From 3fa9c4303621f4c3a6c79dc9dd40e7365f39f2d0 Mon Sep 17 00:00:00 2001
From: jhudsl-robot <itcrtrainingnetwork@gmail.com>
Date: Wed, 25 Oct 2023 18:18:27 +0000
Subject: [PATCH] Render bookdown

---
 docs/404.html               |  11 +-
 docs/About.md               |   2 +-
 docs/about-the-authors.html |  17 +--
 docs/index.html             |  27 +++--
 docs/index.md               |   9 +-
 docs/materials.html         | 209 ++++++++++++++++++++++++++++++++++++
 docs/reference-keys.txt     |   2 +
 docs/references.html        |  21 ++--
 docs/search_index.json      |   2 +-
 9 files changed, 258 insertions(+), 42 deletions(-)
 create mode 100644 docs/materials.html

diff --git a/docs/404.html b/docs/404.html
index 032edcb..af530ef 100644
--- a/docs/404.html
+++ b/docs/404.html
@@ -23,7 +23,7 @@
 
 
 
-<meta name="date" content="2023-10-20" />
+<meta name="date" content="2023-10-25" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />
@@ -83,13 +83,16 @@
 <a href="https://anvilproject.org/" target="_blank"><img src="assets/AnVIL_style/logo-anvil.png" style="width: 80%; padding-left: 15px; padding-top: 8px;"</a>
 
 <li class="divider"></li>
-<li class="chapter" data-level="" data-path="index.html"><a href="index.html"><i class="fa fa-check"></i>About this Resource</a>
+<li class="chapter" data-level="1" data-path="index.html"><a href="index.html"><i class="fa fa-check"></i><b>1</b> Events</a>
 <ul>
 <li class="chapter" data-level="" data-path="index.html"><a href="index.html#upcoming-anvil-events-portal"><i class="fa fa-check"></i>Upcoming AnVIL Events (Portal)</a></li>
-<li class="chapter" data-level="" data-path="index.html"><a href="index.html#anvil-collection"><i class="fa fa-check"></i>AnVIL Collection</a></li>
+</ul></li>
+<li class="chapter" data-level="2" data-path="materials.html"><a href="materials.html"><i class="fa fa-check"></i><b>2</b> Materials</a>
+<ul>
+<li class="chapter" data-level="" data-path="materials.html"><a href="materials.html#anvil-collection"><i class="fa fa-check"></i>AnVIL Collection</a></li>
 </ul></li>
 <li class="chapter" data-level="" data-path="about-the-authors.html"><a href="about-the-authors.html"><i class="fa fa-check"></i>About the Authors</a></li>
-<li class="chapter" data-level="1" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>1</b> References</a></li>
+<li class="chapter" data-level="3" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>3</b> References</a></li>
 <li class="divider"></li>
 <p style="text-align:center;"> <a href="https://github.com/jhudsl/OTTR_Template" target="blank" > This content was published with</a> <a href="https://bookdown.org/" target="blank"> bookdown by: </a> </p>
 <p style="text-align:center;"> <a href="https://hutchdatascience.org/"> The Fred Hutch Data Science Lab </a></p>
diff --git a/docs/About.md b/docs/About.md
index d344cd2..8a39797 100644
--- a/docs/About.md
+++ b/docs/About.md
@@ -53,7 +53,7 @@ These credits are based on our [course contributors table guidelines](https://gi
 ##  collate  en_US.UTF-8                 
 ##  ctype    en_US.UTF-8                 
 ##  tz       Etc/UTC                     
-##  date     2023-10-20                  
+##  date     2023-10-25                  
 ## 
 ## ─ Packages ───────────────────────────────────────────────────────────────────
 ##  package     * version date       lib source                            
diff --git a/docs/about-the-authors.html b/docs/about-the-authors.html
index 18338df..6eeda44 100644
--- a/docs/about-the-authors.html
+++ b/docs/about-the-authors.html
@@ -23,14 +23,14 @@
 
 
 
-<meta name="date" content="2023-10-20" />
+<meta name="date" content="2023-10-25" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />
   <meta name="apple-mobile-web-app-status-bar-style" content="black" />
   
   <link rel="shortcut icon" href="assets/AnVIL_style/anvil_favicon.ico" type="image/x-icon" />
-<link rel="prev" href="index.html"/>
+<link rel="prev" href="materials.html"/>
 <link rel="next" href="references.html"/>
 <script src="libs/header-attrs-2.10/header-attrs.js"></script>
 <script src="libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
@@ -83,13 +83,16 @@
 <a href="https://anvilproject.org/" target="_blank"><img src="assets/AnVIL_style/logo-anvil.png" style="width: 80%; padding-left: 15px; padding-top: 8px;"</a>
 
 <li class="divider"></li>
-<li class="chapter" data-level="" data-path="index.html"><a href="index.html"><i class="fa fa-check"></i>About this Resource</a>
+<li class="chapter" data-level="1" data-path="index.html"><a href="index.html"><i class="fa fa-check"></i><b>1</b> Events</a>
 <ul>
 <li class="chapter" data-level="" data-path="index.html"><a href="index.html#upcoming-anvil-events-portal"><i class="fa fa-check"></i>Upcoming AnVIL Events (Portal)</a></li>
-<li class="chapter" data-level="" data-path="index.html"><a href="index.html#anvil-collection"><i class="fa fa-check"></i>AnVIL Collection</a></li>
+</ul></li>
+<li class="chapter" data-level="2" data-path="materials.html"><a href="materials.html"><i class="fa fa-check"></i><b>2</b> Materials</a>
+<ul>
+<li class="chapter" data-level="" data-path="materials.html"><a href="materials.html#anvil-collection"><i class="fa fa-check"></i>AnVIL Collection</a></li>
 </ul></li>
 <li class="chapter" data-level="" data-path="about-the-authors.html"><a href="about-the-authors.html"><i class="fa fa-check"></i>About the Authors</a></li>
-<li class="chapter" data-level="1" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>1</b> References</a></li>
+<li class="chapter" data-level="3" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>3</b> References</a></li>
 <li class="divider"></li>
 <p style="text-align:center;"> <a href="https://github.com/jhudsl/OTTR_Template" target="blank" > This content was published with</a> <a href="https://bookdown.org/" target="blank"> bookdown by: </a> </p>
 <p style="text-align:center;"> <a href="https://hutchdatascience.org/"> The Fred Hutch Data Science Lab </a></p>
@@ -268,7 +271,7 @@ <h1>About the Authors</h1>
 ##  collate  en_US.UTF-8                 
 ##  ctype    en_US.UTF-8                 
 ##  tz       Etc/UTC                     
-##  date     2023-10-20                  
+##  date     2023-10-25                  
 ## 
 ## ─ Packages ───────────────────────────────────────────────────────────────────
 ##  package     * version date       lib source                            
@@ -340,7 +343,7 @@ <h1>About the Authors</h1>
           </div>
         </div>
       </div>
-<a href="index.html" class="navigation navigation-prev " aria-label="Previous page"><i class="fa fa-angle-left"></i></a>
+<a href="materials.html" class="navigation navigation-prev " aria-label="Previous page"><i class="fa fa-angle-left"></i></a>
 <a href="references.html" class="navigation navigation-next " aria-label="Next page"><i class="fa fa-angle-right"></i></a>
     </div>
   </div>
diff --git a/docs/index.html b/docs/index.html
index 6ce81b5..1888474 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -23,7 +23,7 @@
 
 
 
-<meta name="date" content="2023-10-20" />
+<meta name="date" content="2023-10-25" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />
@@ -31,7 +31,7 @@
   
   <link rel="shortcut icon" href="assets/AnVIL_style/anvil_favicon.ico" type="image/x-icon" />
 
-<link rel="next" href="about-the-authors.html"/>
+<link rel="next" href="materials.html"/>
 <script src="libs/header-attrs-2.10/header-attrs.js"></script>
 <script src="libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
 <script src="https://cdn.jsdelivr.net/npm/fuse.js@6.4.6/dist/fuse.min.js"></script>
@@ -83,13 +83,16 @@
 <a href="https://anvilproject.org/" target="_blank"><img src="assets/AnVIL_style/logo-anvil.png" style="width: 80%; padding-left: 15px; padding-top: 8px;"</a>
 
 <li class="divider"></li>
-<li class="chapter" data-level="" data-path="index.html"><a href="index.html"><i class="fa fa-check"></i>About this Resource</a>
+<li class="chapter" data-level="1" data-path="index.html"><a href="index.html"><i class="fa fa-check"></i><b>1</b> Events</a>
 <ul>
 <li class="chapter" data-level="" data-path="index.html"><a href="index.html#upcoming-anvil-events-portal"><i class="fa fa-check"></i>Upcoming AnVIL Events (Portal)</a></li>
-<li class="chapter" data-level="" data-path="index.html"><a href="index.html#anvil-collection"><i class="fa fa-check"></i>AnVIL Collection</a></li>
+</ul></li>
+<li class="chapter" data-level="2" data-path="materials.html"><a href="materials.html"><i class="fa fa-check"></i><b>2</b> Materials</a>
+<ul>
+<li class="chapter" data-level="" data-path="materials.html"><a href="materials.html#anvil-collection"><i class="fa fa-check"></i>AnVIL Collection</a></li>
 </ul></li>
 <li class="chapter" data-level="" data-path="about-the-authors.html"><a href="about-the-authors.html"><i class="fa fa-check"></i>About the Authors</a></li>
-<li class="chapter" data-level="1" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>1</b> References</a></li>
+<li class="chapter" data-level="3" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>3</b> References</a></li>
 <li class="divider"></li>
 <p style="text-align:center;"> <a href="https://github.com/jhudsl/OTTR_Template" target="blank" > This content was published with</a> <a href="https://bookdown.org/" target="blank"> bookdown by: </a> </p>
 <p style="text-align:center;"> <a href="https://hutchdatascience.org/"> The Fred Hutch Data Science Lab </a></p>
@@ -127,11 +130,10 @@ <h1>
 </div>
 <div id="header">
 <h1 class="title">AnVIL Outreach Dashboard</h1>
-<p class="date"><em>October 20, 2023</em></p>
+<p class="date"><em>October 25, 2023</em></p>
 </div>
-<div id="about-this-resource" class="section level1 unnumbered">
-<h1>About this Resource</h1>
-<p>This is a collection of upcoming opportunities to engage with AnVIL Outreach.</p>
+<div id="events" class="section level1" number="1">
+<h1><span class="header-section-number">Chapter 1</span> Events</h1>
 <div id="upcoming-anvil-events-portal" class="section level2 unnumbered">
 <h2>Upcoming AnVIL Events (Portal)</h2>
 <p>We’d love to see you at an upcoming event! Here are a few upcoming events that might meet your training needs:</p>
@@ -339,11 +341,6 @@ <h2>Upcoming AnVIL Events (Portal)</h2>
 </tr>
 </tbody>
 </table>
-</div>
-<div id="anvil-collection" class="section level2 unnumbered">
-<h2>AnVIL Collection</h2>
-<p>Please check out our full collection of AnVIL and related resources: <a href="https://hutchdatascience.org/AnVIL_Collection/" class="uri">https://hutchdatascience.org/AnVIL_Collection/</a></p>
-
 </div>
 </div>
 <hr>
@@ -360,7 +357,7 @@ <h2>AnVIL Collection</h2>
         </div>
       </div>
 
-<a href="about-the-authors.html" class="navigation navigation-next navigation-unique" aria-label="Next page"><i class="fa fa-angle-right"></i></a>
+<a href="materials.html" class="navigation navigation-next navigation-unique" aria-label="Next page"><i class="fa fa-angle-right"></i></a>
     </div>
   </div>
 <script src="libs/gitbook-2.6.7/js/app.min.js"></script>
diff --git a/docs/index.md b/docs/index.md
index a31c265..0613c41 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -1,6 +1,6 @@
 ---
 title: "AnVIL Outreach Dashboard"
-date: "October 20, 2023"
+date: "October 25, 2023"
 site: bookdown::bookdown_site
 documentclass: book
 bibliography: book.bib
@@ -11,9 +11,7 @@ favicon: assets/AnVIL_style/anvil_favicon.ico
 ---
 
 
-# About this Resource {-}
- 
-This is a collection of upcoming opportunities to engage with AnVIL Outreach.
+# Events
 
 ## Upcoming AnVIL Events (Portal) {-}
 
@@ -116,8 +114,9 @@ We'd love to see you at an upcoming event! Here are a few upcoming events that m
 </tbody>
 </table>
 
+# Materials
+
 ## AnVIL Collection {-}
 
 Please check out our full collection of AnVIL and related resources: https://hutchdatascience.org/AnVIL_Collection/
 
-
diff --git a/docs/materials.html b/docs/materials.html
new file mode 100644
index 0000000..a33fa9e
--- /dev/null
+++ b/docs/materials.html
@@ -0,0 +1,209 @@
+<!DOCTYPE html>
+<html lang="" xml:lang="">
+<head>
+
+  <meta charset="utf-8" />
+  <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+  <title>Chapter 2 Materials | AnVIL Outreach Dashboard</title>
+  <meta name="description" content="Description about Course/Book." />
+  <meta name="generator" content="bookdown 0.24 and GitBook 2.6.7" />
+
+  <meta property="og:title" content="Chapter 2 Materials | AnVIL Outreach Dashboard" />
+  <meta property="og:type" content="book" />
+  
+  
+  <meta property="og:description" content="Description about Course/Book." />
+  
+
+  <meta name="twitter:card" content="summary" />
+  <meta name="twitter:title" content="Chapter 2 Materials | AnVIL Outreach Dashboard" />
+  
+  <meta name="twitter:description" content="Description about Course/Book." />
+  
+
+
+
+<meta name="date" content="2023-10-25" />
+
+  <meta name="viewport" content="width=device-width, initial-scale=1" />
+  <meta name="apple-mobile-web-app-capable" content="yes" />
+  <meta name="apple-mobile-web-app-status-bar-style" content="black" />
+  
+  <link rel="shortcut icon" href="assets/AnVIL_style/anvil_favicon.ico" type="image/x-icon" />
+<link rel="prev" href="index.html"/>
+<link rel="next" href="about-the-authors.html"/>
+<script src="libs/header-attrs-2.10/header-attrs.js"></script>
+<script src="libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
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+<link href="libs/gitbook-2.6.7/css/plugin-search.css" rel="stylesheet" />
+<link href="libs/gitbook-2.6.7/css/plugin-fontsettings.css" rel="stylesheet" />
+<link href="libs/gitbook-2.6.7/css/plugin-clipboard.css" rel="stylesheet" />
+
+
+
+
+
+
+
+
+<link href="libs/anchor-sections-1.0.1/anchor-sections.css" rel="stylesheet" />
+<script src="libs/anchor-sections-1.0.1/anchor-sections.js"></script>
+  
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id={MeasurementID}"></script>
+<script>
+  window.dataLayer = window.dataLayer || [];
+  function gtag(){dataLayer.push(arguments);}
+  gtag('js', new Date());
+
+  gtag('config', '{MeasurementID}');
+</script>
+
+
+
+
+<link rel="stylesheet" href="assets/style.css" type="text/css" />
+<link rel="stylesheet" href="assets/AnVIL_style/anvil.css" type="text/css" />
+</head>
+
+<body>
+
+
+
+  <div class="book without-animation with-summary font-size-2 font-family-1" data-basepath=".">
+
+    <div class="book-summary">
+      <nav role="navigation">
+
+<ul class="summary">
+<a href="https://anvilproject.org/" target="_blank"><img src="assets/AnVIL_style/logo-anvil.png" style="width: 80%; padding-left: 15px; padding-top: 8px;"</a>
+
+<li class="divider"></li>
+<li class="chapter" data-level="1" data-path="index.html"><a href="index.html"><i class="fa fa-check"></i><b>1</b> Events</a>
+<ul>
+<li class="chapter" data-level="" data-path="index.html"><a href="index.html#upcoming-anvil-events-portal"><i class="fa fa-check"></i>Upcoming AnVIL Events (Portal)</a></li>
+</ul></li>
+<li class="chapter" data-level="2" data-path="materials.html"><a href="materials.html"><i class="fa fa-check"></i><b>2</b> Materials</a>
+<ul>
+<li class="chapter" data-level="" data-path="materials.html"><a href="materials.html#anvil-collection"><i class="fa fa-check"></i>AnVIL Collection</a></li>
+</ul></li>
+<li class="chapter" data-level="" data-path="about-the-authors.html"><a href="about-the-authors.html"><i class="fa fa-check"></i>About the Authors</a></li>
+<li class="chapter" data-level="3" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>3</b> References</a></li>
+<li class="divider"></li>
+<p style="text-align:center;"> <a href="https://github.com/jhudsl/OTTR_Template" target="blank" > This content was published with</a> <a href="https://bookdown.org/" target="blank"> bookdown by: </a> </p>
+<p style="text-align:center;"> <a href="https://hutchdatascience.org/"> The Fred Hutch Data Science Lab </a></p>
+<a href="https://hutchdatascience.org/" target="_blank"><img src="https://raw.githubusercontent.com/jhudsl/OTTR_Template/main/style-sets/fhdasl/copy_to_assets/big-dasl-stacked.png" style="width: 80%; padding-left: 34px; padding-top: 8px;"</a>
+<p style="text-align:center; font-size: 12px;"> <a href="https://github.com/rstudio4edu/rstudio4edu-book/"> Style adapted from: rstudio4edu-book </a> <a href ="https://creativecommons.org/licenses/by/2.0/"> (CC-BY 2.0) </a></p>
+<p style="padding-left: 40px;"><div class="trapezoid" style = "padding-left: 40px;"><span><a href="https://docs.google.com/forms/d/e/1FAIpQLScrDVb_utm55pmb_SHx-RgELTEbCCWdLea0T3IzS0Oj00GE4w/viewform?usp=pp_url&entry.1565230805=AnVIL+Outreach+Dashboard"> Click here to provide feedback</a> <img src="assets/itcr_arrow.png" style=" width: 10%" ></span></div></p>
+
+</ul>
+
+      </nav>
+    </div>
+
+    <div class="book-body">
+      <div class="body-inner">
+        <div class="book-header" role="navigation">
+          <h1>
+            <i class="fa fa-circle-o-notch fa-spin"></i><a href="./">AnVIL Outreach Dashboard</a>
+          </h1>
+        </div>
+
+        <div class="page-wrapper" tabindex="-1" role="main">
+          <div class="page-inner">
+
+            <section class="normal" id="section-">
+<head>
+  <meta name="viewport" content="width=device-width,minimum-scale=1.0,maximum-scale=10.0,initial-scale=1.0">
+  <!--script src="https://kit.fontawesome.com/6a26f47516.js"></script-->
+  <!--<script src="assets/hideOutput.js"></script>-->
+</head>
+        
+
+
+<div class="hero-image-container"> 
+  <img class= "hero-image" src="assets/AnVIL_style/dasl_thin_main_image.png">
+</div>
+<div id="materials" class="section level1" number="2">
+<h1><span class="header-section-number">Chapter 2</span> Materials</h1>
+<div id="anvil-collection" class="section level2 unnumbered">
+<h2>AnVIL Collection</h2>
+<p>Please check out our full collection of AnVIL and related resources: <a href="https://hutchdatascience.org/AnVIL_Collection/" class="uri">https://hutchdatascience.org/AnVIL_Collection/</a></p>
+
+</div>
+</div>
+<hr>
+<center> 
+  <div class="footer">
+      All illustrations <a href="https://creativecommons.org/licenses/by/4.0/">CC-BY. </a>
+      <br>
+      All other materials <a href= "https://creativecommons.org/licenses/by/4.0/"> CC-BY </a> unless noted otherwise.
+  </div>
+</center>
+            </section>
+
+          </div>
+        </div>
+      </div>
+<a href="index.html" class="navigation navigation-prev " aria-label="Previous page"><i class="fa fa-angle-left"></i></a>
+<a href="about-the-authors.html" class="navigation navigation-next " aria-label="Next page"><i class="fa fa-angle-right"></i></a>
+    </div>
+  </div>
+<script src="libs/gitbook-2.6.7/js/app.min.js"></script>
+<script src="libs/gitbook-2.6.7/js/clipboard.min.js"></script>
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+<script src="libs/gitbook-2.6.7/js/plugin-fontsettings.js"></script>
+<script src="libs/gitbook-2.6.7/js/plugin-bookdown.js"></script>
+<script src="libs/gitbook-2.6.7/js/jquery.highlight.js"></script>
+<script src="libs/gitbook-2.6.7/js/plugin-clipboard.js"></script>
+<script>
+gitbook.require(["gitbook"], function(gitbook) {
+gitbook.start({
+"sharing": {
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+"facebook": true,
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+"weibo": false,
+"instapaper": false,
+"vk": false,
+"whatsapp": false,
+"all": ["facebook", "twitter", "linkedin", "weibo", "instapaper"]
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+"family": "sans",
+"size": 2
+},
+"edit": {
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+},
+"history": {
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+"view": {
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+"download": null,
+"search": {
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+"toc": {
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+}
+});
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+
+</body>
+
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diff --git a/docs/reference-keys.txt b/docs/reference-keys.txt
index 41b9469..af2ad6f 100644
--- a/docs/reference-keys.txt
+++ b/docs/reference-keys.txt
@@ -1 +1,3 @@
+events
+materials
 references
diff --git a/docs/references.html b/docs/references.html
index c306ba8..aabbd5d 100644
--- a/docs/references.html
+++ b/docs/references.html
@@ -4,11 +4,11 @@
 
   <meta charset="utf-8" />
   <meta http-equiv="X-UA-Compatible" content="IE=edge" />
-  <title>Chapter 1 References | AnVIL Outreach Dashboard</title>
+  <title>Chapter 3 References | AnVIL Outreach Dashboard</title>
   <meta name="description" content="Description about Course/Book." />
   <meta name="generator" content="bookdown 0.24 and GitBook 2.6.7" />
 
-  <meta property="og:title" content="Chapter 1 References | AnVIL Outreach Dashboard" />
+  <meta property="og:title" content="Chapter 3 References | AnVIL Outreach Dashboard" />
   <meta property="og:type" content="book" />
   
   
@@ -16,14 +16,14 @@
   
 
   <meta name="twitter:card" content="summary" />
-  <meta name="twitter:title" content="Chapter 1 References | AnVIL Outreach Dashboard" />
+  <meta name="twitter:title" content="Chapter 3 References | AnVIL Outreach Dashboard" />
   
   <meta name="twitter:description" content="Description about Course/Book." />
   
 
 
 
-<meta name="date" content="2023-10-20" />
+<meta name="date" content="2023-10-25" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />
@@ -83,13 +83,16 @@
 <a href="https://anvilproject.org/" target="_blank"><img src="assets/AnVIL_style/logo-anvil.png" style="width: 80%; padding-left: 15px; padding-top: 8px;"</a>
 
 <li class="divider"></li>
-<li class="chapter" data-level="" data-path="index.html"><a href="index.html"><i class="fa fa-check"></i>About this Resource</a>
+<li class="chapter" data-level="1" data-path="index.html"><a href="index.html"><i class="fa fa-check"></i><b>1</b> Events</a>
 <ul>
 <li class="chapter" data-level="" data-path="index.html"><a href="index.html#upcoming-anvil-events-portal"><i class="fa fa-check"></i>Upcoming AnVIL Events (Portal)</a></li>
-<li class="chapter" data-level="" data-path="index.html"><a href="index.html#anvil-collection"><i class="fa fa-check"></i>AnVIL Collection</a></li>
+</ul></li>
+<li class="chapter" data-level="2" data-path="materials.html"><a href="materials.html"><i class="fa fa-check"></i><b>2</b> Materials</a>
+<ul>
+<li class="chapter" data-level="" data-path="materials.html"><a href="materials.html#anvil-collection"><i class="fa fa-check"></i>AnVIL Collection</a></li>
 </ul></li>
 <li class="chapter" data-level="" data-path="about-the-authors.html"><a href="about-the-authors.html"><i class="fa fa-check"></i>About the Authors</a></li>
-<li class="chapter" data-level="1" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>1</b> References</a></li>
+<li class="chapter" data-level="3" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>3</b> References</a></li>
 <li class="divider"></li>
 <p style="text-align:center;"> <a href="https://github.com/jhudsl/OTTR_Template" target="blank" > This content was published with</a> <a href="https://bookdown.org/" target="blank"> bookdown by: </a> </p>
 <p style="text-align:center;"> <a href="https://hutchdatascience.org/"> The Fred Hutch Data Science Lab </a></p>
@@ -125,8 +128,8 @@ <h1>
 <div class="hero-image-container"> 
   <img class= "hero-image" src="assets/AnVIL_style/dasl_thin_main_image.png">
 </div>
-<div id="references" class="section level1" number="1">
-<h1><span class="header-section-number">Chapter 1</span> References</h1>
+<div id="references" class="section level1" number="3">
+<h1><span class="header-section-number">Chapter 3</span> References</h1>
 
 </div>
 <hr>
diff --git a/docs/search_index.json b/docs/search_index.json
index 8acfe9f..d7bd4ed 100644
--- a/docs/search_index.json
+++ b/docs/search_index.json
@@ -1 +1 @@
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