class="anchor" aria-label="anchor" href="#retrieving-sample-sequencing-data-from-the-facility"></a>
+</section><section><h2 class="section-heading" id="retrieving-sample-sequencing-data-from-the-facility">Retrieving sample sequencing data from the facility<a class="anchor" aria-label="anchor" href="#retrieving-sample-sequencing-data-from-the-facility"></a>
+<a class="anchor" aria-label="anchor" href="#retrieving-sample-sequencing-data-from-the-facility"></a>
 </h2>
 <hr class="half-width">
 <p>When the data come back from the sequencing facility, you will
@@ -759,7 +765,7 @@ <h3 class="callout-title">Exercise<a class="anchor" aria-label="anchor" href="#e
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 <ol style="list-style-type: decimal">
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 </div>
 </div>
 </div>
-</section><section id="storing-data"><h2 class="section-heading">Storing data<a class="anchor" aria-label="anchor" href="#storing-data"></a>
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 </h2>
 <hr class="half-width">
 <p>The raw data you get back from the sequencing center is the
@@ -821,7 +828,8 @@ <h4 id="some-data-storage-solutions">Some data storage solutions<a class="anchor
 to Cloud Computing for Genomics”</a>.</p>
 </div>
 </div>
-</section><section id="summary"><h2 class="section-heading">Summary<a class="anchor" aria-label="anchor" href="#summary"></a>
+</section><section><h2 class="section-heading" id="summary">Summary<a class="anchor" aria-label="anchor" href="#summary"></a>
+<a class="anchor" aria-label="anchor" href="#summary"></a>
 </h2>
 <hr class="half-width">
 <p>Before analysis of data has begun, there are already many potential
@@ -871,7 +879,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
 </section></section><section id="aio-03-ncbi-sra"><p>Content from <a href="03-ncbi-sra.html">Examining Data on the NCBI SRA Database</a></p>
 <hr>
 <p>Last updated on 2023-11-20 |
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         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/episodes/03-ncbi-sra.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <p>Estimated time: <i aria-hidden="true" data-feather="clock"></i> 30 minutes</p>
 <div class="text-end">
@@ -922,7 +930,8 @@ <h3 class="card-title">Objectives</h3>
 (SRA)</a> is the database we will be using for this lesson, but the
 EMBL-EBI’s Nucleotide Archive (ENA) is also useful. The general
 processes are similar for any database.</p>
-<section id="accessing-the-original-archived-data"><h2 class="section-heading">Accessing the original archived data<a class="anchor" aria-label="anchor" href="#accessing-the-original-archived-data"></a>
+<section><h2 class="section-heading" id="accessing-the-original-archived-data">Accessing the original archived data<a class="anchor" aria-label="anchor" href="#accessing-the-original-archived-data"></a>
+<a class="anchor" aria-label="anchor" href="#accessing-the-original-archived-data"></a>
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 <p>The <a href="https://www.datacarpentry.org/organization-genomics/data" class="external-link">sequencing
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 <div class="accordion-body">
 <ol style="list-style-type: decimal">
 <li>Escherichia coli B str. REL606 shown under the “organism” column.
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 changes. If you were to save this file, make sure you save it as a
 text-based <code>.csv</code> file format.</p>
 </div>
-</section><section id="downloading-a-few-sequencing-files-embl-ebi"><h2 class="section-heading">Downloading a few sequencing files: EMBL-EBI<a class="anchor" aria-label="anchor" href="#downloading-a-few-sequencing-files-embl-ebi"></a>
+</section><section><h2 class="section-heading" id="downloading-a-few-sequencing-files-embl-ebi">Downloading a few sequencing files: EMBL-EBI<a class="anchor" aria-label="anchor" href="#downloading-a-few-sequencing-files-embl-ebi"></a>
+<a class="anchor" aria-label="anchor" href="#downloading-a-few-sequencing-files-embl-ebi"></a>
 </h2>
 <hr class="half-width">
 <p>The SRA does not support direct download of fastq files from its
@@ -1107,7 +1117,8 @@ <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 this way. For that, the NCBI has made a software package called the
 <code>sra-toolkit</code>. However, for a couple files, it’s often easier
 to go through the ENA.</p>
-</section><section id="where-to-learn-more"><h2 class="section-heading">Where to learn more<a class="anchor" aria-label="anchor" href="#where-to-learn-more"></a>
+</section><section><h2 class="section-heading" id="where-to-learn-more">Where to learn more<a class="anchor" aria-label="anchor" href="#where-to-learn-more"></a>
+<a class="anchor" aria-label="anchor" href="#where-to-learn-more"></a>
 </h2>
 <hr class="half-width">
 <div class="section level3">
@@ -1122,7 +1133,8 @@ <h3 id="about-the-sequence-read-archive">About the Sequence Read Archive<a class
 </li>
 </ul>
 </div>
-</section><section id="references"><h2 class="section-heading">References<a class="anchor" aria-label="anchor" href="#references"></a>
+</section><section><h2 class="section-heading" id="references">References<a class="anchor" aria-label="anchor" href="#references"></a>
+<a class="anchor" aria-label="anchor" href="#references"></a>
 </h2>
 <hr class="half-width">
 <p>Tenaillon O, Barrick JE, Ribeck N, Deatherage DE, Blanchard JL,
@@ -1159,18 +1171,18 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
 <div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/README.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/datacarpentry/organization-genomics/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/datacarpentry/organization-genomics/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/datacarpentry/organization-genomics/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:team@carpentries.org">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
-        
+
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
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index 0f1e0e29..b20564a2 100644
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       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Data</h1>
         <p>Last updated on 2023-05-02 |
-        
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         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/instructors/data.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
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         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/instructors/data.md" class="external-link">Edit on GitHub</a>
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+
 	
         | <a href="https://github.com/datacarpentry/organization-genomics/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/datacarpentry/organization-genomics/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/datacarpentry/organization-genomics/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:team@carpentries.org">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
-        
+
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
         <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
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         <a href="03-ncbi-sra.html">3. Examining Data on the NCBI SRA Database</a>
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             <hr class="half-width resources"><a href="../instructor/aio.html">See all in one page</a>
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       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Discussion</h1>
         <p>Last updated on 2023-05-02 |
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@@ -317,18 +317,18 @@ <h1>Discussion</h1>
       		<footer class="row footer mx-md-3"><hr><div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/learners/discuss.md" class="external-link">Edit on GitHub</a>
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         | <a href="https://github.com/datacarpentry/organization-genomics/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/datacarpentry/organization-genomics/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/datacarpentry/organization-genomics/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:team@carpentries.org">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
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-        
+
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         <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
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 <div class="col-md-6">
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         <p>
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         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/README.md" class="external-link">Edit on GitHub</a>
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         | <a href="https://github.com/datacarpentry/organization-genomics/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/datacarpentry/organization-genomics/" class="external-link">Source</a></p>
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 			<div class="col-md-6">
-        
+
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
-        
+
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
         <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
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@@ -411,8 +411,8 @@ <h3 id="03-ncbi-sra-figure-5">Figure 5</h3>
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   "identifier": "https://datacarpentry.github.io/organization-genomics/instructor/images.html",
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-  "dateModified": "2024-07-02",
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 }
 
   </script><script>
diff --git a/instructor/index.html b/instructor/index.html
index 21b2930c..45ca7e42 100644
--- a/instructor/index.html
+++ b/instructor/index.html
@@ -46,7 +46,7 @@
             </li>
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-      
+
       <div class="dropdown" id="instructor-dropdown">
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               </div><!--div.sidenav-view-selector -->
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+
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@@ -193,7 +193,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         </span>
       
     </div><!--/div.accordion-header-->
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+
   </div><!--/div.accordion-item-->
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@@ -202,7 +202,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading2">
         <a href="01-tidiness.html">1. Data Tidiness</a>
     </div><!--/div.accordion-header-->
-        
+
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@@ -211,7 +211,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
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         <a href="02-project-planning.html">2. Planning for NGS Projects</a>
     </div><!--/div.accordion-header-->
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+
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@@ -220,7 +220,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading4">
         <a href="03-ncbi-sra.html">3. Examining Data on the NCBI SRA Database</a>
     </div><!--/div.accordion-header-->
-        
+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -252,10 +252,10 @@ <h2 class="accordion-header" id="flush-headingTwelve">
               </div>
             </div>
             <hr class="half-width resources"><a href="../instructor/aio.html">See all in one page</a>
-            
+
 
             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
-            
+
             </div>
           </div><!-- /div.accordion -->
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@@ -413,18 +413,18 @@ <h3 class="callout-title">For Instructors<a class="anchor" aria-label="anchor" h
       		<footer class="row footer mx-md-3"><hr><div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/index.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/datacarpentry/organization-genomics/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/datacarpentry/organization-genomics/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/datacarpentry/organization-genomics/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:team@carpentries.org">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
-        
+
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
         <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
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   "dateCreated": "2015-03-24",
-  "dateModified": "2024-07-02",
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 }
 
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diff --git a/instructor/instructor-notes.html b/instructor/instructor-notes.html
index 62004d8f..1bf660df 100644
--- a/instructor/instructor-notes.html
+++ b/instructor/instructor-notes.html
@@ -65,7 +65,7 @@
           </ul>
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       </div>
-      
+
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           <i aria-hidden="true" class="icon" data-feather="eye"></i> Instructor View <i data-feather="chevron-down"></i>
@@ -207,7 +207,7 @@ <h2 class="accordion-header" id="flush-headingNine">
 <!--div.sidenav-view-selector -->
             </div>
 <!--/div.col -->
-      
+
             <hr>
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 <!--/div.mobile-row -->
@@ -229,7 +229,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         <a href="index.html">Summary and Schedule</a>
     </div>
 <!--/div.accordion-header-->
-        
+
   </div>
 <!--/div.accordion-item-->
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@@ -241,7 +241,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         <a href="01-tidiness.html">1. Data Tidiness</a>
     </div>
 <!--/div.accordion-header-->
-        
+
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 <!--/div.accordion-item-->
 </div>
@@ -253,7 +253,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         <a href="02-project-planning.html">2. Planning for NGS Projects</a>
     </div>
 <!--/div.accordion-header-->
-        
+
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 </div>
@@ -265,7 +265,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         <a href="03-ncbi-sra.html">3. Examining Data on the NCBI SRA Database</a>
     </div>
 <!--/div.accordion-header-->
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@@ -307,11 +307,11 @@ <h2 class="accordion-header" id="flush-headingTwelve">
             </div>
             <hr class="half-width resources">
 <a href="../instructor/aio.html">See all in one page</a>
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+
 
             <hr class="d-none d-sm-block d-md-none">
 <div class="d-grid gap-1">
-            
+
             </div>
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 <!-- /div.accordion -->
@@ -330,15 +330,18 @@ <h2 class="accordion-header" id="flush-headingTwelve">
         <h1>Instructor Notes</h1>
         
 
-<section id="instructor-notes"><h2 class="section-heading">Instructor notes<a class="anchor" aria-label="anchor" href="#instructor-notes"></a>
+<section><h2 class="section-heading" id="instructor-notes">Instructor notes<a class="anchor" aria-label="anchor" href="#instructor-notes"></a>
+<a class="anchor" aria-label="anchor" href="#instructor-notes"></a>
 </h2>
-<hr class="half-width"></section><section id="lesson-motivation-and-learning-objectives"><h2 class="section-heading">Lesson motivation and learning objectives<a class="anchor" aria-label="anchor" href="#lesson-motivation-and-learning-objectives"></a>
+<hr class="half-width"></section><section><h2 class="section-heading" id="lesson-motivation-and-learning-objectives">Lesson motivation and learning objectives<a class="anchor" aria-label="anchor" href="#lesson-motivation-and-learning-objectives"></a>
+<a class="anchor" aria-label="anchor" href="#lesson-motivation-and-learning-objectives"></a>
 </h2>
 <hr class="half-width">
 <p>The purpose of this lesson is <em>not</em> to teach how to do data
 analysis in spreadsheets, but to teach good data organization and how to
 do some data cleaning and quality control in a spreadsheet program.</p>
-</section><section id="lesson-design"><h2 class="section-heading">Lesson design<a class="anchor" aria-label="anchor" href="#lesson-design"></a>
+</section><section><h2 class="section-heading" id="lesson-design">Lesson design<a class="anchor" aria-label="anchor" href="#lesson-design"></a>
+<a class="anchor" aria-label="anchor" href="#lesson-design"></a>
 </h2>
 <hr class="half-width">
 <div class="section level4">
@@ -405,7 +408,8 @@ <h4 id="concluding-points">Concluding points<a class="anchor" aria-label="anchor
 analyses as we’ll see in the rest of the workshop.</li>
 </ul>
 </div>
-</section><section id="working-with-participants-level-of-expertise"><h2 class="section-heading">Working with participants’ level of expertise<a class="anchor" aria-label="anchor" href="#working-with-participants-level-of-expertise"></a>
+</section><section><h2 class="section-heading" id="working-with-participants-level-of-expertise">Working with participants’ level of expertise<a class="anchor" aria-label="anchor" href="#working-with-participants-level-of-expertise"></a>
+<a class="anchor" aria-label="anchor" href="#working-with-participants-level-of-expertise"></a>
 </h2>
 <hr class="half-width">
 <p>Learners may be taking this lesson for many reasons - they may be
@@ -453,14 +457,16 @@ <h4 id="data-tidiness-1">
 survey, then present the range of answers during the class. It can also
 be helpful for instructors and helpers to share what they work on.</p>
 </div>
-</section><section id="technical-tips-and-tricks"><h2 class="section-heading">Technical tips and tricks<a class="anchor" aria-label="anchor" href="#technical-tips-and-tricks"></a>
+</section><section><h2 class="section-heading" id="technical-tips-and-tricks">Technical tips and tricks<a class="anchor" aria-label="anchor" href="#technical-tips-and-tricks"></a>
+<a class="anchor" aria-label="anchor" href="#technical-tips-and-tricks"></a>
 </h2>
 <hr class="half-width">
 <p>Provide information on setting up your environment for learners to
 view your live coding (increasing text size, changing text color, etc),
 as well as general recommendations for working with coding tools to best
 suit the learning environment.</p>
-</section><section id="common-problems"><h2 class="section-heading">Common problems<a class="anchor" aria-label="anchor" href="#common-problems"></a>
+</section><section><h2 class="section-heading" id="common-problems">Common problems<a class="anchor" aria-label="anchor" href="#common-problems"></a>
+<a class="anchor" aria-label="anchor" href="#common-problems"></a>
 </h2>
 <hr class="half-width">
 <div class="section level4">
@@ -501,18 +507,18 @@ <h4 id="people-are-not-interactive-or-responsive-on-the-exercises">People are no
 <div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/README.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/datacarpentry/organization-genomics/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/datacarpentry/organization-genomics/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/datacarpentry/organization-genomics/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:team@carpentries.org">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
-        
+
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
         <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
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@@ -537,8 +543,8 @@ <h4 id="people-are-not-interactive-or-responsive-on-the-exercises">People are no
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   "identifier": "https://datacarpentry.github.io/organization-genomics/instructor/instructor-notes.html",
   "dateCreated": "2015-03-24",
-  "dateModified": "2024-07-02",
-  "datePublished": "2024-07-02"
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+  "datePublished": "2024-07-09"
 }
 
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diff --git a/instructor/key-points.html b/instructor/key-points.html
index c148971d..537c3e63 100644
--- a/instructor/key-points.html
+++ b/instructor/key-points.html
@@ -65,7 +65,7 @@
           </ul>
 </li>
       </div>
-      
+
       <div class="dropdown" id="instructor-dropdown">
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           <i aria-hidden="true" class="icon" data-feather="eye"></i> Instructor View <i data-feather="chevron-down"></i>
@@ -207,7 +207,7 @@ <h2 class="accordion-header" id="flush-headingNine">
 <!--div.sidenav-view-selector -->
             </div>
 <!--/div.col -->
-      
+
             <hr>
 </div>
 <!--/div.mobile-row -->
@@ -229,7 +229,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         <a href="index.html">Summary and Schedule</a>
     </div>
 <!--/div.accordion-header-->
-        
+
   </div>
 <!--/div.accordion-item-->
 </div>
@@ -241,7 +241,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         <a href="01-tidiness.html">1. Data Tidiness</a>
     </div>
 <!--/div.accordion-header-->
-        
+
   </div>
 <!--/div.accordion-item-->
 </div>
@@ -253,7 +253,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         <a href="02-project-planning.html">2. Planning for NGS Projects</a>
     </div>
 <!--/div.accordion-header-->
-        
+
   </div>
 <!--/div.accordion-item-->
 </div>
@@ -265,7 +265,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         <a href="03-ncbi-sra.html">3. Examining Data on the NCBI SRA Database</a>
     </div>
 <!--/div.accordion-header-->
-        
+
   </div>
 <!--/div.accordion-item-->
 </div>
@@ -307,11 +307,11 @@ <h2 class="accordion-header" id="flush-headingTwelve">
             </div>
             <hr class="half-width resources">
 <a href="../instructor/aio.html">See all in one page</a>
-            
+
 
             <hr class="d-none d-sm-block d-md-none">
 <div class="d-grid gap-1">
-            
+
             </div>
           </div>
 <!-- /div.accordion -->
@@ -360,18 +360,18 @@ <h2 class="accordion-header" id="flush-headingTwelve">
 <div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/README.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/datacarpentry/organization-genomics/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/datacarpentry/organization-genomics/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/datacarpentry/organization-genomics/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:team@carpentries.org">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
-        
+
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
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   "identifier": "https://datacarpentry.github.io/organization-genomics/instructor/key-points.html",
   "dateCreated": "2015-03-24",
-  "dateModified": "2024-07-02",
-  "datePublished": "2024-07-02"
+  "dateModified": "2024-07-09",
+  "datePublished": "2024-07-09"
 }
 
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diff --git a/instructor/old-ncbi.html b/instructor/old-ncbi.html
index c9189ace..074310d8 100644
--- a/instructor/old-ncbi.html
+++ b/instructor/old-ncbi.html
@@ -46,7 +46,7 @@
             </li>
           </ul></li>
       </div>
-      
+
       <div class="dropdown" id="instructor-dropdown">
         <button class="btn btn-secondary dropdown-toggle bordered-button" type="button" id="dropdownMenu1" data-bs-toggle="dropdown" aria-expanded="false">
           <i aria-hidden="true" class="icon" data-feather="eye"></i> Instructor View <i data-feather="chevron-down"></i>
@@ -170,7 +170,7 @@ <h2 class="accordion-header" id="flush-headingNine">
                 </div><!--/div.accordion-flush-->
               </div><!--div.sidenav-view-selector -->
             </div><!--/div.col -->
-      
+
             <hr></div><!--/div.mobile-row -->
 
           <div class="accordion accordion-flush" id="accordionFlush11">
@@ -189,7 +189,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading1">
         <a href="index.html">Summary and Schedule</a>
     </div><!--/div.accordion-header-->
-        
+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -198,7 +198,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading2">
         <a href="01-tidiness.html">1. Data Tidiness</a>
     </div><!--/div.accordion-header-->
-        
+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -207,7 +207,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading3">
         <a href="02-project-planning.html">2. Planning for NGS Projects</a>
     </div><!--/div.accordion-header-->
-        
+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -216,7 +216,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading4">
         <a href="03-ncbi-sra.html">3. Examining Data on the NCBI SRA Database</a>
     </div><!--/div.accordion-header-->
-        
+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -248,10 +248,10 @@ <h2 class="accordion-header" id="flush-headingTwelve">
               </div>
             </div>
             <hr class="half-width resources"><a href="../instructor/aio.html">See all in one page</a>
-            
+
 
             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
-            
+
             </div>
           </div><!-- /div.accordion -->
         </div><!-- /div.sidebar-inner -->
@@ -279,20 +279,20 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Old NCBI</h1>
         <p>Last updated on 2023-05-02 |
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/instructors/old-ncbi.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
-        
-        
-        
-        
-        
+
+
+
+
+
         <div class="text-end">
           <button role="button" aria-pressed="false" tabindex="0" id="expand-code" class="pull-right" data-expand="Expand All Solutions " data-collapse="Collapse All Solutions "> Expand All Solutions <i aria-hidden="true" data-feather="plus"></i></button>
         </div>
 
         
-<section id="original-older-ncbi-instructions"><h2 class="section-heading">Original (older) NCBI instructions<a class="anchor" aria-label="anchor" href="#original-older-ncbi-instructions"></a>
-</h2>
+<section><h2 class="section-heading" id="original-older-ncbi-instructions">Original (older) NCBI instructions<a class="anchor" aria-label="anchor" href="#original-older-ncbi-instructions"></a>
+<a class="anchor" aria-label="anchor" href="#original-older-ncbi-instructions"></a></h2>
 <hr class="half-width"><p>These will be phased out of our lesson when NCBI stops supporting the
 old page versions.</p>
 <ol style="list-style-type: decimal"><li><p>Access the Tenaillon dataset from the provided link: <a href="https://trace.ncbi.nlm.nih.gov/Traces/study/?acc=SRP064605" class="external-link">https://trace.ncbi.nlm.nih.gov/Traces/study/?acc=SRP064605</a>.
@@ -339,18 +339,18 @@ <h1>Old NCBI</h1>
       		<footer class="row footer mx-md-3"><hr><div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/instructors/old-ncbi.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/datacarpentry/organization-genomics/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/datacarpentry/organization-genomics/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/datacarpentry/organization-genomics/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:team@carpentries.org">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
-        
+
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
         <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
 			</div>
@@ -375,7 +375,7 @@ <h1>Old NCBI</h1>
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   "dateCreated": "2015-03-24",
   "dateModified": "2023-05-02",
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+  "datePublished": "2024-07-09"
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diff --git a/instructor/profiles.html b/instructor/profiles.html
index aeadbe2d..97b59f8a 100644
--- a/instructor/profiles.html
+++ b/instructor/profiles.html
@@ -46,7 +46,7 @@
             </li>
           </ul></li>
       </div>
-      
+
       <div class="dropdown" id="instructor-dropdown">
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           <i aria-hidden="true" class="icon" data-feather="eye"></i> Instructor View <i data-feather="chevron-down"></i>
@@ -170,7 +170,7 @@ <h2 class="accordion-header" id="flush-headingNine">
                 </div><!--/div.accordion-flush-->
               </div><!--div.sidenav-view-selector -->
             </div><!--/div.col -->
-      
+
             <hr></div><!--/div.mobile-row -->
 
           <div class="accordion accordion-flush" id="accordionFlush11">
@@ -189,7 +189,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading1">
         <a href="index.html">Summary and Schedule</a>
     </div><!--/div.accordion-header-->
-        
+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -198,7 +198,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading2">
         <a href="01-tidiness.html">1. Data Tidiness</a>
     </div><!--/div.accordion-header-->
-        
+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -207,7 +207,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading3">
         <a href="02-project-planning.html">2. Planning for NGS Projects</a>
     </div><!--/div.accordion-header-->
-        
+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -216,7 +216,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading4">
         <a href="03-ncbi-sra.html">3. Examining Data on the NCBI SRA Database</a>
     </div><!--/div.accordion-header-->
-        
+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -248,10 +248,10 @@ <h2 class="accordion-header" id="flush-headingTwelve">
               </div>
             </div>
             <hr class="half-width resources"><a href="../instructor/aio.html">See all in one page</a>
-            
+
 
             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
-            
+
             </div>
           </div><!-- /div.accordion -->
         </div><!-- /div.sidebar-inner -->
@@ -274,18 +274,18 @@ <h1>Learner Profiles</h1>
       		<footer class="row footer mx-md-3"><hr><div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/README.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/datacarpentry/organization-genomics/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/datacarpentry/organization-genomics/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/datacarpentry/organization-genomics/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:team@carpentries.org">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
-        
+
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
         <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
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@@ -309,8 +309,8 @@ <h1>Learner Profiles</h1>
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   "identifier": "https://datacarpentry.github.io/organization-genomics/instructor/profiles.html",
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-  "dateModified": "2024-07-02",
-  "datePublished": "2024-07-02"
+  "dateModified": "2024-07-09",
+  "datePublished": "2024-07-09"
 }
 
   </script><script>
diff --git a/instructor/reference.html b/instructor/reference.html
index 780a28cd..0e9731b5 100644
--- a/instructor/reference.html
+++ b/instructor/reference.html
@@ -46,7 +46,7 @@
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           </ul></li>
       </div>
-      
+
       <div class="dropdown" id="instructor-dropdown">
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           <i aria-hidden="true" class="icon" data-feather="eye"></i> Instructor View <i data-feather="chevron-down"></i>
@@ -170,7 +170,7 @@ <h2 class="accordion-header" id="flush-headingNine">
                 </div><!--/div.accordion-flush-->
               </div><!--div.sidenav-view-selector -->
             </div><!--/div.col -->
-      
+
             <hr></div><!--/div.mobile-row -->
 
           <div class="accordion accordion-flush" id="accordionFlush11">
@@ -189,7 +189,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading1">
         <a href="index.html">Summary and Schedule</a>
     </div><!--/div.accordion-header-->
-        
+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -198,7 +198,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading2">
         <a href="01-tidiness.html">1. Data Tidiness</a>
     </div><!--/div.accordion-header-->
-        
+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -207,7 +207,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading3">
         <a href="02-project-planning.html">2. Planning for NGS Projects</a>
     </div><!--/div.accordion-header-->
-        
+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -216,7 +216,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading4">
         <a href="03-ncbi-sra.html">3. Examining Data on the NCBI SRA Database</a>
     </div><!--/div.accordion-header-->
-        
+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -248,10 +248,10 @@ <h2 class="accordion-header" id="flush-headingTwelve">
               </div>
             </div>
             <hr class="half-width resources"><a href="../instructor/aio.html">See all in one page</a>
-            
+
 
             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
-            
+
             </div>
           </div><!-- /div.accordion -->
         </div><!-- /div.sidebar-inner -->
@@ -279,20 +279,20 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Glossary</h1>
         <p>Last updated on 2023-05-02 |
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/learners/reference.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
-        
-        
-        
-        
-        
+
+
+
+
+
         <div class="text-end">
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         </div>
 
         
-<section id="glossary"><h2 class="section-heading">Glossary<a class="anchor" aria-label="anchor" href="#glossary"></a>
-</h2>
+<section><h2 class="section-heading" id="glossary">Glossary<a class="anchor" aria-label="anchor" href="#glossary"></a>
+<a class="anchor" aria-label="anchor" href="#glossary"></a></h2>
 <hr class="half-width"><p>{:auto_ids}<br>
 accession : a unique identifier assigned to each sequence or set of
 sequences</p>
@@ -415,18 +415,18 @@ <h1>Glossary</h1>
       		<footer class="row footer mx-md-3"><hr><div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/learners/reference.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/datacarpentry/organization-genomics/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/datacarpentry/organization-genomics/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/datacarpentry/organization-genomics/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:team@carpentries.org">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
-        
+
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
         <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
 			</div>
@@ -451,7 +451,7 @@ <h1>Glossary</h1>
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   "dateCreated": "2015-03-24",
   "dateModified": "2023-05-02",
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+  "datePublished": "2024-07-09"
 }
 
   </script><script>
diff --git a/key-points.html b/key-points.html
index 1cc28856..0a1ee03a 100644
--- a/key-points.html
+++ b/key-points.html
@@ -65,7 +65,7 @@
           </ul>
 </li>
       </div>
-      
+
       <div class="dropdown" id="instructor-dropdown">
         <button class="btn btn-secondary dropdown-toggle bordered-button" type="button" id="dropdownMenu1" data-bs-toggle="dropdown" aria-expanded="false">
           <i aria-hidden="true" class="icon" data-feather="eye"></i> Learner View <i data-feather="chevron-down"></i>
@@ -204,7 +204,7 @@ <h2 class="accordion-header" id="flush-headingNine">
 <!--div.sidenav-view-selector -->
             </div>
 <!--/div.col -->
-      
+
             <hr>
 </div>
 <!--/div.mobile-row -->
@@ -226,7 +226,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         <a href="index.html">Summary and Setup</a>
     </div>
 <!--/div.accordion-header-->
-        
+
   </div>
 <!--/div.accordion-item-->
 </div>
@@ -238,7 +238,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         <a href="01-tidiness.html">1. Data Tidiness</a>
     </div>
 <!--/div.accordion-header-->
-        
+
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 <!--/div.accordion-item-->
 </div>
@@ -250,7 +250,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         <a href="02-project-planning.html">2. Planning for NGS Projects</a>
     </div>
 <!--/div.accordion-header-->
-        
+
   </div>
 <!--/div.accordion-item-->
 </div>
@@ -262,7 +262,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         <a href="03-ncbi-sra.html">3. Examining Data on the NCBI SRA Database</a>
     </div>
 <!--/div.accordion-header-->
-        
+
   </div>
 <!--/div.accordion-item-->
 </div>
@@ -301,11 +301,11 @@ <h2 class="accordion-header" id="flush-headingTwelve">
             </div>
             <hr class="half-width resources">
 <a href="aio.html">See all in one page</a>
-            
+
 
             <hr class="d-none d-sm-block d-md-none">
 <div class="d-grid gap-1">
-            
+
             </div>
           </div>
 <!-- /div.accordion -->
@@ -354,18 +354,18 @@ <h2 class="accordion-header" id="flush-headingTwelve">
 <div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/README.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/datacarpentry/organization-genomics/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/datacarpentry/organization-genomics/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/datacarpentry/organization-genomics/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:team@carpentries.org">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
-        
+
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
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@@ -390,8 +390,8 @@ <h2 class="accordion-header" id="flush-headingTwelve">
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   "dateCreated": "2015-03-24",
-  "dateModified": "2024-07-02",
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+  "datePublished": "2024-07-09"
 }
 
   </script><script>
diff --git a/old-ncbi.html b/old-ncbi.html
index 1ede1504..d1116019 100644
--- a/old-ncbi.html
+++ b/old-ncbi.html
@@ -46,7 +46,7 @@
             </li>
           </ul></li>
       </div>
-      
+
       <div class="dropdown" id="instructor-dropdown">
         <button class="btn btn-secondary dropdown-toggle bordered-button" type="button" id="dropdownMenu1" data-bs-toggle="dropdown" aria-expanded="false">
           <i aria-hidden="true" class="icon" data-feather="eye"></i> Learner View <i data-feather="chevron-down"></i>
@@ -170,7 +170,7 @@ <h2 class="accordion-header" id="flush-headingNine">
                 </div><!--/div.accordion-flush-->
               </div><!--div.sidenav-view-selector -->
             </div><!--/div.col -->
-      
+
             <hr></div><!--/div.mobile-row -->
 
           <div class="accordion accordion-flush" id="accordionFlush11">
@@ -189,7 +189,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading1">
         <a href="index.html">Summary and Setup</a>
     </div><!--/div.accordion-header-->
-        
+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -198,7 +198,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading2">
         <a href="01-tidiness.html">1. Data Tidiness</a>
     </div><!--/div.accordion-header-->
-        
+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -207,7 +207,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading3">
         <a href="02-project-planning.html">2. Planning for NGS Projects</a>
     </div><!--/div.accordion-header-->
-        
+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -216,7 +216,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading4">
         <a href="03-ncbi-sra.html">3. Examining Data on the NCBI SRA Database</a>
     </div><!--/div.accordion-header-->
-        
+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -248,10 +248,10 @@ <h2 class="accordion-header" id="flush-headingTwelve">
               </div>
             </div>
             <hr class="half-width resources"><a href="aio.html">See all in one page</a>
-            
+
 
             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
-            
+
             </div>
           </div><!-- /div.accordion -->
         </div><!-- /div.sidebar-inner -->
@@ -279,18 +279,18 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Old NCBI</h1>
         <p>Last updated on 2023-05-02 |
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/instructors/old-ncbi.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
-        
-        
-        
+
+
+
         <div class="text-end">
           <button role="button" aria-pressed="false" tabindex="0" id="expand-code" class="pull-right" data-expand="Expand All Solutions " data-collapse="Collapse All Solutions "> Expand All Solutions <i aria-hidden="true" data-feather="plus"></i></button>
         </div>
 
         
-<section id="original-older-ncbi-instructions"><h2 class="section-heading">Original (older) NCBI instructions<a class="anchor" aria-label="anchor" href="#original-older-ncbi-instructions"></a>
-</h2>
+<section><h2 class="section-heading" id="original-older-ncbi-instructions">Original (older) NCBI instructions<a class="anchor" aria-label="anchor" href="#original-older-ncbi-instructions"></a>
+<a class="anchor" aria-label="anchor" href="#original-older-ncbi-instructions"></a></h2>
 <hr class="half-width"><p>These will be phased out of our lesson when NCBI stops supporting the
 old page versions.</p>
 <ol style="list-style-type: decimal"><li><p>Access the Tenaillon dataset from the provided link: <a href="https://trace.ncbi.nlm.nih.gov/Traces/study/?acc=SRP064605" class="external-link">https://trace.ncbi.nlm.nih.gov/Traces/study/?acc=SRP064605</a>.
@@ -337,18 +337,18 @@ <h1>Old NCBI</h1>
       		<footer class="row footer mx-md-3"><hr><div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/instructors/old-ncbi.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/datacarpentry/organization-genomics/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/datacarpentry/organization-genomics/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/datacarpentry/organization-genomics/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:team@carpentries.org">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
-        
+
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
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@@ -373,7 +373,7 @@ <h1>Old NCBI</h1>
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diff --git a/pkgdown.yml b/pkgdown.yml
index 99d5f1ac..a63693d8 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
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diff --git a/profiles.html b/profiles.html
index 60b212c8..75604507 100644
--- a/profiles.html
+++ b/profiles.html
@@ -46,7 +46,7 @@
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               </div><!--div.sidenav-view-selector -->
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-      
+
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     <div class="accordion-header" id="flush-heading1">
         <a href="index.html">Summary and Setup</a>
     </div><!--/div.accordion-header-->
-        
+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -198,7 +198,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading2">
         <a href="01-tidiness.html">1. Data Tidiness</a>
     </div><!--/div.accordion-header-->
-        
+
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@@ -207,7 +207,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading3">
         <a href="02-project-planning.html">2. Planning for NGS Projects</a>
     </div><!--/div.accordion-header-->
-        
+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -216,7 +216,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
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         <a href="03-ncbi-sra.html">3. Examining Data on the NCBI SRA Database</a>
     </div><!--/div.accordion-header-->
-        
+
   </div><!--/div.accordion-item-->
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@@ -248,10 +248,10 @@ <h2 class="accordion-header" id="flush-headingTwelve">
               </div>
             </div>
             <hr class="half-width resources"><a href="aio.html">See all in one page</a>
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@@ -274,18 +274,18 @@ <h1>Learner Profiles</h1>
       		<footer class="row footer mx-md-3"><hr><div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/README.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/datacarpentry/organization-genomics/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
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 				<p><a href="https://github.com/datacarpentry/organization-genomics/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:team@carpentries.org">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
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+
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   "identifier": "https://datacarpentry.github.io/organization-genomics/profiles.html",
   "dateCreated": "2015-03-24",
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diff --git a/reference.html b/reference.html
index c77f5be6..b159b4d1 100644
--- a/reference.html
+++ b/reference.html
@@ -46,7 +46,7 @@
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+
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           <div class="accordion accordion-flush" id="accordionFlush11">
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         <a href="index.html">Summary and Setup</a>
     </div><!--/div.accordion-header-->
-        
+
   </div><!--/div.accordion-item-->
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@@ -198,7 +198,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading2">
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     </div><!--/div.accordion-header-->
-        
+
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@@ -207,7 +207,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
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         <a href="02-project-planning.html">2. Planning for NGS Projects</a>
     </div><!--/div.accordion-header-->
-        
+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -216,7 +216,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
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         <a href="03-ncbi-sra.html">3. Examining Data on the NCBI SRA Database</a>
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+
   </div><!--/div.accordion-item-->
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@@ -248,10 +248,10 @@ <h2 class="accordion-header" id="flush-headingTwelve">
               </div>
             </div>
             <hr class="half-width resources"><a href="aio.html">See all in one page</a>
-            
+
 
             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
-            
+
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         <h1>Glossary</h1>
         <p>Last updated on 2023-05-02 |
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+
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-        
-        
-        
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+
+
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-<section id="glossary"><h2 class="section-heading">Glossary<a class="anchor" aria-label="anchor" href="#glossary"></a>
-</h2>
+<section><h2 class="section-heading" id="glossary">Glossary<a class="anchor" aria-label="anchor" href="#glossary"></a>
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 <hr class="half-width"><p>{:auto_ids}<br>
 accession : a unique identifier assigned to each sequence or set of
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@@ -413,18 +413,18 @@ <h1>Glossary</h1>
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         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/learners/reference.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/datacarpentry/organization-genomics/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/datacarpentry/organization-genomics/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/datacarpentry/organization-genomics/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:team@carpentries.org">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
-        
+
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