diff --git a/AMI-setup.html b/AMI-setup.html
index b8057ee4..9014c770 100644
--- a/AMI-setup.html
+++ b/AMI-setup.html
@@ -333,7 +333,7 @@ <h3 class="accordion-header" id="headingSpoiler1">
   Connect to your Amazon Instance (MacOS/Linux)
   </h3>
 </button>
-<div id="collapseSpoiler1" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
+<div id="collapseSpoiler1" class="accordion-collapse collapse" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
 <div class="accordion-body">
 <ol style="list-style-type: decimal"><li><p>Log into your AWC EC2 Dashboard <a href="https://console.aws.amazon.com/ec2/" class="external-link">https://console.aws.amazon.com/ec2/</a></p></li>
 <li><p>You should see that you have one instance. To proceed, the
@@ -390,7 +390,7 @@ <h3 class="accordion-header" id="headingSpoiler2">
   Connect to your Amazon instance (Windows)
   </h3>
 </button>
-<div id="collapseSpoiler2" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler2" aria-labelledby="headingSpoiler2">
+<div id="collapseSpoiler2" class="accordion-collapse collapse" aria-labelledby="headingSpoiler2" data-bs-parent="#accordionSpoiler2">
 <div class="accordion-body">
 <ol style="list-style-type: decimal"><li><p>Download the PuTTY application at: <a href="https://the.earth.li/~sgtatham/putty/latest/x86/putty.exe" class="external-link">http://the.earth.li/~sgtatham/putty/latest/x86/putty.exe</a></p></li>
 <li><p>Log into your AWC EC2 Dashboard <a href="https://console.aws.amazon.com/ec2/" class="external-link">https://console.aws.amazon.com/ec2/</a></p></li>
diff --git a/index.html b/index.html
index 6adc7ab2..f72a68e5 100644
--- a/index.html
+++ b/index.html
@@ -291,22 +291,22 @@ <h3 class="callout-title">Data<a class="anchor" aria-label="anchor" href="#data"
 <h1 id="workshop-overview">Workshop Overview<a class="anchor" aria-label="anchor" href="#workshop-overview"></a></h1>
 <table class="table"><colgroup><col width="49%"><col width="50%"></colgroup><thead><tr class="header"><th>Lesson</th>
 <th>Overview</th>
-</tr></thead><tbody><tr class="odd"><td><a href="https://%7B%7Bpage.base_url%7D%7D/organization-genomics/" class="external-link">Project
+</tr></thead><tbody><tr class="odd"><td><a href="https://gwu-libraries.github.io/organization-genomics/" class="external-link">Project
 organization and management</a></td>
 <td>Learn how to structure your metadata, organize and document your
 genomics data and bioinformatics workflow, and access data on the NCBI
 sequence read archive (SRA) database.</td>
-</tr><tr class="even"><td><a href="https://%7B%7Bpage.base_url%7D%7D/shell-genomics/" class="external-link">Introduction to
+</tr><tr class="even"><td><a href="https://gwu-libraries.github.io/shell-genomics/" class="external-link">Introduction to
 the command line</a></td>
 <td>Learn to navigate your file system, create, copy, move, and remove
 files and directories, and automate repetitive tasks using scripts and
 wildcards.</td>
-</tr><tr class="odd"><td><a href="https://%7B%7Bpage.base_url%7D%7D/wrangling-genomics/" class="external-link">Data
+</tr><tr class="odd"><td><a href="https://gwu-libraries.github.io/wrangling-genomics/" class="external-link">Data
 wrangling and processing</a></td>
 <td>Use command-line tools to perform quality control, align reads to a
 reference genome, and identify and visualize between-sample
 variation.</td>
-</tr><tr class="even"><td><a href="https://%7B%7Bpage.base_url%7D%7D/cloud-genomics/" class="external-link">Introduction to
+</tr><tr class="even"><td><a href="https://gwu-libraries.github.io/cloud-genomics/" class="external-link">Introduction to
 cloud computing for genomics</a></td>
 <td>Learn how to work with Amazon AWS cloud computing and how to
 transfer data between your local computer and cloud resources.</td>
@@ -315,8 +315,8 @@ <h1 id="workshop-overview">Workshop Overview<a class="anchor" aria-label="anchor
 <h1 id="optional-additional-lessons">Optional Additional Lessons<a class="anchor" aria-label="anchor" href="#optional-additional-lessons"></a></h1>
 <table class="table"><colgroup><col width="49%"><col width="50%"></colgroup><thead><tr class="header"><th>Lesson</th>
 <th>Overview</th>
-</tr></thead><tbody><tr class="odd"><td><a href="https://%7B%7Bpage.base_url%7D%7D/genomics-r-intro/" class="external-link">Intro
-to R and RStudio for Genomics</a></td>
+</tr></thead><tbody><tr class="odd"><td><a href="https://gwu-libraries.github.io/genomics-r-intro/" class="external-link">Intro to
+R and RStudio for Genomics</a></td>
 <td>Use R to analyze and visualize between-sample variation.</td>
 </tr></tbody></table></div>
 <div class="section level1">
@@ -331,40 +331,40 @@ <h1 id="teaching-platform">Teaching Platform<a class="anchor" aria-label="anchor
 <h1 id="common-schedules">Common Schedules<a class="anchor" aria-label="anchor" href="#common-schedules"></a></h1>
 <div class="section level3">
 <h3 id="schedule-a-2-days-or-4-half-days">Schedule A (2 days OR 4 half days)<a class="anchor" aria-label="anchor" href="#schedule-a-2-days-or-4-half-days"></a></h3>
-<ul><li>Half-day 1: <a href="https://datacarpentry.github.io/organization-genomics/" class="external-link">Project
-organization and management</a> &amp; <a href="https://datacarpentry.github.io/shell-genomics/" class="external-link">Introduction to
+<ul><li>Half-day 1: <a href="https://gwu-libraries.github.io/organization-genomics/" class="external-link">Project
+organization and management</a> &amp; <a href="https://gwu-libraries.github.io/shell-genomics/" class="external-link">Introduction to
 the command line</a>
 </li>
-<li>Half-day 2: <a href="https://datacarpentry.github.io/shell-genomics/" class="external-link">Introduction to
+<li>Half-day 2: <a href="https://gwu-libraries.github.io/shell-genomics/" class="external-link">Introduction to
 the command line</a> (continued).</li>
-<li>Half-day 3 &amp; 4 : <a href="https://datacarpentry.github.io/wrangling-genomics/" class="external-link">Data
+<li>Half-day 3 &amp; 4 : <a href="https://gwu-libraries.github.io/wrangling-genomics/" class="external-link">Data
 wrangling and processing</a>
 </li>
 </ul></div>
 <div class="section level3">
 <h3 id="schedule-b-2-days-or-4-half-days">Schedule B (2 days OR 4 half days)<a class="anchor" aria-label="anchor" href="#schedule-b-2-days-or-4-half-days"></a></h3>
-<ul><li>Half-day 1: <a href="https://datacarpentry.github.io/organization-genomics/" class="external-link">Project
-organization and management</a> &amp; <a href="https://datacarpentry.github.io/shell-genomics/" class="external-link">Introduction to
+<ul><li>Half-day 1: <a href="https://gwu-libraries.github.io/organization-genomics/" class="external-link">Project
+organization and management</a> &amp; <a href="https://gwu-libraries.github.io/shell-genomics/" class="external-link">Introduction to
 the command line</a>
 </li>
-<li>Half-day 2: <a href="https://datacarpentry.github.io/shell-genomics/" class="external-link">Introduction to
+<li>Half-day 2: <a href="https://gwu-libraries.github.io/shell-genomics/" class="external-link">Introduction to
 the command line</a> (continued)</li>
-<li>Half-day 3 &amp; 4: <a href="https://datacarpentry.org/genomics-r-intro/" class="external-link">Intro to R and
+<li>Half-day 3 &amp; 4: <a href="https://gwu-libraries.github.io/genomics-r-intro/" class="external-link">Intro to R and
 RStudio for Genomics</a>
 </li>
 </ul></div>
 <div class="section level3">
 <h3 id="schedule-c-3-days-or-6-half-days">Schedule C (3 days OR 6 half days)<a class="anchor" aria-label="anchor" href="#schedule-c-3-days-or-6-half-days"></a></h3>
-<ul><li>Half-day 1: <a href="https://datacarpentry.github.io/organization-genomics/" class="external-link">Project
-organization and management</a> &amp; <a href="https://datacarpentry.github.io/shell-genomics/" class="external-link">Introduction to
+<ul><li>Half-day 1: <a href="https://gwu-libraries.github.io/organization-genomics/" class="external-link">Project
+organization and management</a> &amp; <a href="https://gwu-libraries.github.io/shell-genomics/" class="external-link">Introduction to
 the command line</a>
 </li>
-<li>Half-day 2: <a href="https://datacarpentry.github.io/shell-genomics/" class="external-link">Introduction to
+<li>Half-day 2: <a href="https://gwu-libraries.github.io/shell-genomics/" class="external-link">Introduction to
 the command line</a> (continued)</li>
-<li>Half-day 3 &amp; 4 : <a href="https://datacarpentry.github.io/wrangling-genomics/" class="external-link">Data
+<li>Half-day 3 &amp; 4 : <a href="https://gwu-libraries.github.io/wrangling-genomics/" class="external-link">Data
 wrangling and processing</a>
 </li>
-<li>Half-day 5 &amp; 6: <a href="https://datacarpentry.org/genomics-r-intro/" class="external-link">Intro to R and
+<li>Half-day 5 &amp; 6: <a href="https://gwu-libraries.github.io/genomics-r-intro/" class="external-link">Intro to R and
 RStudio for Genomics</a>
 </li>
 </ul></div>
@@ -399,7 +399,7 @@ <h3 class="accordion-header" id="headingSpoiler1">
   Windows
   </h3>
 </button>
-<div id="collapseSpoiler1" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
+<div id="collapseSpoiler1" class="accordion-collapse collapse" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
 <div class="accordion-body">
 <ul><li>Visit <a href="https://www.libreoffice.org/download/libreoffice-fresh/" class="external-link">the
 LibreOffice installation page</a>. The version for Windows should
@@ -479,7 +479,7 @@ <h3 class="accordion-header" id="headingSpoiler2">
   Mac OS X
   </h3>
 </button>
-<div id="collapseSpoiler2" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler2" aria-labelledby="headingSpoiler2">
+<div id="collapseSpoiler2" class="accordion-collapse collapse" aria-labelledby="headingSpoiler2" data-bs-parent="#accordionSpoiler2">
 <div class="accordion-body">
 <ul><li>Visit <a href="https://www.libreoffice.org/download/libreoffice-fresh/" class="external-link">the
 LibreOffice installation page</a>. The version for Mac should
@@ -501,7 +501,7 @@ <h3 class="accordion-header" id="headingSpoiler3">
   Linux
   </h3>
 </button>
-<div id="collapseSpoiler3" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler3" aria-labelledby="headingSpoiler3">
+<div id="collapseSpoiler3" class="accordion-collapse collapse" aria-labelledby="headingSpoiler3" data-bs-parent="#accordionSpoiler3">
 <div class="accordion-body">
 <ul><li>Visit <a href="https://www.libreoffice.org/download/libreoffice-fresh/" class="external-link">the
 LibreOffice installation page</a>. The version for Linux should
@@ -621,7 +621,7 @@ <h3 class="accordion-header" id="headingSpoiler4">
   Linux
   </h3>
 </button>
-<div id="collapseSpoiler4" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler4" aria-labelledby="headingSpoiler4">
+<div id="collapseSpoiler4" class="accordion-collapse collapse" aria-labelledby="headingSpoiler4" data-bs-parent="#accordionSpoiler4">
 <div class="accordion-body">
 <p>To install Conda, type:</p>
 <div class="codewrapper sourceCode" id="cb1">
@@ -644,7 +644,7 @@ <h3 class="accordion-header" id="headingSpoiler5">
   MacOS
   </h3>
 </button>
-<div id="collapseSpoiler5" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler5" aria-labelledby="headingSpoiler5">
+<div id="collapseSpoiler5" class="accordion-collapse collapse" aria-labelledby="headingSpoiler5" data-bs-parent="#accordionSpoiler5">
 <div class="accordion-body">
 <p>To install Conda, type:</p>
 <div class="codewrapper sourceCode" id="cb2">
@@ -670,7 +670,7 @@ <h3 class="accordion-header" id="headingSpoiler6">
   MacOS
   </h3>
 </button>
-<div id="collapseSpoiler6" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler6" aria-labelledby="headingSpoiler6">
+<div id="collapseSpoiler6" class="accordion-collapse collapse" aria-labelledby="headingSpoiler6" data-bs-parent="#accordionSpoiler6">
 <div class="accordion-body">
 <p>To install FastQC, type:</p>
 <div class="codewrapper sourceCode" id="cb3">
@@ -690,7 +690,7 @@ <h3 class="accordion-header" id="headingSpoiler7">
   FastQC Source Code Installation
   </h3>
 </button>
-<div id="collapseSpoiler7" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler7" aria-labelledby="headingSpoiler7">
+<div id="collapseSpoiler7" class="accordion-collapse collapse" aria-labelledby="headingSpoiler7" data-bs-parent="#accordionSpoiler7">
 <div class="accordion-body">
 <p>If you prefer to install from source, follow the directions
 below:</p>
@@ -736,7 +736,7 @@ <h3 class="accordion-header" id="headingSpoiler8">
   MacOS
   </h3>
 </button>
-<div id="collapseSpoiler8" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler8" aria-labelledby="headingSpoiler8">
+<div id="collapseSpoiler8" class="accordion-collapse collapse" aria-labelledby="headingSpoiler8" data-bs-parent="#accordionSpoiler8">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb8">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -755,7 +755,7 @@ <h3 class="accordion-header" id="headingSpoiler9">
   Trimmomatic Source Code Installation
   </h3>
 </button>
-<div id="collapseSpoiler9" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler9" aria-labelledby="headingSpoiler9">
+<div id="collapseSpoiler9" class="accordion-collapse collapse" aria-labelledby="headingSpoiler9" data-bs-parent="#accordionSpoiler9">
 <div class="accordion-body">
 <p>If you prefer to install from source, follow the directions
 below:</p>
@@ -794,7 +794,7 @@ <h3 class="accordion-header" id="headingSpoiler10">
   Simplify the Invocation, or to Test your installation if you installed with miniconda3:
   </h3>
 </button>
-<div id="collapseSpoiler10" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler10" aria-labelledby="headingSpoiler10">
+<div id="collapseSpoiler10" class="accordion-collapse collapse" aria-labelledby="headingSpoiler10" data-bs-parent="#accordionSpoiler10">
 <div class="accordion-body">
 <p>To simplify the invocation you could also create a script in the
 ~/bin folder:</p>
@@ -826,7 +826,7 @@ <h3 class="accordion-header" id="headingSpoiler11">
   MacOS
   </h3>
 </button>
-<div id="collapseSpoiler11" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler11" aria-labelledby="headingSpoiler11">
+<div id="collapseSpoiler11" class="accordion-collapse collapse" aria-labelledby="headingSpoiler11" data-bs-parent="#accordionSpoiler11">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb15">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -845,7 +845,7 @@ <h3 class="accordion-header" id="headingSpoiler12">
   BWA Source Code Installation
   </h3>
 </button>
-<div id="collapseSpoiler12" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler12" aria-labelledby="headingSpoiler12">
+<div id="collapseSpoiler12" class="accordion-collapse collapse" aria-labelledby="headingSpoiler12" data-bs-parent="#accordionSpoiler12">
 <div class="accordion-body">
 <p>If you prefer to install from source, follow the instructions
 below:</p>
@@ -880,7 +880,7 @@ <h3 class="accordion-header" id="headingSpoiler13">
   MacOS
   </h3>
 </button>
-<div id="collapseSpoiler13" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler13" aria-labelledby="headingSpoiler13">
+<div id="collapseSpoiler13" class="accordion-collapse collapse" aria-labelledby="headingSpoiler13" data-bs-parent="#accordionSpoiler13">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb18">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -915,7 +915,7 @@ <h3 class="accordion-header" id="headingSpoiler14">
   SAMtools Source Code Installation
   </h3>
 </button>
-<div id="collapseSpoiler14" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler14" aria-labelledby="headingSpoiler14">
+<div id="collapseSpoiler14" class="accordion-collapse collapse" aria-labelledby="headingSpoiler14" data-bs-parent="#accordionSpoiler14">
 <div class="accordion-body">
 <p>If you prefer to install from source, follow the instructions
 below:</p>
@@ -956,7 +956,7 @@ <h3 class="accordion-header" id="headingSpoiler15">
   MacOS
   </h3>
 </button>
-<div id="collapseSpoiler15" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler15" aria-labelledby="headingSpoiler15">
+<div id="collapseSpoiler15" class="accordion-collapse collapse" aria-labelledby="headingSpoiler15" data-bs-parent="#accordionSpoiler15">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb22">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -975,7 +975,7 @@ <h3 class="accordion-header" id="headingSpoiler16">
   BCF tools Source Code Installation
   </h3>
 </button>
-<div id="collapseSpoiler16" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler16" aria-labelledby="headingSpoiler16">
+<div id="collapseSpoiler16" class="accordion-collapse collapse" aria-labelledby="headingSpoiler16" data-bs-parent="#accordionSpoiler16">
 <div class="accordion-body">
 <p>If you prefer to install from source, follow the instructions
 below:</p>
diff --git a/instructor/AMI-setup.html b/instructor/AMI-setup.html
index 73d67077..670bb16f 100644
--- a/instructor/AMI-setup.html
+++ b/instructor/AMI-setup.html
@@ -329,7 +329,7 @@ <h3 class="accordion-header" id="headingSpoiler1">
   Connect to your Amazon Instance (MacOS/Linux)
   </h3>
 </button>
-<div id="collapseSpoiler1" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
+<div id="collapseSpoiler1" class="accordion-collapse collapse" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
 <div class="accordion-body">
 <ol style="list-style-type: decimal"><li><p>Log into your AWC EC2 Dashboard <a href="https://console.aws.amazon.com/ec2/" class="external-link">https://console.aws.amazon.com/ec2/</a></p></li>
 <li><p>You should see that you have one instance. To proceed, the
@@ -386,7 +386,7 @@ <h3 class="accordion-header" id="headingSpoiler2">
   Connect to your Amazon instance (Windows)
   </h3>
 </button>
-<div id="collapseSpoiler2" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler2" aria-labelledby="headingSpoiler2">
+<div id="collapseSpoiler2" class="accordion-collapse collapse" aria-labelledby="headingSpoiler2" data-bs-parent="#accordionSpoiler2">
 <div class="accordion-body">
 <ol style="list-style-type: decimal"><li><p>Download the PuTTY application at: <a href="https://the.earth.li/~sgtatham/putty/latest/x86/putty.exe" class="external-link">http://the.earth.li/~sgtatham/putty/latest/x86/putty.exe</a></p></li>
 <li><p>Log into your AWC EC2 Dashboard <a href="https://console.aws.amazon.com/ec2/" class="external-link">https://console.aws.amazon.com/ec2/</a></p></li>
diff --git a/instructor/index.html b/instructor/index.html
index 19ecc2fd..d6fd4201 100644
--- a/instructor/index.html
+++ b/instructor/index.html
@@ -285,22 +285,22 @@ <h3 class="callout-title">Data<a class="anchor" aria-label="anchor" href="#data"
 <h1 id="workshop-overview">Workshop Overview<a class="anchor" aria-label="anchor" href="#workshop-overview"></a></h1>
 <table class="table"><colgroup><col width="49%"><col width="50%"></colgroup><thead><tr class="header"><th>Lesson</th>
 <th>Overview</th>
-</tr></thead><tbody><tr class="odd"><td><a href="https://%7B%7Bpage.base_url%7D%7D/organization-genomics/" class="external-link">Project
+</tr></thead><tbody><tr class="odd"><td><a href="https://gwu-libraries.github.io/organization-genomics/" class="external-link">Project
 organization and management</a></td>
 <td>Learn how to structure your metadata, organize and document your
 genomics data and bioinformatics workflow, and access data on the NCBI
 sequence read archive (SRA) database.</td>
-</tr><tr class="even"><td><a href="https://%7B%7Bpage.base_url%7D%7D/shell-genomics/" class="external-link">Introduction to
+</tr><tr class="even"><td><a href="https://gwu-libraries.github.io/shell-genomics/" class="external-link">Introduction to
 the command line</a></td>
 <td>Learn to navigate your file system, create, copy, move, and remove
 files and directories, and automate repetitive tasks using scripts and
 wildcards.</td>
-</tr><tr class="odd"><td><a href="https://%7B%7Bpage.base_url%7D%7D/wrangling-genomics/" class="external-link">Data
+</tr><tr class="odd"><td><a href="https://gwu-libraries.github.io/wrangling-genomics/" class="external-link">Data
 wrangling and processing</a></td>
 <td>Use command-line tools to perform quality control, align reads to a
 reference genome, and identify and visualize between-sample
 variation.</td>
-</tr><tr class="even"><td><a href="https://%7B%7Bpage.base_url%7D%7D/cloud-genomics/" class="external-link">Introduction to
+</tr><tr class="even"><td><a href="https://gwu-libraries.github.io/cloud-genomics/" class="external-link">Introduction to
 cloud computing for genomics</a></td>
 <td>Learn how to work with Amazon AWS cloud computing and how to
 transfer data between your local computer and cloud resources.</td>
@@ -309,8 +309,8 @@ <h1 id="workshop-overview">Workshop Overview<a class="anchor" aria-label="anchor
 <h1 id="optional-additional-lessons">Optional Additional Lessons<a class="anchor" aria-label="anchor" href="#optional-additional-lessons"></a></h1>
 <table class="table"><colgroup><col width="49%"><col width="50%"></colgroup><thead><tr class="header"><th>Lesson</th>
 <th>Overview</th>
-</tr></thead><tbody><tr class="odd"><td><a href="https://%7B%7Bpage.base_url%7D%7D/genomics-r-intro/" class="external-link">Intro
-to R and RStudio for Genomics</a></td>
+</tr></thead><tbody><tr class="odd"><td><a href="https://gwu-libraries.github.io/genomics-r-intro/" class="external-link">Intro to
+R and RStudio for Genomics</a></td>
 <td>Use R to analyze and visualize between-sample variation.</td>
 </tr></tbody></table></div>
 <div class="section level1">
@@ -325,40 +325,40 @@ <h1 id="teaching-platform">Teaching Platform<a class="anchor" aria-label="anchor
 <h1 id="common-schedules">Common Schedules<a class="anchor" aria-label="anchor" href="#common-schedules"></a></h1>
 <div class="section level3">
 <h3 id="schedule-a-2-days-or-4-half-days">Schedule A (2 days OR 4 half days)<a class="anchor" aria-label="anchor" href="#schedule-a-2-days-or-4-half-days"></a></h3>
-<ul><li>Half-day 1: <a href="https://datacarpentry.github.io/organization-genomics/" class="external-link">Project
-organization and management</a> &amp; <a href="https://datacarpentry.github.io/shell-genomics/" class="external-link">Introduction to
+<ul><li>Half-day 1: <a href="https://gwu-libraries.github.io/organization-genomics/" class="external-link">Project
+organization and management</a> &amp; <a href="https://gwu-libraries.github.io/shell-genomics/" class="external-link">Introduction to
 the command line</a>
 </li>
-<li>Half-day 2: <a href="https://datacarpentry.github.io/shell-genomics/" class="external-link">Introduction to
+<li>Half-day 2: <a href="https://gwu-libraries.github.io/shell-genomics/" class="external-link">Introduction to
 the command line</a> (continued).</li>
-<li>Half-day 3 &amp; 4 : <a href="https://datacarpentry.github.io/wrangling-genomics/" class="external-link">Data
+<li>Half-day 3 &amp; 4 : <a href="https://gwu-libraries.github.io/wrangling-genomics/" class="external-link">Data
 wrangling and processing</a>
 </li>
 </ul></div>
 <div class="section level3">
 <h3 id="schedule-b-2-days-or-4-half-days">Schedule B (2 days OR 4 half days)<a class="anchor" aria-label="anchor" href="#schedule-b-2-days-or-4-half-days"></a></h3>
-<ul><li>Half-day 1: <a href="https://datacarpentry.github.io/organization-genomics/" class="external-link">Project
-organization and management</a> &amp; <a href="https://datacarpentry.github.io/shell-genomics/" class="external-link">Introduction to
+<ul><li>Half-day 1: <a href="https://gwu-libraries.github.io/organization-genomics/" class="external-link">Project
+organization and management</a> &amp; <a href="https://gwu-libraries.github.io/shell-genomics/" class="external-link">Introduction to
 the command line</a>
 </li>
-<li>Half-day 2: <a href="https://datacarpentry.github.io/shell-genomics/" class="external-link">Introduction to
+<li>Half-day 2: <a href="https://gwu-libraries.github.io/shell-genomics/" class="external-link">Introduction to
 the command line</a> (continued)</li>
-<li>Half-day 3 &amp; 4: <a href="https://datacarpentry.org/genomics-r-intro/" class="external-link">Intro to R and
+<li>Half-day 3 &amp; 4: <a href="https://gwu-libraries.github.io/genomics-r-intro/" class="external-link">Intro to R and
 RStudio for Genomics</a>
 </li>
 </ul></div>
 <div class="section level3">
 <h3 id="schedule-c-3-days-or-6-half-days">Schedule C (3 days OR 6 half days)<a class="anchor" aria-label="anchor" href="#schedule-c-3-days-or-6-half-days"></a></h3>
-<ul><li>Half-day 1: <a href="https://datacarpentry.github.io/organization-genomics/" class="external-link">Project
-organization and management</a> &amp; <a href="https://datacarpentry.github.io/shell-genomics/" class="external-link">Introduction to
+<ul><li>Half-day 1: <a href="https://gwu-libraries.github.io/organization-genomics/" class="external-link">Project
+organization and management</a> &amp; <a href="https://gwu-libraries.github.io/shell-genomics/" class="external-link">Introduction to
 the command line</a>
 </li>
-<li>Half-day 2: <a href="https://datacarpentry.github.io/shell-genomics/" class="external-link">Introduction to
+<li>Half-day 2: <a href="https://gwu-libraries.github.io/shell-genomics/" class="external-link">Introduction to
 the command line</a> (continued)</li>
-<li>Half-day 3 &amp; 4 : <a href="https://datacarpentry.github.io/wrangling-genomics/" class="external-link">Data
+<li>Half-day 3 &amp; 4 : <a href="https://gwu-libraries.github.io/wrangling-genomics/" class="external-link">Data
 wrangling and processing</a>
 </li>
-<li>Half-day 5 &amp; 6: <a href="https://datacarpentry.org/genomics-r-intro/" class="external-link">Intro to R and
+<li>Half-day 5 &amp; 6: <a href="https://gwu-libraries.github.io/genomics-r-intro/" class="external-link">Intro to R and
 RStudio for Genomics</a>
 </li>
 </ul></div>
@@ -398,7 +398,7 @@ <h3 class="accordion-header" id="headingSpoiler1">
   Windows
   </h3>
 </button>
-<div id="collapseSpoiler1" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
+<div id="collapseSpoiler1" class="accordion-collapse collapse" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
 <div class="accordion-body">
 <ul><li>Visit <a href="https://www.libreoffice.org/download/libreoffice-fresh/" class="external-link">the
 LibreOffice installation page</a>. The version for Windows should
@@ -478,7 +478,7 @@ <h3 class="accordion-header" id="headingSpoiler2">
   Mac OS X
   </h3>
 </button>
-<div id="collapseSpoiler2" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler2" aria-labelledby="headingSpoiler2">
+<div id="collapseSpoiler2" class="accordion-collapse collapse" aria-labelledby="headingSpoiler2" data-bs-parent="#accordionSpoiler2">
 <div class="accordion-body">
 <ul><li>Visit <a href="https://www.libreoffice.org/download/libreoffice-fresh/" class="external-link">the
 LibreOffice installation page</a>. The version for Mac should
@@ -500,7 +500,7 @@ <h3 class="accordion-header" id="headingSpoiler3">
   Linux
   </h3>
 </button>
-<div id="collapseSpoiler3" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler3" aria-labelledby="headingSpoiler3">
+<div id="collapseSpoiler3" class="accordion-collapse collapse" aria-labelledby="headingSpoiler3" data-bs-parent="#accordionSpoiler3">
 <div class="accordion-body">
 <ul><li>Visit <a href="https://www.libreoffice.org/download/libreoffice-fresh/" class="external-link">the
 LibreOffice installation page</a>. The version for Linux should
@@ -620,7 +620,7 @@ <h3 class="accordion-header" id="headingSpoiler4">
   Linux
   </h3>
 </button>
-<div id="collapseSpoiler4" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler4" aria-labelledby="headingSpoiler4">
+<div id="collapseSpoiler4" class="accordion-collapse collapse" aria-labelledby="headingSpoiler4" data-bs-parent="#accordionSpoiler4">
 <div class="accordion-body">
 <p>To install Conda, type:</p>
 <div class="codewrapper sourceCode" id="cb1">
@@ -643,7 +643,7 @@ <h3 class="accordion-header" id="headingSpoiler5">
   MacOS
   </h3>
 </button>
-<div id="collapseSpoiler5" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler5" aria-labelledby="headingSpoiler5">
+<div id="collapseSpoiler5" class="accordion-collapse collapse" aria-labelledby="headingSpoiler5" data-bs-parent="#accordionSpoiler5">
 <div class="accordion-body">
 <p>To install Conda, type:</p>
 <div class="codewrapper sourceCode" id="cb2">
@@ -669,7 +669,7 @@ <h3 class="accordion-header" id="headingSpoiler6">
   MacOS
   </h3>
 </button>
-<div id="collapseSpoiler6" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler6" aria-labelledby="headingSpoiler6">
+<div id="collapseSpoiler6" class="accordion-collapse collapse" aria-labelledby="headingSpoiler6" data-bs-parent="#accordionSpoiler6">
 <div class="accordion-body">
 <p>To install FastQC, type:</p>
 <div class="codewrapper sourceCode" id="cb3">
@@ -689,7 +689,7 @@ <h3 class="accordion-header" id="headingSpoiler7">
   FastQC Source Code Installation
   </h3>
 </button>
-<div id="collapseSpoiler7" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler7" aria-labelledby="headingSpoiler7">
+<div id="collapseSpoiler7" class="accordion-collapse collapse" aria-labelledby="headingSpoiler7" data-bs-parent="#accordionSpoiler7">
 <div class="accordion-body">
 <p>If you prefer to install from source, follow the directions
 below:</p>
@@ -735,7 +735,7 @@ <h3 class="accordion-header" id="headingSpoiler8">
   MacOS
   </h3>
 </button>
-<div id="collapseSpoiler8" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler8" aria-labelledby="headingSpoiler8">
+<div id="collapseSpoiler8" class="accordion-collapse collapse" aria-labelledby="headingSpoiler8" data-bs-parent="#accordionSpoiler8">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb8">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -754,7 +754,7 @@ <h3 class="accordion-header" id="headingSpoiler9">
   Trimmomatic Source Code Installation
   </h3>
 </button>
-<div id="collapseSpoiler9" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler9" aria-labelledby="headingSpoiler9">
+<div id="collapseSpoiler9" class="accordion-collapse collapse" aria-labelledby="headingSpoiler9" data-bs-parent="#accordionSpoiler9">
 <div class="accordion-body">
 <p>If you prefer to install from source, follow the directions
 below:</p>
@@ -793,7 +793,7 @@ <h3 class="accordion-header" id="headingSpoiler10">
   Simplify the Invocation, or to Test your installation if you installed with miniconda3:
   </h3>
 </button>
-<div id="collapseSpoiler10" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler10" aria-labelledby="headingSpoiler10">
+<div id="collapseSpoiler10" class="accordion-collapse collapse" aria-labelledby="headingSpoiler10" data-bs-parent="#accordionSpoiler10">
 <div class="accordion-body">
 <p>To simplify the invocation you could also create a script in the
 ~/bin folder:</p>
@@ -825,7 +825,7 @@ <h3 class="accordion-header" id="headingSpoiler11">
   MacOS
   </h3>
 </button>
-<div id="collapseSpoiler11" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler11" aria-labelledby="headingSpoiler11">
+<div id="collapseSpoiler11" class="accordion-collapse collapse" aria-labelledby="headingSpoiler11" data-bs-parent="#accordionSpoiler11">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb15">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -844,7 +844,7 @@ <h3 class="accordion-header" id="headingSpoiler12">
   BWA Source Code Installation
   </h3>
 </button>
-<div id="collapseSpoiler12" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler12" aria-labelledby="headingSpoiler12">
+<div id="collapseSpoiler12" class="accordion-collapse collapse" aria-labelledby="headingSpoiler12" data-bs-parent="#accordionSpoiler12">
 <div class="accordion-body">
 <p>If you prefer to install from source, follow the instructions
 below:</p>
@@ -879,7 +879,7 @@ <h3 class="accordion-header" id="headingSpoiler13">
   MacOS
   </h3>
 </button>
-<div id="collapseSpoiler13" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler13" aria-labelledby="headingSpoiler13">
+<div id="collapseSpoiler13" class="accordion-collapse collapse" aria-labelledby="headingSpoiler13" data-bs-parent="#accordionSpoiler13">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb18">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -914,7 +914,7 @@ <h3 class="accordion-header" id="headingSpoiler14">
   SAMtools Source Code Installation
   </h3>
 </button>
-<div id="collapseSpoiler14" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler14" aria-labelledby="headingSpoiler14">
+<div id="collapseSpoiler14" class="accordion-collapse collapse" aria-labelledby="headingSpoiler14" data-bs-parent="#accordionSpoiler14">
 <div class="accordion-body">
 <p>If you prefer to install from source, follow the instructions
 below:</p>
@@ -955,7 +955,7 @@ <h3 class="accordion-header" id="headingSpoiler15">
   MacOS
   </h3>
 </button>
-<div id="collapseSpoiler15" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler15" aria-labelledby="headingSpoiler15">
+<div id="collapseSpoiler15" class="accordion-collapse collapse" aria-labelledby="headingSpoiler15" data-bs-parent="#accordionSpoiler15">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb22">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -974,7 +974,7 @@ <h3 class="accordion-header" id="headingSpoiler16">
   BCF tools Source Code Installation
   </h3>
 </button>
-<div id="collapseSpoiler16" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler16" aria-labelledby="headingSpoiler16">
+<div id="collapseSpoiler16" class="accordion-collapse collapse" aria-labelledby="headingSpoiler16" data-bs-parent="#accordionSpoiler16">
 <div class="accordion-body">
 <p>If you prefer to install from source, follow the instructions
 below:</p>
diff --git a/md5sum.txt b/md5sum.txt
index 4925b178..724ad1d1 100644
--- a/md5sum.txt
+++ b/md5sum.txt
@@ -2,7 +2,7 @@
 "CODE_OF_CONDUCT.md" "d4d213107229d04d444bd8f94cbe2c42" "site/built/CODE_OF_CONDUCT.md" "2023-09-19"
 "LICENSE.md" "8040c7857a1f2f328144193eef549203" "site/built/LICENSE.md" "2023-09-19"
 "config.yaml" "e0f88b2fa9a955366790c7554c781b0d" "site/built/config.yaml" "2023-09-19"
-"index.md" "48dd341443c95f48c19f94746ecd785b" "site/built/index.md" "2024-07-08"
+"index.md" "2be9d09cbcf4412e953b6dc9412261ad" "site/built/index.md" "2024-07-08"
 "instructors/AMI-setup.md" "64ecb146cd91d020872034b88ed145b7" "site/built/AMI-setup.md" "2023-09-19"
 "instructors/faq.md" "fb685c501943b1679eff3f491651824d" "site/built/faq.md" "2024-01-08"
 "instructors/instructor-notes.md" "b963ac0859abcde3d03bb7c14fa38f69" "site/built/instructor-notes.md" "2023-09-19"
diff --git a/pkgdown.yml b/pkgdown.yml
index 98c152db..038579bb 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -2,4 +2,4 @@ pandoc: 3.1.11
 pkgdown: 2.1.0
 pkgdown_sha: ~
 articles: {}
-last_built: 2024-07-08T12:31Z
+last_built: 2024-07-08T12:35Z

Lesson	Overview
Project +
Project organization and management	Learn how to structure your metadata, organize and document your genomics data and bioinformatics workflow, and access data on the NCBI sequence read archive (SRA) database.
Introduction to +
Introduction to the command line	Learn to navigate your file system, create, copy, move, and remove files and directories, and automate repetitive tasks using scripts and wildcards.
Data +
Data wrangling and processing	Use command-line tools to perform quality control, align reads to a reference genome, and identify and visualize between-sample variation.
Introduction to +
Introduction to cloud computing for genomics	Learn how to work with Amazon AWS cloud computing and how to transfer data between your local computer and cloud resources.
Lesson	Overview
Intro -to R and RStudio for Genomics
Intro to +R and RStudio for Genomics	Use R to analyze and visualize between-sample variation.